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Sample records for fmri adaptation reveals

  1. Asymmetric fMRI adaptation reveals no evidence for mirror neurons in humans.

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    Lingnau, Angelika; Gesierich, Benno; Caramazza, Alfonso

    2009-06-16

    Neurons in macaque ventral premotor cortex and inferior parietal lobe discharge during both the observation and the execution of motor acts. It has been claimed that these so-called mirror neurons form the basis of action understanding by matching the visual input with the corresponding motor program (direct matching). Functional magnetic resonance imaging (fMRI) adaptation can be used to test the direct matching account of action recognition by determining whether putative mirror neurons show adaptation for repeated motor acts independently of whether they are observed or executed. An unambiguous test of the hypothesis requires that the motor acts be meaningless to ensure that any adaptation effect is directly because of movement recognition/motor execution and not contextually determined inferences. We found adaptation for motor acts that were repeatedly observed or repeatedly executed. We also found adaptation for motor acts that were first observed and then executed, as would be expected if a previously seen act primed the subsequent execution of that act. Crucially, we found no signs of adaptation for motor acts that were first executed and then observed. Failure to find cross-modal adaptation for executed and observed motor acts is not compatible with the core assumption of mirror neuron theory, which holds that action recognition and understanding are based on motor simulation.

  2. Face processing changes in normal aging revealed by fMRI adaptation.

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    Lee, Yunjo; Grady, Cheryl L; Habak, Claudine; Wilson, Hugh R; Moscovitch, Morris

    2011-11-01

    We investigated the neural correlates of facial processing changes in healthy aging using fMRI and an adaptation paradigm. In the scanner, participants were successively presented with faces that varied in identity, viewpoint, both, or neither and performed a head size detection task independent of identity or viewpoint. In right fusiform face area (FFA), older adults failed to show adaptation to the same face repeatedly presented in the same view, which elicited the most adaptation in young adults. We also performed a multivariate analysis to examine correlations between whole-brain activation patterns and behavioral performance in a face-matching task tested outside the scanner. Despite poor neural adaptation in right FFA, high-performing older adults engaged the same face-processing network as high-performing young adults across conditions, except the one presenting a same facial identity across different viewpoints. Low-performing older adults used this network to a lesser extent. Additionally, high-performing older adults uniquely recruited a set of areas related to better performance across all conditions, indicating age-specific involvement of this added network. This network did not include the core ventral face-processing areas but involved the left inferior occipital gyrus, frontal, and parietal regions. Although our adaptation results show that the neuronal representations of the core face-preferring areas become less selective with age, our multivariate analysis indicates that older adults utilize a distinct network of regions associated with better face matching performance, suggesting that engaging this network may compensate for deficiencies in ventral face processing regions.

  3. fMRI adaptation reveals mirror neurons in human inferior parietal cortex.

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    Chong, Trevor T-J; Cunnington, Ross; Williams, Mark A; Kanwisher, Nancy; Mattingley, Jason B

    2008-10-28

    Mirror neurons, as originally described in the macaque, have two defining properties [1, 2]: They respond specifically to a particular action (e.g., bringing an object to the mouth), and they produce their action-specific responses independent of whether the monkey executes the action or passively observes a conspecific performing the same action. In humans, action observation and action execution engage a network of frontal, parietal, and temporal areas. However, it is unclear whether these responses reflect the activity of a single population that represents both observed and executed actions in a common neural code or the activity of distinct but overlapping populations of exclusively perceptual and motor neurons [3]. Here, we used fMRI adaptation to show that the right inferior parietal lobe (IPL) responds independently to specific actions regardless of whether they are observed or executed. Specifically, responses in the right IPL were attenuated when participants observed a recently executed action relative to one that had not previously been performed. This adaptation across action and perception demonstrates that the right IPL responds selectively to the motoric and perceptual representations of actions and is the first evidence for a neural response in humans that shows both defining properties of mirror neurons.

  4. fMRI adaptation revisited.

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    Larsson, Jonas; Solomon, Samuel G; Kohn, Adam

    2016-07-01

    Adaptation has been widely used in functional magnetic imaging (fMRI) studies to infer neuronal response properties in human cortex. fMRI adaptation has been criticized because of the complex relationship between fMRI adaptation effects and the multiple neuronal effects that could underlie them. Many of the longstanding concerns about fMRI adaptation have received empirical support from neurophysiological studies over the last decade. We review these studies here, and also consider neuroimaging studies that have investigated how fMRI adaptation effects are influenced by high-level perceptual processes. The results of these studies further emphasize the need to interpret fMRI adaptation results with caution, but they also provide helpful guidance for more accurate interpretation and better experimental design. In addition, we argue that rather than being used as a proxy for measurements of neuronal stimulus selectivity, fMRI adaptation may be most useful for studying population-level adaptation effects across cortical processing hierarchies.

  5. fMRI repetition suppression: neuronal adaptation or stimulus expectation?

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    Larsson, Jonas; Smith, Andrew T

    2012-03-01

    Measurements of repetition suppression with functional magnetic resonance imaging (fMRI adaptation) have been used widely to probe neuronal population response properties in human cerebral cortex. fMRI adaptation techniques assume that fMRI repetition suppression reflects neuronal adaptation, an assumption that has been challenged on the basis of evidence that repetition-related response changes may reflect unrelated factors, such as attention and stimulus expectation. Specifically, Summerfield et al. (Summerfield C, Trittschuh EH, Monti JM, Mesulam MM, Egner T. 2008. Neural repetition suppression reflects fulfilled perceptual expectations. Nat Neurosci. 11:1004-1006) reported that the relative frequency of stimulus repetitions and non-repetitions influenced the magnitude of repetition suppression in the fusiform face area, suggesting that stimulus expectation accounted for most of the effect of repetition. We confirm that stimulus expectation can significantly influence fMRI repetition suppression throughout visual cortex and show that it occurs with long as well as short adaptation durations. However, the effect was attention dependent: When attention was diverted away from the stimuli, the effects of stimulus expectation completely disappeared. Nonetheless, robust and significant repetition suppression was still evident. These results suggest that fMRI repetition suppression reflects a combination of neuronal adaptation and attention-dependent expectation effects that can be experimentally dissociated. This implies that with an appropriate experimental design, fMRI adaptation can provide valid measures of neuronal adaptation and hence response specificity.

  6. Letter representations in writing: An fMRI adaptation approach

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    Olivier eDufor

    2013-10-01

    Full Text Available Abstract:Behavioral and neuropsychological research in reading and spelling has provided evidence for the role of the following types of orthographic representations in letter writing: letter forms, letter case, and abstract letter identities. We report on the results of an fMRI investigation designed to identify the neural substrates of these different representational types. Using a neural adaptation paradigm we examined the neural distribution of inhibition and release from inhibition in a letter-writing task in which, on every trial, participants produced three repetitions of the same letter and a fourth letter that was either identical to (no-change trial or different from the previous three (change trial. Change trials involved a change in the shape, case and/or identity of the letter. After delineating the general letter writing network by identifying areas that exhibited significant neural adaptation effects on no-change trials, we used deconvolution analysis to examine this network for effects of release from inhibition on change trials. In this way we identified regions specifically associated with the representation of letter shape (left SFS and SFG/pre-CG and letter identity (left fusiform gyrus or both (cerebellum, post-central gyrus and middle frontal gyrus. No regions were associated with the representation of letter case. This study showcases an investigational approach that allows for the differentiation of the neurotopography of the representational types that are key to our ability to produce written language.

  7. Studying the neural bases of prism adaptation using fMRI: A technical and design challenge.

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    Bultitude, Janet H; Farnè, Alessandro; Salemme, Romeo; Ibarrola, Danielle; Urquizar, Christian; O'Shea, Jacinta; Luauté, Jacques

    2016-12-30

    Prism adaptation induces rapid recalibration of visuomotor coordination. The neural mechanisms of prism adaptation have come under scrutiny since the observations that the technique can alleviate hemispatial neglect following stroke, and can alter spatial cognition in healthy controls. Relative to non-imaging behavioral studies, fMRI investigations of prism adaptation face several challenges arising from the confined physical environment of the scanner and the supine position of the participants. Any researcher who wishes to administer prism adaptation in an fMRI environment must adjust their procedures enough to enable the experiment to be performed, but not so much that the behavioral task departs too much from true prism adaptation. Furthermore, the specific temporal dynamics of behavioral components of prism adaptation present additional challenges for measuring their neural correlates. We developed a system for measuring the key features of prism adaptation behavior within an fMRI environment. To validate our configuration, we present behavioral (pointing) and head movement data from 11 right-hemisphere lesioned patients and 17 older controls who underwent sham and real prism adaptation in an MRI scanner. Most participants could adapt to prismatic displacement with minimal head movements, and the procedure was well tolerated. We propose recommendations for fMRI studies of prism adaptation based on the design-specific constraints and our results.

  8. Simulating fiction: individual differences in literature comprehension revealed with FMRI.

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    Annabel D Nijhof

    Full Text Available When we read literary fiction, we are transported to fictional places, and we feel and think along with the characters. Despite the importance of narrative in adult life and during development, the neurocognitive mechanisms underlying fiction comprehension are unclear. We used functional magnetic resonance imaging (fMRI to investigate how individuals differently employ neural networks important for understanding others' beliefs and intentions (mentalizing, and for sensori-motor simulation while listening to excerpts from literary novels. Localizer tasks were used to localize both the cortical motor network and the mentalizing network in participants after they listened to excerpts from literary novels. Results show that participants who had high activation in anterior medial prefrontal cortex (aMPFC; part of the mentalizing network when listening to mentalizing content of literary fiction, had lower motor cortex activity when they listened to action-related content of the story, and vice versa. This qualifies how people differ in their engagement with fiction: some people are mostly drawn into a story by mentalizing about the thoughts and beliefs of others, whereas others engage in literature by simulating more concrete events such as actions. This study provides on-line neural evidence for the existence of qualitatively different styles of moving into literary worlds, and adds to a growing body of literature showing the potential to study narrative comprehension with neuroimaging methods.

  9. Simulating fiction: individual differences in literature comprehension revealed with FMRI.

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    Nijhof, Annabel D; Willems, Roel M

    2015-01-01

    When we read literary fiction, we are transported to fictional places, and we feel and think along with the characters. Despite the importance of narrative in adult life and during development, the neurocognitive mechanisms underlying fiction comprehension are unclear. We used functional magnetic resonance imaging (fMRI) to investigate how individuals differently employ neural networks important for understanding others' beliefs and intentions (mentalizing), and for sensori-motor simulation while listening to excerpts from literary novels. Localizer tasks were used to localize both the cortical motor network and the mentalizing network in participants after they listened to excerpts from literary novels. Results show that participants who had high activation in anterior medial prefrontal cortex (aMPFC; part of the mentalizing network) when listening to mentalizing content of literary fiction, had lower motor cortex activity when they listened to action-related content of the story, and vice versa. This qualifies how people differ in their engagement with fiction: some people are mostly drawn into a story by mentalizing about the thoughts and beliefs of others, whereas others engage in literature by simulating more concrete events such as actions. This study provides on-line neural evidence for the existence of qualitatively different styles of moving into literary worlds, and adds to a growing body of literature showing the potential to study narrative comprehension with neuroimaging methods.

  10. Long timescale fMRI neuronal adaptation effects in human amblyopic cortex.

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    Xingfeng Li

    Full Text Available An investigation of long timescale (5 minutes fMRI neuronal adaptation effects, based on retinotopic mapping and spatial frequency stimuli, is presented in this paper. A hierarchical linear model was developed to quantify the adaptation effects in the visual cortex. The analysis of data involved studying the retinotopic mapping and spatial frequency adaptation effects in the amblyopic cortex. Our results suggest that, firstly, there are many cortical regions, including V1, where neuronal adaptation effects are reduced in the cortex in response to amblyopic eye stimulation. Secondly, our results show the regional contribution is different, and it seems to start from V1 and spread to the extracortex regions. Thirdly, our results show that there is greater adaptation to broadband retinotopic mapping as opposed to narrowband spatial frequency stimulation of the amblyopic eye, and we find significant correlation between fMRI response and the magnitude of the adaptation effect, suggesting that the reduced adaptation may be a consequence of the reduced response to different stimuli reported for amblyopic eyes.

  11. A pilot study for investigating cortical binocularity in humans using fMRI adaptation.

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    Jurcoane, Alina; Choubey, Bhaskar; Muckli, Lars; Sireteanu, Ruxandra

    2007-01-01

    Disrupted stereovision is a feature that accompanies strabismus. This study uses an fMRI adaptation paradigm to assess the amount of cortical binocularity in subjects with normal or impaired stereopsis. We present data from a pilot study of two normally-sighted and one stereodeficient subject with alternating fixation. We adapted one eye to diagonally oriented sinusoidal gratings and tested either the same (monocular test) or the other eye (interocular transfer), using either the same or an orthogonal orientation. In normally-sighted subjects, we observed monocular adaptation but only weak interocular transfer in the striate cortex, whereas in the extrastriate cortex we found strong monocular as well as interocular adaptation. In the stereodeficient subject, monocular adaptation but no interocular transfer was obtained in the extrastriate cortex. These results suggest that impaired stereopsis is related to reduced interocular transfer of adaptation at higher levels of the cortical visual pathway.

  12. Adaptive thresholding for reliable topological inference in single subject fMRI analysis

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    Krzysztof eGorgolewski

    2012-08-01

    Full Text Available Single subject fMRI has proved to be a useful tool for mapping functional areas in clinical procedures such as tumour resection. Using fMRI data, clinicians assess the risk, plan and execute such procedures based on thresholded statistical maps. However, because current thresholding methods were developed mainly in the context of cognitive neuroscience group studies, most single subject fMRI maps are thresholded manually to satisfy specific criteria related to single subject analyses. Here, we propose a new adaptive thresholding method which combines Gamma-Gaussian mixture modelling with topological thresholding to improve cluster delineation. In a series of simulations we show that by adapting to the signal and noise properties, the new method performs well in terms of the trade-off between false negative and positive cluster error rates as well as in terms of over and underestimation of the true activation border. We also show through simulations and a motor test-retest study on ten volunteer subjects that adaptive thresholding improves reliability, mainly by accounting for the global signal variance. This in turn increases the likelihood that the true activation pattern can be determined.

  13. Flexible adaptive paradigms for fMRI using a novel software package 'Brain Analysis in Real-Time' (BART.

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    Lydia Hellrung

    Full Text Available In this work we present a new open source software package offering a unified framework for the real-time adaptation of fMRI stimulation procedures. The software provides a straightforward setup and highly flexible approach to adapt fMRI paradigms while the experiment is running. The general framework comprises the inclusion of parameters from subject's compliance, such as directing gaze to visually presented stimuli and physiological fluctuations, like blood pressure or pulse. Additionally, this approach yields possibilities to investigate complex scientific questions, for example the influence of EEG rhythms or fMRI signals results themselves. To prove the concept of this approach, we used our software in a usability example for an fMRI experiment where the presentation of emotional pictures was dependent on the subject's gaze position. This can have a significant impact on the results. So far, if this is taken into account during fMRI data analysis, it is commonly done by the post-hoc removal of erroneous trials. Here, we propose an a priori adaptation of the paradigm during the experiment's runtime. Our fMRI findings clearly show the benefits of an adapted paradigm in terms of statistical power and higher effect sizes in emotion-related brain regions. This can be of special interest for all experiments with low statistical power due to a limited number of subjects, a limited amount of time, costs or available data to analyze, as is the case with real-time fMRI.

  14. Neural correlates of intelligence as revealed by fMRI of fluid analogies.

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    Geake, John G; Hansen, Peter C

    2005-06-01

    It has been conjectured that the cognitive basis of intelligence is the ability to make fluid or creative analogical relationships between distantly related concepts or pieces of information (Hofstadter, D.R. 1995. Fluid Concepts and Creative Analogies. Basic Books, New York., Hofstadter, D.R. 2001. Analogy as the Core of Cognition. In The Analogical Mind: Perspectives from Cognitive Science (D. Gentner, K. J. Holyoak and B. N. Kokinov, Ed.). pp. 504-537. MIT Press, Cambridge, Mass.). We hypothesised that fluid analogy-making tasks would activate specific regions of frontal cortex that were common to those of previous inferential reasoning tasks. We report here a novel self-paced event-related fMRI study employed to investigate the neural correlates of intelligence associated with undertaking fluid letter string analogy tasks. Stimuli were adapted from items of the AI program Copycat (Mitchell, M. 1993. Analogy-making as Perception: A computer model. The MIT Press, Cambridge MA.). Twelve right-handed adults chose their own "best" completions from four plausible response choices to 55 fluid letter string analogies across a range of analogical depths. An analysis using covariates determined per subject by analogical depth revealed significant bilateral neural activations in the superior, inferior, and middle frontal gyri and in the anterior cingulate/paracingulate cortex. These frontal areas have been previously associated with reasoning tasks involving inductive syllogisms, syntactic hierarchies, and linguistic creativity. A higher-order analysis covarying participants' verbal intelligence measures found correlations with individual BOLD activation strengths in two ROIs within BA 9 and BA 45/46. This is a provocative result given that verbal intelligence is conceptualised as being a measure of crystallised intelligence, while analogy making is conceptualised as requiring fluid intelligence. The results therefore support the conjecture that fluid analogising could

  15. fMRI study of the role of glutamate NMDA receptor in the olfactory adaptation in rats: Insights into cellular and molecular mechanisms of olfactory adaptation.

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    Zhao, Fuqiang; Wang, Xiaohai; Zariwala, Hatim A; Uslaner, Jason M; Houghton, Andrea K; Evelhoch, Jeffrey L; Hostetler, Eric; Winkelmann, Christopher T; Hines, Catherine D G

    2017-02-03

    Olfactory adaptation, characterized by attenuation of response to repeated odor stimulations or continuous odor exposure, is an intrinsic feature of olfactory processing. Adaptation can be induced by either "synaptic depression" due to depletion of neurotransmitters, or "enhanced inhibition" onto principle neurons by local inhibitory interneurons in olfactory structures. It is not clear which mechanism plays a major role in olfactory adaptation. More importantly, molecular sources of enhanced inhibition have not been identified. In this study, olfactory responses to either repeated 40-s stimulations with interstimulus intervals (ISI) of 140-s or 30-min, or a single prolonged 200-s stimulus were measured by fMRI in different naïve rats. Olfactory adaptations in the olfactory bulb (OB), anterior olfactory nucleus (AON), and piriform cortex (PC) were observed only with repeated 40-s odor stimulations, and no olfactory adaptations were detected during the prolonged 200-s stimulation. Interestingly, in responses to repeated 40-s odor stimulations in the PC, the first odor stimulation induced positive activations, and odor stimulations under adapted condition induced negative activations. The negative activations suggest that "sparse coding" and "global inhibition" are the characteristics of olfactory processing in PC, and the global inhibition manifests only under an adapted condition, not a naïve condition. Further, we found that these adaptations were NMDA receptor dependent; an NMDA receptor antagonist (MK801) blocked the adaptations. Based on the mechanism that glutamate NMDA receptor plays a role in the inhibition onto principle neurons by interneurons, our data suggest that the olfactory adaptations are caused by enhanced inhibition from interneurons. Combined with the necessity of the interruption of odor stimulation to observe the adaptations, the molecular source for the enhanced inhibition is most likely an increased glutamate release from presynaptic

  16. Revealing the functional neuroanatomy of intrinsic alertness using fMRI: methodological peculiarities.

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    Benjamin Clemens

    Full Text Available Clinical observations and neuroimaging data revealed a right-hemisphere fronto-parietal-thalamic-brainstem network for intrinsic alertness, and additional left fronto-parietal activity during phasic alertness. The primary objective of this fMRI study was to map the functional neuroanatomy of intrinsic alertness as precisely as possible in healthy participants, using a novel assessment paradigm already employed in clinical settings. Both the paradigm and the experimental design were optimized to specifically assess intrinsic alertness, while at the same time controlling for sensory-motor processing. The present results suggest that the processing of intrinsic alertness is accompanied by increased activity within the brainstem, thalamus, anterior cingulate gyrus, right insula, and right parietal cortex. Additionally, we found increased activation in the left hemisphere around the middle frontal gyrus (BA 9, the insula, the supplementary motor area, and the cerebellum. Our results further suggest that rather minute aspects of the experimental design may induce aspects of phasic alertness, which in turn might lead to additional brain activation in left-frontal areas not normally involved in intrinsic alertness. Accordingly, left BA 9 activation may be related to co-activation of the phasic alertness network due to the switch between rest and task conditions functioning as an external warning cue triggering the phasic alertness network. Furthermore, activation of the intrinsic alertness network during fixation blocks due to enhanced expectancy shortly before the switch to the task block might, when subtracted from the task block, lead to diminished activation in the typical right hemisphere intrinsic alertness network. Thus, we cautiously suggest that--as a methodological artifact--left frontal activations might show up due to phasic alertness involvement and intrinsic alertness activations might be weakened due to contrasting with fixation blocks

  17. Combined eye tracking and fMRI reveals neural basis of linguistic predictions during sentence comprehension.

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    Bonhage, Corinna E; Mueller, Jutta L; Friederici, Angela D; Fiebach, Christian J

    2015-07-01

    It is widely agreed upon that linguistic predictions are an integral part of language comprehension. Yet, experimental proof of their existence remains challenging. Here, we introduce a new predictive eye gaze reading task combining eye tracking and functional magnetic resonance imaging (fMRI) that allows us to infer the existence and timing of linguistic predictions via anticipatory eye-movements. Participants read different types of word sequences (i.e., regular sentences, meaningless jabberwocky sentences, non-word lists) up to the pre-final word. The final target word was displayed with a temporal delay and its screen position was dependent on the syntactic word category (nouns vs verbs). During the delay, anticipatory eye-movements into the correct target word area were indicative of linguistic predictions. For fMRI analysis, the predictive sentence conditions were contrasted to the non-word condition, with the anticipatory eye-movements specifying differences in timing across conditions. A conjunction analysis of both sentence conditions revealed the neural substrate of word category prediction, namely a distributed network of cortical and subcortical brain regions including language systems, basal ganglia, thalamus, and hippocampus. Direct contrasts between the regular sentence condition and the jabberwocky condition indicate that prediction of word category in meaningless jabberwocky sentences relies on classical left-hemispheric language systems involving Brodman's area 44/45 in the left inferior frontal gyrus, left superior temporal areas, and the dorsal caudate nucleus. Regular sentences, in contrast, allowed for the prediction of specific words. Word-specific predictions were specifically associated with more widely distributed temporal and parietal cortical systems, most prominently in the right hemisphere. Our results support the presence of linguistic predictions during sentence processing and demonstrate the validity of the predictive eye gaze

  18. Revealing the functional neuroanatomy of intrinsic alertness using fMRI: methodological peculiarities.

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    Clemens, Benjamin; Zvyagintsev, Mikhail; Sack, Alexander T; Sack, Alexander; Heinecke, Armin; Willmes, Klaus; Sturm, Walter

    2011-01-01

    Clinical observations and neuroimaging data revealed a right-hemisphere fronto-parietal-thalamic-brainstem network for intrinsic alertness, and additional left fronto-parietal activity during phasic alertness. The primary objective of this fMRI study was to map the functional neuroanatomy of intrinsic alertness as precisely as possible in healthy participants, using a novel assessment paradigm already employed in clinical settings. Both the paradigm and the experimental design were optimized to specifically assess intrinsic alertness, while at the same time controlling for sensory-motor processing. The present results suggest that the processing of intrinsic alertness is accompanied by increased activity within the brainstem, thalamus, anterior cingulate gyrus, right insula, and right parietal cortex. Additionally, we found increased activation in the left hemisphere around the middle frontal gyrus (BA 9), the insula, the supplementary motor area, and the cerebellum. Our results further suggest that rather minute aspects of the experimental design may induce aspects of phasic alertness, which in turn might lead to additional brain activation in left-frontal areas not normally involved in intrinsic alertness. Accordingly, left BA 9 activation may be related to co-activation of the phasic alertness network due to the switch between rest and task conditions functioning as an external warning cue triggering the phasic alertness network. Furthermore, activation of the intrinsic alertness network during fixation blocks due to enhanced expectancy shortly before the switch to the task block might, when subtracted from the task block, lead to diminished activation in the typical right hemisphere intrinsic alertness network. Thus, we cautiously suggest that--as a methodological artifact--left frontal activations might show up due to phasic alertness involvement and intrinsic alertness activations might be weakened due to contrasting with fixation blocks, when assessing the

  19. fMRI of Simultaneous Interpretation Reveals the Neural Basis of Extreme Language Control.

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    Hervais-Adelman, Alexis; Moser-Mercer, Barbara; Michel, Christoph M; Golestani, Narly

    2015-12-01

    We used functional magnetic resonance imaging (fMRI) to examine the neural basis of extreme multilingual language control in a group of 50 multilingual participants. Comparing brain responses arising during simultaneous interpretation (SI) with those arising during simultaneous repetition revealed activation of regions known to be involved in speech perception and production, alongside a network incorporating the caudate nucleus that is known to be implicated in domain-general cognitive control. The similarity between the networks underlying bilingual language control and general executive control supports the notion that the frequently reported bilingual advantage on executive tasks stems from the day-to-day demands of language control in the multilingual brain. We examined neural correlates of the management of simultaneity by correlating brain activity during interpretation with the duration of simultaneous speaking and hearing. This analysis showed significant modulation of the putamen by the duration of simultaneity. Our findings suggest that, during SI, the caudate nucleus is implicated in the overarching selection and control of the lexico-semantic system, while the putamen is implicated in ongoing control of language output. These findings provide the first clear dissociation of specific dorsal striatum structures in polyglot language control, roles that are consistent with previously described involvement of these regions in nonlinguistic executive control.

  20. The neural substrates of musical memory revealed by fMRI and two semantic tasks.

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    Groussard, M; Rauchs, G; Landeau, B; Viader, F; Desgranges, B; Eustache, F; Platel, H

    2010-12-01

    Recognizing a musical excerpt without necessarily retrieving its title typically reflects the existence of a memory system dedicated to the retrieval of musical knowledge. The functional distinction between musical and verbal semantic memory has seldom been investigated. In this fMRI study, we directly compared the musical and verbal memory of 20 nonmusicians, using a congruence task involving automatic semantic retrieval and a familiarity task requiring more thorough semantic retrieval. In the former, participants had to access their semantic store to retrieve musical or verbal representations of melodies or expressions they heard, in order to decide whether these were then given the right ending or not. In the latter, they had to judge the level of familiarity of musical excerpts and expressions. Both tasks revealed activation of the left inferior frontal and posterior middle temporal cortices, suggesting that executive and selection processes are common to both verbal and musical retrievals. Distinct patterns of activation were observed within the left temporal cortex, with musical material mainly activating the superior temporal gyrus and verbal material the middle and inferior gyri. This cortical organization of musical and verbal semantic representations could explain clinical dissociations featuring selective disturbances for musical or verbal material. Copyright © 2010 Elsevier Inc. All rights reserved.

  1. Awake fMRI reveals a specialized region in dog temporal cortex for face processing

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    Dilks, Daniel D.; Cook, Peter; Weiller, Samuel K.; Berns, Helen P.; Spivak, Mark

    2015-01-01

    Recent behavioral evidence suggests that dogs, like humans and monkeys, are capable of visual face recognition. But do dogs also exhibit specialized cortical face regions similar to humans and monkeys? Using functional magnetic resonance imaging (fMRI) in six dogs trained to remain motionless during scanning without restraint or sedation, we found a region in the canine temporal lobe that responded significantly more to movies of human faces than to movies of everyday objects. Next, using a new stimulus set to investigate face selectivity in this predefined candidate dog face area, we found that this region responded similarly to images of human faces and dog faces, yet significantly more to both human and dog faces than to images of objects. Such face selectivity was not found in dog primary visual cortex. Taken together, these findings: (1) provide the first evidence for a face-selective region in the temporal cortex of dogs, which cannot be explained by simple low-level visual feature extraction; (2) reveal that neural machinery dedicated to face processing is not unique to primates; and (3) may help explain dogs’ exquisite sensitivity to human social cues. PMID:26290784

  2. Neural adaptation to thin and fat bodies in the fusiform body area and middle occipital gyrus: an fMRI adaptation study.

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    Hummel, Dennis; Rudolf, Anne K; Brandi, Marie-Luise; Untch, Karl-Heinz; Grabhorn, Ralph; Hampel, Harald; Mohr, Harald M

    2013-12-01

    Visual perception can be strongly biased due to exposure to specific stimuli in the environment, often causing neural adaptation and visual aftereffects. In this study, we investigated whether adaptation to certain body shapes biases the perception of the own body shape. Furthermore, we aimed to evoke neural adaptation to certain body shapes. Participants completed a behavioral experiment (n = 14) to rate manipulated pictures of their own bodies after adaptation to demonstratively thin or fat pictures of their own bodies. The same stimuli were used in a second experiment (n = 16) using functional magnetic resonance imaging (fMRI) adaptation. In the behavioral experiment, after adapting to a thin picture of the own body participants also judged a thinner than actual body picture to be the most realistic and vice versa, resembling a typical aftereffect. The fusiform body area (FBA) and the right middle occipital gyrus (rMOG) show neural adaptation to specific body shapes while the extrastriate body area (EBA) bilaterally does not. The rMOG cluster is highly selective for bodies and perhaps body parts. The findings of the behavioral experiment support the existence of a perceptual body shape aftereffect, resulting from a specific adaptation to thin and fat pictures of one's own body. The fMRI results imply that body shape adaptation occurs in the FBA and the rMOG. The role of the EBA in body shape processing remains unclear. The results are also discussed in the light of clinical body image disturbances.

  3. Sentence Syntax and Content in the Human Temporal Lobe: An fMRI Adaptation Study in Auditory and Visual Modalities

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    Devauchelle, A.D.; Dehaene, S.; Pallier, C. [INSERM, Gif sur Yvette (France); Devauchelle, A.D.; Dehaene, S.; Pallier, C. [CEA, DSV, I2BM, NeuroSpin, F-91191 Gif Sur Yvette (France); Devauchelle, A.D.; Pallier, C. [Univ. Paris 11, Orsay (France); Oppenheim, C. [Univ Paris 05, Ctr Hosp St Anne, Paris (France); Rizzi, L. [Univ Siena, CISCL, I-53100 Siena (Italy); Dehaene, S. [Coll France, F-75231 Paris (France)

    2009-07-01

    Priming effects have been well documented in behavioral psycho-linguistics experiments: The processing of a word or a sentence is typically facilitated when it shares lexico-semantic or syntactic features with a previously encountered stimulus. Here, we used fMRI priming to investigate which brain areas show adaptation to the repetition of a sentence's content or syntax. Participants read or listened to sentences organized in series which could or not share similar syntactic constructions and/or lexico-semantic content. The repetition of lexico-semantic content yielded adaptation in most of the temporal and frontal sentence processing network, both in the visual and the auditory modalities, even when the same lexico-semantic content was expressed using variable syntactic constructions. No fMRI adaptation effect was observed when the same syntactic construction was repeated. Yet behavioral priming was observed at both syntactic and semantic levels in a separate experiment where participants detected sentence endings. We discuss a number of possible explanations for the absence of syntactic priming in the fMRI experiments, including the possibility that the conglomerate of syntactic properties defining 'a construction' is not an actual object assembled during parsing. (authors)

  4. Adaptive changes in early and late blind: a fMRI study of Braille reading.

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    Burton, H; Snyder, A Z; Conturo, T E; Akbudak, E; Ollinger, J M; Raichle, M E

    2002-01-01

    Braille reading depends on remarkable adaptations that connect the somatosensory system to language. We hypothesized that the pattern of cortical activations in blind individuals reading Braille would reflect these adaptations. Activations in visual (occipital-temporal), frontal-language, and somatosensory cortex in blind individuals reading Braille were examined for evidence of differences relative to previously reported studies of sighted subjects reading print or receiving tactile stimulation. Nine congenitally blind and seven late-onset blind subjects were studied with fMRI as they covertly performed verb generation in response to reading Braille embossed nouns. The control task was reading the nonlexical Braille string "######". This study emphasized image analysis in individual subjects rather than pooled data. Group differences were examined by comparing magnitudes and spatial extent of activated regions first determined to be significant using the general linear model. The major adaptive change was robust activation of visual cortex despite the complete absence of vision in all subjects. This included foci in peri-calcarine, lingual, cuneus and fusiform cortex, and in the lateral and superior occipital gyri encompassing primary (V1), secondary (V2), and higher tier (VP, V4v, LO and possibly V3A) visual areas previously identified in sighted subjects. Subjects who never had vision differed from late blind subjects in showing even greater activity in occipital-temporal cortex, provisionally corresponding to V5/MT and V8. In addition, the early blind had stronger activation of occipital cortex located contralateral to the hand used for reading Braille. Responses in frontal and parietal cortex were nearly identical in both subject groups. There was no evidence of modifications in frontal cortex language areas (inferior frontal gyrus and dorsolateral prefrontal cortex). Surprisingly, there was also no evidence of an adaptive expansion of the somatosensory or

  5. Adaptive changes in early and late blind: a FMRI study of verb generation to heard nouns.

    Science.gov (United States)

    Burton, H; Snyder, A Z; Diamond, J B; Raichle, M E

    2002-12-01

    Literacy for blind people requires learning Braille. Along with others, we have shown that reading Braille activates visual cortex. This includes striate cortex (V1), i.e., banks of calcarine sulcus, and several higher visual areas in lingual, fusiform, cuneus, lateral occipital, inferior temporal, and middle temporal gyri. The spatial extent and magnitude of magnetic resonance (MR) signals in visual cortex is greatest for those who became blind early in life. Individuals who lost sight as adults, and subsequently learned Braille, still exhibited activity in some of the same visual cortex regions, especially V1. These findings suggest these visual cortex regions become adapted to processing tactile information and that this cross-modal neural change might support Braille literacy. Here we tested the alternative hypothesis that these regions directly respond to linguistic aspects of a task. Accordingly, language task performance by blind persons should activate the same visual cortex regions regardless of input modality. Specifically, visual cortex activity in blind people ought to arise during a language task involving heard words. Eight early blind, six late blind, and eight sighted subjects were studied using functional magnetic resonance imaging (fMRI) during covert generation of verbs to heard nouns. The control task was passive listening to indecipherable sounds (reverse words) matched to the nouns in sound intensity, duration, and spectral content. Functional responses were analyzed at the level of individual subjects using methods based on the general linear model and at the group level, using voxel based ANOVA and t-test analyses. Blind and sighted subjects showed comparable activation of language areas in left inferior frontal, dorsolateral prefrontal, and left posterior superior temporal gyri. The main distinction was bilateral, left dominant activation of the same visual cortex regions previously noted with Braille reading in all blind subjects. The

  6. fMRI reveals reciprocal inhibition between social and physical cognitive domains

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    Jack, Anthony I.; Dawson, Abigail; Begany, Katelyn; Leckie, Regina L.; Barry, Kevin; Ciccia, Angela; Snyder, Abraham

    2012-01-01

    Two lines of evidence indicate that there exists a reciprocal inhibitory relationship between opposed brain networks. First, most attention-demanding cognitive tasks activate a stereotypical set of brain areas, known as the task-positive network and simultaneously deactivate a different set of brain regions, commonly referred to as the task negative or default mode network. Second, functional connectivity analyses show that these same opposed networks are anti-correlated in the resting state. We hypothesize that these reciprocally inhibitory effects reflect two incompatible cognitive modes, each of which is directed towards understanding the external world. Thus, engaging one mode activates one set of regions and suppresses activity in the other. We test this hypothesis by identifying two types of problem-solving task which, on the basis of prior work, have been consistently associated with the task positive and task negative regions: tasks requiring social cognition, i.e., reasoning about the mental states of other persons, and tasks requiring physical cognition, i.e., reasoning about the causal/mechanical properties of inanimate objects. Social and mechanical reasoning tasks were presented to neurologically normal participants during fMRI. Each task type was presented using both text and video clips. Regardless of presentation modality, we observed clear evidence of reciprocal suppression: social tasks deactivated regions associated with mechanical reasoning and mechanical tasks deactivated regions associated with social reasoning. These findings are not explained by self-referential processes, task engagement, mental simulation, mental time travel or external vs. internal attention, all factors previously hypothesized to explain default mode network activity. Analyses of resting state data revealed a close match between the regions our tasks identified as reciprocally inhibitory and regions of maximal anti-correlation in the resting state. These results indicate

  7. The contribution of primary and secondary somatosensory cortices to the representation of body parts and body sides: an fMRI adaptation study.

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    Tamè, Luigi; Braun, Christoph; Lingnau, Angelika; Schwarzbach, Jens; Demarchi, Gianpaolo; Li Hegner, Yiwen; Farnè, Alessandro; Pavani, Francesco

    2012-12-01

    Although the somatosensory homunculus is a classically used description of the way somatosensory inputs are processed in the brain, the actual contributions of primary (SI) and secondary (SII) somatosensory cortices to the spatial coding of touch remain poorly understood. We studied adaptation of the fMRI BOLD response in the somatosensory cortex by delivering pairs of vibrotactile stimuli to the finger tips of the index and middle fingers. The first stimulus (adaptor) was delivered either to the index or to the middle finger of the right or left hand, and the second stimulus (test) was always administered to the left index finger. The overall BOLD response evoked by the stimulation was primarily contralateral in SI and was more bilateral in SII. However, our fMRI adaptation approach also revealed that both somatosensory cortices were sensitive to ipsilateral as well as to contralateral inputs. SI and SII adapted more after subsequent stimulation of homologous as compared with nonhomologous fingers, showing a distinction between different fingers. Most importantly, for both somatosensory cortices, this finger-specific adaptation occurred irrespective of whether the tactile stimulus was delivered to the same or to different hands. This result implies integration of contralateral and ipsilateral somatosensory inputs in SI as well as in SII. Our findings suggest that SI is more than a simple relay for sensory information and that both SI and SII contribute to the spatial coding of touch by discriminating between body parts (fingers) and by integrating the somatosensory input from the two sides of the body (hands).

  8. The selectivity of responses to red-green colour and achromatic contrast in the human visual cortex: an fMRI adaptation study.

    Science.gov (United States)

    Mullen, Kathy T; Chang, Dorita H F; Hess, Robert F

    2015-12-01

    There is controversy as to how responses to colour in the human brain are organized within the visual pathways. A key issue is whether there are modular pathways that respond selectively to colour or whether there are common neural substrates for both colour and achromatic (Ach) contrast. We used functional magnetic resonance imaging (fMRI) adaptation to investigate the responses of early and extrastriate visual areas to colour and Ach contrast. High-contrast red-green (RG) and Ach sinewave rings (0.5 cycles/degree, 2 Hz) were used as both adapting stimuli and test stimuli in a block design. We found robust adaptation to RG or Ach contrast in all visual areas. Cross-adaptation between RG and Ach contrast occurred in all areas indicating the presence of integrated, colour and Ach responses. Notably, we revealed contrasting trends for the two test stimuli. For the RG test, unselective processing (robust adaptation to both RG and Ach contrast) was most evident in the early visual areas (V1 and V2), but selective responses, revealed as greater adaptation between the same stimuli than cross-adaptation between different stimuli, emerged in the ventral cortex, in V4 and VO in particular. For the Ach test, unselective responses were again most evident in early visual areas but Ach selectivity emerged in the dorsal cortex (V3a and hMT+). Our findings support a strong presence of integrated mechanisms for colour and Ach contrast across the visual hierarchy, with a progression towards selective processing in extrastriate visual areas. © 2015 The Authors. European Journal of Neuroscience published by Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  9. Flexible Adaptive Paradigms for fMRI Using a Novel Software Package ‘Brain Analysis in Real-Time’ (BART)

    Science.gov (United States)

    Hellrung, Lydia; Hollmann, Maurice; Zscheyge, Oliver; Schlumm, Torsten; Kalberlah, Christian; Roggenhofer, Elisabeth; Okon-Singer, Hadas; Villringer, Arno; Horstmann, Annette

    2015-01-01

    In this work we present a new open source software package offering a unified framework for the real-time adaptation of fMRI stimulation procedures. The software provides a straightforward setup and highly flexible approach to adapt fMRI paradigms while the experiment is running. The general framework comprises the inclusion of parameters from subject’s compliance, such as directing gaze to visually presented stimuli and physiological fluctuations, like blood pressure or pulse. Additionally, this approach yields possibilities to investigate complex scientific questions, for example the influence of EEG rhythms or fMRI signals results themselves. To prove the concept of this approach, we used our software in a usability example for an fMRI experiment where the presentation of emotional pictures was dependent on the subject’s gaze position. This can have a significant impact on the results. So far, if this is taken into account during fMRI data analysis, it is commonly done by the post-hoc removal of erroneous trials. Here, we propose an a priori adaptation of the paradigm during the experiment’s runtime. Our fMRI findings clearly show the benefits of an adapted paradigm in terms of statistical power and higher effect sizes in emotion-related brain regions. This can be of special interest for all experiments with low statistical power due to a limited number of subjects, a limited amount of time, costs or available data to analyze, as is the case with real-time fMRI. PMID:25837719

  10. Intrinsic brain network abnormalities in migraines without aura revealed in resting-state fMRI.

    Directory of Open Access Journals (Sweden)

    Ting Xue

    Full Text Available BACKGROUND: Previous studies have defined low-frequency, spatially consistent intrinsic connectivity networks (ICN in resting functional magnetic resonance imaging (fMRI data which reflect functional interactions among distinct brain areas. We sought to explore whether and how repeated migraine attacks influence intrinsic brain connectivity, as well as how activity in these networks correlates with clinical indicators of migraine. METHODS/PRINCIPAL FINDINGS: Resting-state fMRI data in twenty-three patients with migraines without aura (MwoA and 23 age- and gender-matched healthy controls (HC were analyzed using independent component analysis (ICA, in combination with a "dual-regression" technique to identify the group differences of three important pain-related networks [default mode network (DMN, bilateral central executive network (CEN, salience network (SN] between the MwoA patients and HC. Compared with the HC, MwoA patients showed aberrant intrinsic connectivity within the bilateral CEN and SN, and greater connectivity between both the DMN and right CEN (rCEN and the insula cortex - a critical region involving in pain processing. Furthermore, greater connectivity between both the DMN and rCEN and the insula correlated with duration of migraine. CONCLUSIONS: Our findings may provide new insights into the characterization of migraine as a condition affecting brain activity in intrinsic connectivity networks. Moreover, the abnormalities may be the consequence of a persistent central neural system dysfunction, reflecting cumulative brain insults due to frequent ongoing migraine attacks.

  11. Time, space and emotion: fMRI reveals content-specific activation during text comprehension.

    Science.gov (United States)

    Ferstl, Evelyn C; von Cramon, D Yves

    2007-11-12

    Story comprehension involves building a situation model of the text, i.e., a representation containing information on the who, where, when and why of the story. Using fMRI at 3T, domain-specific activations for three different information aspects were sought. Twenty participants read two sentence stories half of which contained inconsistencies concerning emotional, temporal or spatial information. Partly replicating previous results [E.C. Ferstl, M. Rinck, D.Y. von Cramon, Emotional and temporal aspects of situation model processing during text comprehension: an event-related fMRI study, J. Cogn. Neurosci. 17 (2005) 724-739], the anterior lateral prefrontal cortex/orbito-frontal cortex proved important for processing temporal information. The left anterior temporal lobe was particularly important during emotional stories. Most importantly, spatial information elicited bilateral activation in the collateral sulci and the posterior cingulate cortex, areas important for visuo-spatial cognition. These findings provide further evidence for content-specific processes during text comprehension.

  12. fMRI Study Revealing Neural Mechanisms of the Functions of SOA in Spatial Orienting

    Institute of Scientific and Technical Information of China (English)

    Yin Tian; Qian Zhang; De-Zhong Yao

    2009-01-01

    It is well documented that orienting attention plays an important role in visual search. However, it remains unclear how the executive brain regions will act when two different stimulus onset asynchrony (SOA) are used in visual search. In this work, event-related fMRI was used to investigate neural mechanisms on the functions of SOA in endogenous and exogenous orienting. The results showed that in the endogenous orienting, long SOA versus short SOA resulted in widespread cortical activation mainly including right medial frontal gyrus and bilateral middle frontal gyri. Conversely, in exogenous orienting, long SOA compared to short SOA resulted in only activations in bilateral middle frontal gyri. These findings indicated that these two spatial orienting involved different brain areas and neural mechanisms.

  13. Aberrant Processing of Deviant Stimuli in Schizophrenia Revealed by Fusion of FMRI and EEG Data.

    Science.gov (United States)

    Calhoun, Vd; Wu, L; Kiehl, Ka; Eichele, T; Pearlson, Gd

    2010-06-01

    BACKGROUND: Aberrant electrophysiological and hemodynamic processing of auditory oddball stimuli is among the most robustly documented findings in patients with schizophrenia. However, no study to date has directly examined linked patterns of electrical and hemodynamic differences in patients and controls. METHODS: In a recent paper we demonstrated a data-driven approach, joint independent component analysis (jICA) to fuse together functional magnetic resonance imaging (fMRI) and event-related potential (ERP) data and elucidated the chronometry of auditory oddball target detection in healthy control subjects. In this paper we extend our fusion method to identify specific differences in the neuronal chronometry of target detection for chronic schizophrenia patients compared to healthy controls. RESULTS: We found one linked source, consistent with the N2 response, known to be related to cognitive processing of deviant stimuli, spatially localized to bilateral fronto-temporal regions. This source showed significant between-group differences both in amplitude response and in the fMRI/ERP distribution pattern. These findings are consistent with previous work showing N2 amplitude and latency abnormalities in schizophrenia, and provide new information about the linkage between the two. CONCLUSIONS: In summary, we use a novel approach to isolate and identify a linked fMRI/ERP component which shows marked differences in chronic schizophrenia patients. We also demonstrate that jointly using both fMRI and ERP measures provides a fully picture of the underlying hemodynamic and electrical changes which are present in patients. Our approach also has broad applicability to other diseases such as autism, Alzheimer's disease, or bipolar disorder.

  14. Adaptive covariance estimation of non-stationary processes and its application to infer dynamic connectivity from fMRI.

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    Fu, Zening; Chan, Shing-Chow; Di, Xin; Biswal, Bharat; Zhang, Zhiguo

    2014-04-01

    Time-varying covariance is an important metric to measure the statistical dependence between non-stationary biological processes. Time-varying covariance is conventionally estimated from short-time data segments within a window having a certain bandwidth, but it is difficult to choose an appropriate bandwidth to estimate covariance with different degrees of non-stationarity. This paper introduces a local polynomial regression (LPR) method to estimate time-varying covariance and performs an asymptotic analysis of the LPR covariance estimator to show that both the estimation bias and variance are functions of the bandwidth and there exists an optimal bandwidth to minimize the mean square error (MSE) locally. A data-driven variable bandwidth selection method, namely the intersection of confidence intervals (ICI), is adopted in LPR for adaptively determining the local optimal bandwidth that minimizes the MSE. Experimental results on simulated signals show that the LPR-ICI method can achieve robust and reliable performance in estimating time-varying covariance with different degrees of variations and under different noise scenarios, making it a powerful tool to study the dynamic relationship between non-stationary biomedical signals. Further, we apply the LPR-ICI method to estimate time-varying covariance of functional magnetic resonance imaging (fMRI) signals in a visual task for the inference of dynamic functional brain connectivity. The results show that the LPR-ICI method can effectively capture the transient connectivity patterns from fMRI.

  15. The compensatory dynamic of inter-hemispheric interactions in visuospatial attention revealed using rTMS and fMRI

    Directory of Open Access Journals (Sweden)

    Ela B Plow

    2014-04-01

    Full Text Available A balance of mutual tonic inhibition between bi-hemispheric posterior parietal cortices is believed to play an important role in bilateral visual attention. However, experimental support for this notion has been mainly drawn from clinical models of unilateral damage. We have previously shown that low-frequency repetitive TMS (rTMS over the intraparietal sulcus (IPS generates a contralateral attentional deficit in bilateral visual tracking. Here, we used functional Magnetic Resonance Imaging (fMRI to study whether rTMS temporarily disrupts the inter-hemispheric balance between bilateral IPS in visual attention. Following application of 1 Hz rTMS over the left IPS, subjects performed a bilateral visual tracking task while their brain activity was recorded using fMRI. Behaviorally, tracking accuracy was reduced immediately following rTMS. Areas ventro-lateral to left IPS, including inferior parietal lobule (IPL, lateral IPS (LIPS, and middle occipital gyrus (MoG, showed decreased activity following rTMS, while dorsomedial areas, such as Superior Parietal Lobule (SPL, Superior occipital gyrus (SoG, and lingual gyrus, as well as middle temporal areas (MT+, showed higher activity. The brain activity of the homologues of these regions in the un-stimulated, right hemisphere was reversed. Interestingly, the evolution of network-wide activation related to attentional behavior following rTMS showed that activation of most occipital synergists adaptively compensated for contralateral and ipsilateral decrement after rTMS, but that of parietal synergists, and SoG remained competing. This pattern of ipsilateral and contralateral activations empirically supports the hypothesized loss of inter-hemispheric balance that underlies clinical manifestation of visual attentional extinction.

  16. The compensatory dynamic of inter-hemispheric interactions in visuospatial attention revealed using rTMS and fMRI

    Science.gov (United States)

    Plow, Ela B.; Cattaneo, Zaira; Carlson, Thomas A.; Alvarez, George A.; Pascual-Leone, Alvaro; Battelli, Lorella

    2014-01-01

    A balance of mutual tonic inhibition between bi-hemispheric posterior parietal cortices is believed to play an important role in bilateral visual attention. However, experimental support for this notion has been mainly drawn from clinical models of unilateral damage. We have previously shown that low-frequency repetitive TMS (rTMS) over the intraparietal sulcus (IPS) generates a contralateral attentional deficit in bilateral visual tracking. Here, we used functional magnetic resonance imaging (fMRI) to study whether rTMS temporarily disrupts the inter-hemispheric balance between bilateral IPS in visual attention. Following application of 1 Hz rTMS over the left IPS, subjects performed a bilateral visual tracking task while their brain activity was recorded using fMRI. Behaviorally, tracking accuracy was reduced immediately following rTMS. Areas ventro-lateral to left IPS, including inferior parietal lobule (IPL), lateral IPS (LIPS), and middle occipital gyrus (MoG), showed decreased activity following rTMS, while dorsomedial areas, such as Superior Parietal Lobule (SPL), Superior occipital gyrus (SoG), and lingual gyrus, as well as middle temporal areas (MT+), showed higher activity. The brain activity of the homologues of these regions in the un-stimulated, right hemisphere was reversed. Interestingly, the evolution of network-wide activation related to attentional behavior following rTMS showed that activation of most occipital synergists adaptively compensated for contralateral and ipsilateral decrement after rTMS, while activation of parietal synergists, and SoG remained competing. This pattern of ipsilateral and contralateral activations empirically supports the hypothesized loss of inter-hemispheric balance that underlies clinical manifestation of visual attentional extinction. PMID:24860462

  17. FMRI-adaptation to highly-rendered color photographs of animals and manipulable artifacts during a classification task.

    Science.gov (United States)

    Chouinard, Philippe A; Goodale, Melvyn A

    2012-02-01

    We used fMRI to identify brain areas that adapted to either animals or manipulable artifacts while participants classified highly-rendered color photographs into subcategories. Several key brain areas adapted more strongly to one class of objects compared to the other. Namely, we observed stronger adaptation for animals in the lingual gyrus bilaterally, which are known to analyze the color of objects, and in the right frontal operculum and in the anterior insular cortex bilaterally, which are known to process emotional content. In contrast, the left anterior intraparietal sulcus, which is important for configuring the hand to match the three-dimensional structure of objects during grasping, adapted more strongly to manipulable artifacts. Contrary to what a previous study has found using gray-scale photographs, we did not replicate categorical-specific adaptation in the lateral fusiform gyrus for animals and categorical-specific adaptation in the medial fusiform gyrus for manipulable artifacts. Both categories of objects adapted strongly in the fusiform gyrus without any clear preference in location along its medial-lateral axis. We think that this is because the fusiform gyrus has an important role to play in color processing and hence its responsiveness to color stimuli could be very different than its responsiveness to gray-scale photographs. Nevertheless, on the basis of what we found, we propose that the recognition and subsequent classification of animals may depend primarily on perceptual properties, such as their color, and on their emotional content whereas other factors, such as their function, may play a greater role for classifying manipulable artifacts.

  18. Functional Connectivity Estimated from Resting-State fMRI Reveals Selective Alterations in Male Adolescents with Pure Conduct Disorder.

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    Feng-Mei Lu

    Full Text Available Conduct disorder (CD is characterized by a persistent pattern of antisocial behavior and aggression in childhood and adolescence. Previous task-based and resting-state functional magnetic resonance imaging (fMRI studies have revealed widespread brain regional abnormalities in adolescents with CD. However, whether the resting-state networks (RSNs are altered in adolescents with CD remains unknown. In this study, resting-state fMRI data were first acquired from eighteen male adolescents with pure CD and eighteen age- and gender-matched typically developing (TD individuals. Independent component analysis (ICA was implemented to extract nine representative RSNs, and the generated RSNs were then compared to show the differences between the CD and TD groups. Interestingly, it was observed from the brain mapping results that compared with the TD group, the CD group manifested decreased functional connectivity in four representative RSNs: the anterior default mode network (left middle frontal gyrus, which is considered to be correlated with impaired social cognition, the somatosensory network (bilateral supplementary motor area and right postcentral gyrus, the lateral visual network (left superior occipital gyrus, and the medial visual network (right fusiform, left lingual gyrus and right calcarine, which are expected to be relevant to the perceptual systems responsible for perceptual dysfunction in male adolescents with CD. Importantly, the novel findings suggested that male adolescents with pure CD were identified to have dysfunctions in both low-level perceptual networks (the somatosensory network and visual network and a high-order cognitive network (the default mode network. Revealing the changes in the functional connectivity of these RSNs enhances our understanding of the neural mechanisms underlying the modulation of emotion and social cognition and the regulation of perception in adolescents with CD.

  19. Functional Connectivity Estimated from Resting-State fMRI Reveals Selective Alterations in Male Adolescents with Pure Conduct Disorder.

    Science.gov (United States)

    Lu, Feng-Mei; Zhou, Jian-Song; Zhang, Jiang; Xiang, Yu-Tao; Zhang, Jian; Liu, Qi; Wang, Xiao-Ping; Yuan, Zhen

    2015-01-01

    Conduct disorder (CD) is characterized by a persistent pattern of antisocial behavior and aggression in childhood and adolescence. Previous task-based and resting-state functional magnetic resonance imaging (fMRI) studies have revealed widespread brain regional abnormalities in adolescents with CD. However, whether the resting-state networks (RSNs) are altered in adolescents with CD remains unknown. In this study, resting-state fMRI data were first acquired from eighteen male adolescents with pure CD and eighteen age- and gender-matched typically developing (TD) individuals. Independent component analysis (ICA) was implemented to extract nine representative RSNs, and the generated RSNs were then compared to show the differences between the CD and TD groups. Interestingly, it was observed from the brain mapping results that compared with the TD group, the CD group manifested decreased functional connectivity in four representative RSNs: the anterior default mode network (left middle frontal gyrus), which is considered to be correlated with impaired social cognition, the somatosensory network (bilateral supplementary motor area and right postcentral gyrus), the lateral visual network (left superior occipital gyrus), and the medial visual network (right fusiform, left lingual gyrus and right calcarine), which are expected to be relevant to the perceptual systems responsible for perceptual dysfunction in male adolescents with CD. Importantly, the novel findings suggested that male adolescents with pure CD were identified to have dysfunctions in both low-level perceptual networks (the somatosensory network and visual network) and a high-order cognitive network (the default mode network). Revealing the changes in the functional connectivity of these RSNs enhances our understanding of the neural mechanisms underlying the modulation of emotion and social cognition and the regulation of perception in adolescents with CD.

  20. An fMRI Study of Audiovisual Speech Perception Reveals Multisensory Interactions in Auditory Cortex.

    Science.gov (United States)

    Okada, Kayoko; Venezia, Jonathan H; Matchin, William; Saberi, Kourosh; Hickok, Gregory

    2013-01-01

    Research on the neural basis of speech-reading implicates a network of auditory language regions involving inferior frontal cortex, premotor cortex and sites along superior temporal cortex. In audiovisual speech studies, neural activity is consistently reported in posterior superior temporal Sulcus (pSTS) and this site has been implicated in multimodal integration. Traditionally, multisensory interactions are considered high-level processing that engages heteromodal association cortices (such as STS). Recent work, however, challenges this notion and suggests that multisensory interactions may occur in low-level unimodal sensory cortices. While previous audiovisual speech studies demonstrate that high-level multisensory interactions occur in pSTS, what remains unclear is how early in the processing hierarchy these multisensory interactions may occur. The goal of the present fMRI experiment is to investigate how visual speech can influence activity in auditory cortex above and beyond its response to auditory speech. In an audiovisual speech experiment, subjects were presented with auditory speech with and without congruent visual input. Holding the auditory stimulus constant across the experiment, we investigated how the addition of visual speech influences activity in auditory cortex. We demonstrate that congruent visual speech increases the activity in auditory cortex.

  1. Human fMRI reveals that delayed action re-recruits visual perception.

    Science.gov (United States)

    Singhal, Anthony; Monaco, Simona; Kaufman, Liam D; Culham, Jody C

    2013-01-01

    Behavioral and neuropsychological research suggests that delayed actions rely on different neural substrates than immediate actions; however, the specific brain areas implicated in the two types of actions remain unknown. We used functional magnetic resonance imaging (fMRI) to measure human brain activation during delayed grasping and reaching. Specifically, we examined activation during visual stimulation and action execution separated by a 18-s delay interval in which subjects had to remember an intended action toward the remembered object. The long delay interval enabled us to unambiguously distinguish visual, memory-related, and action responses. Most strikingly, we observed reactivation of the lateral occipital complex (LOC), a ventral-stream area implicated in visual object recognition, and early visual cortex (EVC) at the time of action. Importantly this reactivation was observed even though participants remained in complete darkness with no visual stimulation at the time of the action. Moreover, within EVC, higher activation was observed for grasping than reaching during both vision and action execution. Areas in the dorsal visual stream were activated during action execution as expected and, for some, also during vision. Several areas, including the anterior intraparietal sulcus (aIPS), dorsal premotor cortex (PMd), primary motor cortex (M1) and the supplementary motor area (SMA), showed sustained activation during the delay phase. We propose that during delayed actions, dorsal-stream areas plan and maintain coarse action goals; however, at the time of execution, motor programming requires re-recruitment of detailed visual information about the object through reactivation of (1) ventral-stream areas involved in object perception and (2) early visual areas that contain richly detailed visual representations, particularly for grasping.

  2. Cognitive control mechanisms revealed by ERP and fMRI: evidence from repeated task-switching.

    Science.gov (United States)

    Swainson, R; Cunnington, R; Jackson, G M; Rorden, C; Peters, A M; Morris, P G; Jackson, S R

    2003-08-15

    We investigated the extent to which a common neural mechanism is involved in task set-switching and response withholding, factors that are frequently confounded in task-switching and go/no-go paradigms. Subjects' brain activity was measured using event-related electrical potentials (ERPs) and event-related functional MRI (fMRI) neuroimaging in separate studies using the same cognitive paradigm. Subjects made compatible left/right keypress responses to left/right arrow stimuli of 1000 msec duration; they switched every two trials between responding at stimulus onset (GO task-green arrows) and stimulus offset (WAIT task-red arrows). With-holding an immediate response (WAIT vs. GO) elicited an enhancement of the frontal N2 ERP and lateral PFC activation of the right hemisphere, both previously associated with the "no-go" response, but only on switch trials. Task-switching (switch vs. nonswitch) was associated with frontal N2 amplification and right hemisphere ventrolateral PFC activation, but only for the WAIT task. The anterior cingulate cortex (ACC) was the only brain region to be activated for both types of task switch, but this activation was located more rostrally for the WAIT than for the GO switch trials. We conclude that the frontal N2 ERP and lateral PFC activation are not markers for withholding an immediate response or switching tasks per se, but are associated with switching into a response-suppression mode. Different regions within the ACC may be involved in two processes integral to task-switching: processing response conflict (rostral ACC) and overcoming prior response suppression (caudal ACC).

  3. Human fMRI reveals that delayed action re-recruits visual perception.

    Directory of Open Access Journals (Sweden)

    Anthony Singhal

    Full Text Available Behavioral and neuropsychological research suggests that delayed actions rely on different neural substrates than immediate actions; however, the specific brain areas implicated in the two types of actions remain unknown. We used functional magnetic resonance imaging (fMRI to measure human brain activation during delayed grasping and reaching. Specifically, we examined activation during visual stimulation and action execution separated by a 18-s delay interval in which subjects had to remember an intended action toward the remembered object. The long delay interval enabled us to unambiguously distinguish visual, memory-related, and action responses. Most strikingly, we observed reactivation of the lateral occipital complex (LOC, a ventral-stream area implicated in visual object recognition, and early visual cortex (EVC at the time of action. Importantly this reactivation was observed even though participants remained in complete darkness with no visual stimulation at the time of the action. Moreover, within EVC, higher activation was observed for grasping than reaching during both vision and action execution. Areas in the dorsal visual stream were activated during action execution as expected and, for some, also during vision. Several areas, including the anterior intraparietal sulcus (aIPS, dorsal premotor cortex (PMd, primary motor cortex (M1 and the supplementary motor area (SMA, showed sustained activation during the delay phase. We propose that during delayed actions, dorsal-stream areas plan and maintain coarse action goals; however, at the time of execution, motor programming requires re-recruitment of detailed visual information about the object through reactivation of (1 ventral-stream areas involved in object perception and (2 early visual areas that contain richly detailed visual representations, particularly for grasping.

  4. Resting State fMRI in Mice Reveals Anesthesia Specific Signatures of Brain Functional Networks and Their Interactions

    Science.gov (United States)

    Bukhari, Qasim; Schroeter, Aileen; Cole, David M.; Rudin, Markus

    2017-01-01

    fMRI studies in mice typically require the use of anesthetics. Yet, it is known that anesthesia alters responses to stimuli or functional networks at rest. In this work, we have used Dual Regression analysis Network Modeling to investigate the effects of two commonly used anesthetics, isoflurane and medetomidine, on rs-fMRI derived functional networks, and in particular to what extent anesthesia affected the interaction within and between these networks. Experimental data have been used from a previous study (Grandjean et al., 2014). We applied multivariate ICA analysis and Dual Regression to infer the differences in functional connectivity between isoflurane- and medetomidine-anesthetized mice. Further network analysis was performed to investigate within- and between-network connectivity differences between these anesthetic regimens. The results revealed five major networks in the mouse brain: lateral cortical, associative cortical, default mode, subcortical, and thalamic network. The anesthesia regime had a profound effect both on within- and between-network interactions. Under isoflurane anesthesia predominantly intra- and inter-cortical interactions have been observed, with only minor interactions involving subcortical structures and in particular attenuated cortico-thalamic connectivity. In contrast, medetomidine-anesthetized mice displayed subcortical functional connectivity including interactions between cortical and thalamic ICA components. Combining the two anesthetics at low dose resulted in network interaction that constituted the superposition of the interaction observed for each anesthetic alone. The study demonstrated that network modeling is a promising tool for analyzing the brain functional architecture in mice and comparing alterations therein caused by different physiological or pathological states. Understanding the differential effects of anesthetics on brain networks and their interaction is essential when interpreting fMRI data recorded under

  5. Resting State fMRI in Mice Reveals Anesthesia Specific Signatures of Brain Functional Networks and Their Interactions.

    Science.gov (United States)

    Bukhari, Qasim; Schroeter, Aileen; Cole, David M; Rudin, Markus

    2017-01-01

    fMRI studies in mice typically require the use of anesthetics. Yet, it is known that anesthesia alters responses to stimuli or functional networks at rest. In this work, we have used Dual Regression analysis Network Modeling to investigate the effects of two commonly used anesthetics, isoflurane and medetomidine, on rs-fMRI derived functional networks, and in particular to what extent anesthesia affected the interaction within and between these networks. Experimental data have been used from a previous study (Grandjean et al., 2014). We applied multivariate ICA analysis and Dual Regression to infer the differences in functional connectivity between isoflurane- and medetomidine-anesthetized mice. Further network analysis was performed to investigate within- and between-network connectivity differences between these anesthetic regimens. The results revealed five major networks in the mouse brain: lateral cortical, associative cortical, default mode, subcortical, and thalamic network. The anesthesia regime had a profound effect both on within- and between-network interactions. Under isoflurane anesthesia predominantly intra- and inter-cortical interactions have been observed, with only minor interactions involving subcortical structures and in particular attenuated cortico-thalamic connectivity. In contrast, medetomidine-anesthetized mice displayed subcortical functional connectivity including interactions between cortical and thalamic ICA components. Combining the two anesthetics at low dose resulted in network interaction that constituted the superposition of the interaction observed for each anesthetic alone. The study demonstrated that network modeling is a promising tool for analyzing the brain functional architecture in mice and comparing alterations therein caused by different physiological or pathological states. Understanding the differential effects of anesthetics on brain networks and their interaction is essential when interpreting fMRI data recorded under

  6. Regional Coherence Alterations Revealed by Resting-State fMRI in Post-Stroke Patients with Cognitive Dysfunction

    National Research Council Canada - National Science Library

    Peng, Cheng-Yu; Chen, Yu-Chen; Cui, Ying; Zhao, Deng-Ling; Jiao, Yun; Tang, Tian-Yu; Ju, Shenghong; Teng, Gao-Jun

    2016-01-01

    ...) to investigate the alterations in regional coherence in patients after subcortical stroke. Resting-state fMRI measurements were acquired from 16 post-stroke patients with poor cognitive function (PSPC...

  7. Adaptive coding of the value of social cues with oxytocin, an fMRI study in autism spectrum disorder.

    Science.gov (United States)

    Andari, Elissar; Richard, Nathalie; Leboyer, Marion; Sirigu, Angela

    2016-03-01

    The neuropeptide oxytocin (OT) is one of the major targets of research in neuroscience, with respect to social functioning. Oxytocin promotes social skills and improves the quality of face processing in individuals with social dysfunctions such as autism spectrum disorder (ASD). Although one of OT's key functions is to promote social behavior during dynamic social interactions, the neural correlates of this function remain unknown. Here, we combined acute intranasal OT (IN-OT) administration (24 IU) and fMRI with an interactive ball game and a face-matching task in individuals with ASD (N = 20). We found that IN-OT selectively enhanced the brain activity of early visual areas in response to faces as compared to non-social stimuli. OT inhalation modulated the BOLD activity of amygdala and hippocampus in a context-dependent manner. Interestingly, IN-OT intake enhanced the activity of mid-orbitofrontal cortex in response to a fair partner, and insula region in response to an unfair partner. These OT-induced neural responses were accompanied by behavioral improvements in terms of allocating appropriate feelings of trust toward different partners' profiles. Our findings suggest that OT impacts the brain activity of key areas implicated in attention and emotion regulation in an adaptive manner, based on the value of social cues. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Wechsler Memory Scale Revised Edition: neural correlates of the visual paired associates subtest adapted for fMRI.

    Science.gov (United States)

    Neuner, Irene; Stöcker, Tony; Kellermann, Thilo; Kircher, Tilo; Zilles, Karl; Schneider, Frank; Shah, N Jon

    2007-10-26

    Memory deficits in neurological and psychiatric patients are evaluated by neuropsychological tests such as the Wechsler Memory Scale Revised Edition (WMS-R). Neuropsychological data from patients with circumscribed lesions point to single elements of the underlying neural network but fail to identify its whole extent. We report the fMRI adaptation of a subtest of the WMS-R, the Visual Paired Associates. Fifteen healthy, right-handed male volunteers were studied using a 1.5T MRI scanner. The encoding of the combination between a shape and a colour, the assessment of the retrieval of this combination immediately after encoding took place, and the underlying network employed during retrieval a second time after approximately 25 min were investigated. The results show a fronto-parieto-occipital network with left frontal accentuation for encoding and a fronto-parieto-occipital network for immediate and delayed retrieval. Noteworthy is the specific role of the thalamus. During immediate retrieval, the thalamus showed significant bilateral activation; during delayed retrieval, there was no significant activation. The thalami are part of an extended hippocampal-diencephalic system which is critical for efficient encoding and normal retrieval of new episodic information. We describe the probability of thalamocortical connections during retrieval based on the Thalamus Connectivity Atlas. The cerebellum showed significant activation in all conditions; its part in higher cognitive functions such as memory was thereby confirmed.

  9. Pain facilitation brain regions activated by nalbuphine are revealed by pharmacological fMRI.

    Directory of Open Access Journals (Sweden)

    Robert Gear

    Full Text Available Nalbuphine, an agonist-antagonist kappa-opioid, produces brief analgesia followed by enhanced pain/hyperalgesia in male postsurgical patients. However, it produces profound analgesia without pain enhancement when co-administration with low dose naloxone. To examine the effect of nalbuphine or nalbuphine plus naloxone on activity in brain regions that may explain these differences, we employed pharmacological magnetic resonance imaging (phMRI in a double blind cross-over study with 13 healthy male volunteers. In separate imaging sessions subjects were administered nalbuphine (5 mg/70 kg preceded by either saline (Sal-Nalb or naloxone 0.4 mg (Nalox-Nalb. Blood oxygen level-dependent (BOLD activation maps followed by contrast and connectivity analyses revealed marked differences. Sal-Nalb produced significantly increased activity in 60 brain regions and decreased activity in 9; in contrast, Nalox-Nalb activated only 14 regions and deactivated only 3. Nalbuphine, like morphine in a previous study, attenuated activity in the inferior orbital cortex, and, like noxious stimulation, increased activity in temporal cortex, insula, pulvinar, caudate, and pons. Co-administration/pretreatment of naloxone selectively blocked activity in pulvinar, pons and posterior insula. Nalbuphine induced functional connectivity between caudate and regions in the frontal, occipital, temporal, insular, middle cingulate cortices, and putamen; naloxone co-admistration reduced all connectivity to non-significant levels, and, like phMRI measures of morphine, increased activation in other areas (e.g., putamen. Naloxone pretreatment to nalbuphine produced changes in brain activity possess characteristics of both analgesia and algesia; naloxone selectively blocks activity in areas associated with algesia. Given these findings, we suggest that nalbuphine interacts with a pain salience system, which can modulate perceived pain intensity.

  10. Sequencing of 50 human exomes reveals adaptation to high altitude

    DEFF Research Database (Denmark)

    Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia

    2010-01-01

    represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency...... difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus...

  11. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    Science.gov (United States)

    2012-01-01

    Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed. PMID:22401625

  12. Comparative genomics reveals evidence of marine adaptation in Salinispora species.

    Science.gov (United States)

    Penn, Kevin; Jensen, Paul R

    2012-03-08

    Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed.

  13. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    Directory of Open Access Journals (Sweden)

    Penn Kevin

    2012-03-01

    Full Text Available Abstract Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed.

  14. Separate channels for processing form, texture, and color: evidence from FMRI adaptation and visual object agnosia.

    Science.gov (United States)

    Cavina-Pratesi, C; Kentridge, R W; Heywood, C A; Milner, A D

    2010-10-01

    Previous neuroimaging research suggests that although object shape is analyzed in the lateral occipital cortex, surface properties of objects, such as color and texture, are dealt with in more medial areas, close to the collateral sulcus (CoS). The present study sought to determine whether there is a single medial region concerned with surface properties in general or whether instead there are multiple foci independently extracting different surface properties. We used stimuli varying in their shape, texture, or color, and tested healthy participants and 2 object-agnosic patients, in both a discrimination task and a functional MR adaptation paradigm. We found a double dissociation between medial and lateral occipitotemporal cortices in processing surface (texture or color) versus geometric (shape) properties, respectively. In Experiment 2, we found that the medial occipitotemporal cortex houses separate foci for color (within anterior CoS and lingual gyrus) and texture (caudally within posterior CoS). In addition, we found that areas selective for shape, texture, and color individually were quite distinct from those that respond to all of these features together (shape and texture and color). These latter areas appear to correspond to those associated with the perception of complex stimuli such as faces and places.

  15. Task-Related Edge Density (TED-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.

    Directory of Open Access Journals (Sweden)

    Gabriele Lohmann

    Full Text Available The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach "Task-related Edge Density" (TED. TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function.

  16. Task-Related Edge Density (TED)-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.

    Science.gov (United States)

    Lohmann, Gabriele; Stelzer, Johannes; Zuber, Verena; Buschmann, Tilo; Margulies, Daniel; Bartels, Andreas; Scheffler, Klaus

    2016-01-01

    The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach "Task-related Edge Density" (TED). TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function.

  17. Brain-decoding fMRI reveals how wholes relate to the sum of parts.

    Science.gov (United States)

    Kubilius, Jonas; Baeck, Annelies; Wagemans, Johan; Op de Beeck, Hans P

    2015-11-01

    The human brain performs many nonlinear operations in order to extract relevant information from local inputs. How can we observe and quantify these effects within and across large patches of cortex? In this paper, we discuss the application of multi-voxel pattern analysis (MVPA) in functional magnetic resonance imaging (fMRI) to address this issue. Specifically, we show how MVPA (i) allows to compare various possibilities of part combinations into wholes, such as taking the mean, weighted mean, or the maximum of responses to the parts; (ii) can be used to quantify the parameters of these combinations; and (iii) can be applied in various experimental paradigms. Through these procedures, fMRI helps to obtain a computational understanding of how local information is integrated into larger wholes in various cortical regions.

  18. The neural substrates of musical memory revealed by fMRI and two semantic tasks. : Neural substrates of musical memory

    OpenAIRE

    Groussard, Mathilde; Rauchs, Géraldine; Landeau, Brigitte; Viader, Fausto; Desgranges, Béatrice; Eustache, Francis; Platel, Hervé

    2010-01-01

    International audience; Recognizing a musical excerpt without necessarily retrieving its title typically reflects the existence of a memory system dedicated to the retrieval of musical knowledge. The functional distinction between musical and verbal semantic memory has seldom been investigated. In this fMRI study, we directly compared the musical and verbal memory of 20 nonmusicians, using a congruence task involving automatic semantic retrieval and a familiarity task requiring more thorough ...

  19. Lateral visual field stimulation reveals extrastriate cortical activation in the contralateral hemisphere: an fMRI study.

    Science.gov (United States)

    Schiffer, Fredric; Mottaghy, Felix M; Pandey Vimal, Ram Lakhan; Renshaw, Perry F; Cowan, Ronald; Pascual-Leone, Alvaro; Teicher, Martin; Valente, Elizabeth; Rohan, Michael

    2004-05-30

    We examined whether lateral visual field stimulation (LSTM) could activate contralateral extrastriate cortical areas as predicted by a large experimental literature. We asked seven unscreened, control subjects to wear glasses designed to allow vision out of either the left (LVF) or right lateral visual field (RVF) depending upon which side the subject looked toward. Each subject participated in a block design functional magnetic resonance imaging (fMRI) study with alternating 30-s epochs in which he was asked to look to one side and then the other for a total of five epochs. On each side of the bore of the scanner, we taped a photograph for the subject to view in the LVF and RVF. The data were analyzed with SPM99 using a fixed effect, box-car design with contrasts for the LVF and the RVF conditions. Both LVF and RVF conditions produced the strongest fMRI activation in the contralateral occipitotemporal and posterior parietal areas as well as the contralateral dorsolateral prefrontal cortex. LSTM appears to increase contralateral fMRI activation in striate and extrastriate cortical areas as predicted by earlier studies reporting differential cognitive and/or emotional effects from unilateral sensory or motor stimulation.

  20. Functional dissociation of transient and sustained fMRI BOLD components in human auditory cortex revealed with a streaming paradigm based on interaural time differences.

    Science.gov (United States)

    Schadwinkel, Stefan; Gutschalk, Alexander

    2010-12-01

    A number of physiological studies suggest that feature-selective adaptation is relevant to the pre-processing for auditory streaming, the perceptual separation of overlapping sound sources. Most of these studies are focused on spectral differences between streams, which are considered most important for streaming. However, spatial cues also support streaming, alone or in combination with spectral cues, but physiological studies of spatial cues for streaming remain scarce. Here, we investigate whether the tuning of selective adaptation for interaural time differences (ITD) coincides with the range where streaming perception is observed. FMRI activation that has been shown to adapt depending on the repetition rate was studied with a streaming paradigm where two tones were differently lateralized by ITD. Listeners were presented with five different ΔITD conditions (62.5, 125, 187.5, 343.75, or 687.5 μs) out of an active baseline with no ΔITD during fMRI. The results showed reduced adaptation for conditions with ΔITD ≥ 125 μs, reflected by enhanced sustained BOLD activity. The percentage of streaming perception for these stimuli increased from approximately 20% for ΔITD = 62.5 μs to > 60% for ΔITD = 125 μs. No further sustained BOLD enhancement was observed when the ΔITD was increased beyond ΔITD = 125 μs, whereas the streaming probability continued to increase up to 90% for ΔITD = 687.5 μs. Conversely, the transient BOLD response, at the transition from baseline to ΔITD blocks, increased most prominently as ΔITD was increased from 187.5 to 343.75 μs. These results demonstrate a clear dissociation of transient and sustained components of the BOLD activity in auditory cortex.

  1. High field fMRI reveals thalamocortical integration of segregated cognitive and emotional processing in mediodorsal and intralaminar thalamic nuclei

    Directory of Open Access Journals (Sweden)

    Coraline Danielle Metzger

    2010-11-01

    Full Text Available Thalamocortical loops, connecting functionally segregated, higher order cortical regions and basal ganglia, have been proposed not only for well described motor and sensory regions, but also for limbic and prefrontal areas relevant for affective and cognitive processes. These functions are, however, more specific to humans, rendering most invasive neuroanatomical approaches impossible and interspecies translations difficult. In contrast, non invasive imaging of functional neuroanatomy using fMRI allows for the development of elaborate task paradigms capable of testing the specific functionalities proposed for these circuits. Until recently, spatial resolution largely limited the anatomical definition of functional clusters at the level of distinct thalamic nuclei. Since their anatomical distinction seems crucial not only for the segregation of cognitive and limbic loops but also for the detection of their functional interaction during cognitive-emotional integration, we applied high resolution fMRI on 7 Tesla.Using an event related design, we could isolate thalamic effects for preceding attention as well as experience of erotic stimuli. We could demonstrate specific thalamic effects of general emotional arousal in mediodorsal nucleus and effects specific to preceding attention and expectancy in intralaminar centromedian/parafascicular complex (CM/PF. These thalamic effects were paralleled by specific coactivations in the head of caudate nucleus as well as segregated portions of rostral or caudal cingulate cortex and anterior insula supporting distinct thalamo-striato-cortical loops. In addition to predescribed effects of sexual arousal in hypothalamus and ventral striatum, high resolution fMRI could extent this network to paraventricular thalamus encompassing laterodorsal and parataenial nuclei. We could lend evidence to segregated subcortical loops which integrate cognitive and emotional aspects of basic human behaviour such as sexual

  2. Naturalistic fMRI Mapping Reveals Superior Temporal Sulcus as the Hub for the Distributed Brain Network for Social Perception

    Science.gov (United States)

    Lahnakoski, Juha M.; Glerean, Enrico; Salmi, Juha; Jääskeläinen, Iiro P.; Sams, Mikko; Hari, Riitta; Nummenmaa, Lauri

    2012-01-01

    Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-T functional magnetic resonance imaging (fMRI), a set of 137 short (approximately 16 s each, total 27 min) audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech) and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action, and non-human sounds) lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS) responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: (1) a fronto-temporal network responding to multiple social categories, (2) a fronto-parietal network preferentially activated to bodies, motion, and pain, (3) a temporo-amygdalar network responding to faces, social interaction, and speech, and (4) a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the pSTS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life. PMID:22905026

  3. Naturalistic FMRI mapping reveals superior temporal sulcus as the hub for the distributed brain network for social perception.

    Science.gov (United States)

    Lahnakoski, Juha M; Glerean, Enrico; Salmi, Juha; Jääskeläinen, Iiro P; Sams, Mikko; Hari, Riitta; Nummenmaa, Lauri

    2012-01-01

    Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-T functional magnetic resonance imaging (fMRI), a set of 137 short (approximately 16 s each, total 27 min) audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech) and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action, and non-human sounds) lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS) responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: (1) a fronto-temporal network responding to multiple social categories, (2) a fronto-parietal network preferentially activated to bodies, motion, and pain, (3) a temporo-amygdalar network responding to faces, social interaction, and speech, and (4) a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the pSTS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life.

  4. Naturalistic fMRI mapping reveals superior temporal sulcus as the hub for the distributed brain network for social perception

    Directory of Open Access Journals (Sweden)

    Juha Marko Lahnakoski

    2012-08-01

    Full Text Available Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-tesla functional magnetic imaging (fMRI, a set of 137 short (~16 s each, total 27 min audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action and non-human sounds lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: 1 a fronto-temporal network responding to multiple social categories, 2 a fronto-parietal network preferentially activated to bodies, motion and pain, 3 a temporo-amygdalar network responding to faces, social interaction and speech, and 4 a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the posterior STS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life.

  5. High Field fMRI Reveals Thalamocortical Integration of Segregated Cognitive and Emotional Processing in Mediodorsal and Intralaminar Thalamic Nuclei

    Science.gov (United States)

    Metzger, C. D.; Eckert, U.; Steiner, J.; Sartorius, A.; Buchmann, J. E.; Stadler, J.; Tempelmann, C.; Speck, O.; Bogerts, B.; Abler, B.; Walter, M.

    2010-01-01

    Thalamocortical loops, connecting functionally segregated, higher order cortical regions, and basal ganglia, have been proposed not only for well described motor and sensory regions, but also for limbic and prefrontal areas relevant for affective and cognitive processes. These functions are, however, more specific to humans, rendering most invasive neuroanatomical approaches impossible and interspecies translations difficult. In contrast, non-invasive imaging of functional neuroanatomy using fMRI allows for the development of elaborate task paradigms capable of testing the specific functionalities proposed for these circuits. Until recently, spatial resolution largely limited the anatomical definition of functional clusters at the level of distinct thalamic nuclei. Since their anatomical distinction seems crucial not only for the segregation of cognitive and limbic loops but also for the detection of their functional interaction during cognitive–emotional integration, we applied high resolution fMRI on 7 Tesla. Using an event-related design, we could isolate thalamic effects for preceding attention as well as experience of erotic stimuli. We could demonstrate specific thalamic effects of general emotional arousal in mediodorsal nucleus and effects specific to preceding attention and expectancy in intralaminar centromedian/parafascicular complex. These thalamic effects were paralleled by specific coactivations in the head of caudate nucleus as well as segregated portions of rostral or caudal cingulate cortex and anterior insula supporting distinct thalamo–striato–cortical loops. In addition to predescribed effects of sexual arousal in hypothalamus and ventral striatum, high resolution fMRI could extent this network to paraventricular thalamus encompassing laterodorsal and parataenial nuclei. We could lend evidence to segregated subcortical loops which integrate cognitive and emotional aspects of basic human behavior such as sexual processing. PMID:21088699

  6. Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation.

    Science.gov (United States)

    Kurczy, Michael E; Forsberg, Erica M; Thorgersen, Michael P; Poole, Farris L; Benton, H Paul; Ivanisevic, Julijana; Tran, Minerva L; Wall, Judy D; Elias, Dwayne A; Adams, Michael W W; Siuzdak, Gary

    2016-06-17

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.

  7. Impossible expectations: fMRI adaptation in the lateral occipital complex (LOC) is modulated by the statistical regularities of 3D structural information.

    Science.gov (United States)

    Freud, Erez; Ganel, Tzvi; Avidan, Galia

    2015-11-15

    fMRI adaptation (fMRIa), the attenuation of fMRI signal which follows repeated presentation of a stimulus, is a well-documented phenomenon. Yet, the underlying neural mechanisms supporting this effect are not fully understood. Recently, short-term perceptual expectations, induced by specific experimental settings, were shown to play an important modulating role in fMRIa. Here we examined the role of long-term expectations, based on 3D structural statistical regularities, in the modulation of fMRIa. To this end, human participants underwent fMRI scanning while performing a same-different task on pairs of possible (regular, expected) objects and spatially impossible (irregular, unexpected) objects. We hypothesized that given the spatial irregularity of impossible objects in relation to real-world visual experience, the visual system would always generate a prediction which is biased to the possible version of the objects. Consistently, fMRIa effects in the lateral occipital cortex (LOC) were found for possible, but not for impossible objects. Additionally, in alternating trials the order of stimulus presentation modulated LOC activity. That is, reduced activation was observed in trials in which the impossible version of the object served as the prime object (i.e. first object) and was followed by the possible version compared to the reverse order. These results were also supported by the behavioral advantage observed for trials that were primed by possible objects. Together, these findings strongly emphasize the importance of perceptual expectations in object representation and provide novel evidence for the role of real-world statistical regularities in eliciting fMRIa.

  8. Regional Coherence Alterations Revealed by Resting-State fMRI in Post-Stroke Patients with Cognitive Dysfunction.

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    Cheng-Yu Peng

    Full Text Available Post-stroke cognitive dysfunction greatly influences patients' quality of life after stroke. However, its neurophysiological basis remains unknown. This study utilized resting-state functional magnetic resonance imaging (fMRI to investigate the alterations in regional coherence in patients after subcortical stroke.Resting-state fMRI measurements were acquired from 16 post-stroke patients with poor cognitive function (PSPC, 16 post-stroke patients with good cognitive function (PSGC and 30 well-matched healthy controls (HC. Regional homogeneity (ReHo was used to detect alterations in regional coherence. Abnormalities in regional coherence correlated with scores on neuropsychological scales.Compared to the HC and the PSGC, the PSPC showed remarkably decreased ReHo in the bilateral anterior cingulate cortex and the left posterior cingulate cortex/precuneus. ReHo in the bilateral anterior cingulate cortex positively correlated with the scores on the Symbol Digit Modalities Test (r = 0.399, P = 0.036 and the Complex Figure Test-delayed recall subtest (r = 0.397, P = 0.036 in all post-stroke patients. Moreover, ReHo in the left posterior cingulate cortex/precuneus positively correlated with the scores on the Forward Digit Span Test (r = 0.485, P = 0.009 in all post-stroke patients.Aberrant regional coherence was observed in the anterior and posterior cingulate cortices in post-stroke patients with cognitive dysfunction. ReHo could represent a promising indicator of neurobiological deficiencies in post-stroke patients.

  9. Recent seizure activity alters motor organization in frontal lobe epilepsy as revealed by task-based fMRI.

    Science.gov (United States)

    Woodward, Kristine E; Gaxiola-Valdez, Ismael; Mainprize, David; Grossi, Matthew; Goodyear, Bradley G; Federico, Paolo

    2014-10-01

    Patients with frontal lobe epilepsy (FLE) commonly demonstrate motor impairments, suggesting that frontal lobe seizures affect motor function. However, the underlying mechanisms of these deficits are not known, nor has any study systematically examined motor organization in these patients. We therefore examined cortical motor organization in a group of adult patients with FLE, using task-based fMRI. Eleven right FLE patients, six left FLE patients, and ten control subjects underwent task-based fMRI. Two tasks were performed using the right and left hands separately, and both hands together. The first task was a finger-tapping task and the second task was a more complex coordination task. Functional MR data were compared between patient groups and controls. A laterality index of brain activation was also calculated between the epileptic and healthy hemisphere to determine hemispheric dominance during task performance to explore its relationship with a variety of patient-specific epilepsy factors. Overall, right FLE patients demonstrated decreased BOLD activity in the epileptic hemisphere and increased BOLD activity in the healthy hemisphere compared to controls (pseizure in both patient groups (right FLE: rs=0.779, left FLE: rs=0.943). Patients that had experienced a recent seizure relied more on the sensorimotor cortex of the healthy hemisphere during task performance, compared to those that were relatively seizure free (pseizure freedom. These results demonstrate the presence of seizure-related alteration of cortical motor organization in FLE, which may underlie the motor deficits seen in these patients. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Framing effects reveal discrete lexical-semantic and sublexical procedures in reading: an fMRI study.

    Science.gov (United States)

    Danelli, Laura; Marelli, Marco; Berlingeri, Manuela; Tettamanti, Marco; Sberna, Maurizio; Paulesu, Eraldo; Luzzatti, Claudio

    2015-01-01

    According to the dual-route model, a printed string of letters can be processed by either a grapheme-to-phoneme conversion (GPC) route or a lexical-semantic route. Although meta-analyses of the imaging literature support the existence of distinct but interacting reading procedures, individual neuroimaging studies that explored neural correlates of reading yielded inconclusive results. We used a list-manipulation paradigm to provide a fresh empirical look at this issue and to isolate specific areas that underlie the two reading procedures. In a lexical condition, we embedded disyllabic Italian words (target stimuli) in lists of either loanwords or trisyllabic Italian words with unpredictable stress position. In a GPC condition, similar target stimuli were included within lists of pseudowords. The procedure was designed to induce participants to emphasize either the lexical-semantic or the GPC reading procedure, while controlling for possible linguistic confounds and keeping the reading task requirements stable across the two conditions. Thirty-three adults participated in the behavioral study, and 20 further adult participants were included in the fMRI study. At the behavioral level, we found sizeable effects of the framing manipulations that included slower voice onset times for stimuli in the pseudoword frames. At the functional anatomical level, the occipital and temporal regions, and the intraparietal sulcus were specifically activated when subjects were reading target words in a lexical frame. The inferior parietal and anterior fusiform cortex were specifically activated in the GPC condition. These patterns of activation represented a valid classifying model of fMRI images associated with target reading in both frames in the multi-voxel pattern analyses. Further activations were shared by the two procedures in the occipital and inferior parietal areas, in the premotor cortex, in the frontal regions and the left supplementary motor area. These regions are most

  11. Framing effects reveal discrete lexical-semantic and sublexical procedures in reading: an fMRI study

    Directory of Open Access Journals (Sweden)

    Laura eDanelli

    2015-09-01

    Full Text Available According to the dual-route model, a printed string of letters can be processed by either a grapheme-to-phoneme conversion (GPC route or a lexical-semantic route. Although meta-analyses of the imaging literature support the existence of distinct but interacting reading procedures, individual neuroimaging studies that explored neural correlates of reading yielded inconclusive results. We used a list-manipulation paradigm to provide a fresh empirical look at this issue and to isolate specific areas that underlie the two reading procedures. In a lexical condition, we embedded disyllabic Italian words (target stimuli in lists of either loanwords or trisyllabic Italian words with an unpredictable stress position. In a GPC condition, similar target stimuli were mixed into lists of pseudowords. The procedure was designed to induce participants to emphasize a lexical-semantic or a GPC reading procedure, while controlling for possible linguistic confounds and keeping the reading task requirements stable across the two conditions. Thirty-three adults participated in the behavioral study, and 20 other adult participants were included in the fMRI study. At the behavioral level, we found sizeable effects of the framing manipulations that included slower voice onset times for stimuli in the pseudoword frames. At the functional anatomical level, the occipital and temporal regions, and the intraparietal sulcus were specifically activated when subjects were reading target words in a lexical frame. The inferior parietal and anterior fusiform cortex was specifically activated in the GPC condition. These patterns of activation represented a valid classifying model of fMRI images associated with target reading in both frames in the multi-voxel pattern analyses. Further activations were shared by the two procedures in the occipital and inferior parietal areas, in the premotor cortex, in the frontal regions and the left supplementary motor area. These regions are most

  12. The role of left superior parietal lobe in male sexual behavior: dynamics of distinct components revealed by FMRI.

    Science.gov (United States)

    Cera, Nicoletta; Di Pierro, Ezio D; Sepede, Gianna; Gambi, Francesco; Perrucci, Mauro Gianni; Merla, Arcangelo; Tartaro, Armando; Del Gratta, Cosimo; Galatioto Paradiso, Giuseppe; Vicentini, Carlo; Romani, Gian Luca; Ferretti, Antonio

    2012-06-01

    Despite the interest for the brain correlates of male sexual arousal, few studies investigated neural mechanisms underlying psychogenic erectile dysfunction (ED). Although these studies showed several brain regions active in ED patients during visual erotic stimulation, the dynamics of inhibition of sexual response is still unclear. This study investigated the dynamics of brain regions involved in the psychogenic ED. Functional magnetic resonance imaging (fMRI) and simultaneous penile tumescence (PT) were used to study brain activity evoked in 17 outpatients with psychogenic ED and 19 healthy controls during visual erotic stimulation. Patterns of brain activation related to different phases of sexual response in the two groups were compared. Simultaneous recording of blood oxygen level-dependent fMRI responses and PT during visual erotic stimulation. During visual erotic stimuli, a larger activation was observed for the patient group in the left superior parietal lobe, ventromedial prefrontal cortex, and posterior cingulate cortex, whereas the control group showed larger activation in the right middle insula and dorsal anterior cingulate cortex and hippocampus. Moreover, the left superior parietal lobe showed a larger activation in patients than controls especially during the later stage of sexual response. Our results suggest that, among regions more active in patient group, the left superior parietal lobe plays a crucial role in inhibition of sexual response. Previous studies showed that left superior parietal lobe is involved in monitoring of internal body representation. The larger activation of this region in patients during later stages of sexual response suggests a high monitoring of the internal body representation, possibly affecting the behavioral response. These findings provide insight on brain mechanisms involved in psychogenic ED. © 2012 International Society for Sexual Medicine.

  13. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana.

    Science.gov (United States)

    Ågrena, Jon; Oakley, Christopher G; McKay, John K; Lovell, John T; Schemske, Douglas W

    2013-12-24

    Organisms inhabiting different environments are often locally adapted, and yet despite a considerable body of theory, the genetic basis of local adaptation is poorly understood. Unanswered questions include the number and effect sizes of adaptive loci, whether locally favored loci reduce fitness elsewhere (i.e., fitness tradeoffs), and whether a lack of genetic variation limits adaptation. To address these questions, we mapped quantitative trait loci (QTL) for total fitness in 398 recombinant inbred lines derived from a cross between locally adapted populations of the highly selfing plant Arabidopsis thaliana from Sweden and Italy and grown for 3 consecutive years at the parental sites (>40,000 plants monitored). We show that local adaptation is controlled by relatively few genomic regions of small to modest effect. A third of the 15 fitness QTL we detected showed evidence of tradeoffs, which contrasts with the minimal evidence for fitness tradeoffs found in previous studies. This difference may reflect the power of our multiyear study to distinguish conditionally neutral QTL from those that reflect fitness tradeoffs. In Sweden, but not in Italy, the local genotype underlying fitness QTL was often maladaptive, suggesting that adaptation there is constrained by a lack of adaptive genetic variation, attributable perhaps to genetic bottlenecks during postglacial colonization of Scandinavia or to recent changes in selection regime caused by climate change. Our results suggest that adaptation to markedly different environments can be achieved through changes in relatively few genomic regions, that fitness tradeoffs are common, and that lack of genetic variation can limit adaptation.

  14. Response inhibition results in the emotional devaluation of faces: neural correlates as revealed by fMRI.

    Science.gov (United States)

    Doallo, Sonia; Raymond, Jane E; Shapiro, Kimron L; Kiss, Monika; Eimer, Martin; Nobre, Anna C

    2012-08-01

    Although it is well established that prior experience with faces determines their subsequent social-emotional evaluation, recent work shows that top-down inhibitory mechanisms, including response inhibition, can lead to social devaluation after even a single, brief exposure. These rapidly induced effects indicate interplay among perceptual, attentional, response-selection and social-emotional networks; yet, the brain mechanisms underlying this are not well understood. This study used functional magnetic resonance imaging (fMRI) to investigate the neural mechanism mediating the relationship between inhibitory control and emotional devaluation. Participants performed two tasks: (i) a Go/No-Go task in response to faces and (ii) a trustworthiness rating task involving the previously seen faces. No-Go faces were rated as significantly less trustworthy than Go faces. By examining brain activations during Task 1, behavioral measures and brain activations obtained in Task 2 could be predicted. Specifically, activity in brain areas during Task 1 associated with (i) executive control and response suppression (i.e. lateral prefrontal cortex) and (ii) affective responses and value representation (i.e. orbitofrontal cortex), systematically covaried with behavioral ratings and amygdala activity obtained during Task 2. The present findings offer insights into the neural mechanisms linking inhibitory processes to affective responses.

  15. Distinct BOLD fMRI Responses of Capsaicin-Induced Thermal Sensation Reveal Pain-Related Brain Activation in Nonhuman Primates.

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    Abu Bakar Ali Asad

    Full Text Available Approximately 20% of the adult population suffer from chronic pain that is not adequately treated by current therapies, highlighting a great need for improved treatment options. To develop effective analgesics, experimental human and animal models of pain are critical. Topically/intra-dermally applied capsaicin induces hyperalgesia and allodynia to thermal and tactile stimuli that mimics chronic pain and is a useful translation from preclinical research to clinical investigation. Many behavioral and self-report studies of pain have exploited the use of the capsaicin pain model, but objective biomarker correlates of the capsaicin augmented nociceptive response in nonhuman primates remains to be explored.Here we establish an aversive capsaicin-induced fMRI model using non-noxious heat stimuli in Cynomolgus monkeys (n = 8. BOLD fMRI data were collected during thermal challenge (ON:20 s/42°C; OFF:40 s/35°C, 4-cycle at baseline and 30 min post-capsaicin (0.1 mg, topical, forearm application. Tail withdrawal behavioral studies were also conducted in the same animals using 42°C or 48°C water bath pre- and post- capsaicin application (0.1 mg, subcutaneous, tail.Group comparisons between pre- and post-capsaicin application revealed significant BOLD signal increases in brain regions associated with the 'pain matrix', including somatosensory, frontal, and cingulate cortices, as well as the cerebellum (paired t-test, p<0.02, n = 8, while no significant change was found after the vehicle application. The tail withdrawal behavioral study demonstrated a significant main effect of temperature and a trend towards capsaicin induced reduction of latency at both temperatures.These findings provide insights into the specific brain regions involved with aversive, 'pain-like', responses in a nonhuman primate model. Future studies may employ both behavioral and fMRI measures as translational biomarkers to gain deeper understanding of pain processing and evaluate

  16. Brain-based translation: fMRI decoding of spoken words in bilinguals reveals language-independent semantic representations in anterior temporal lobe.

    Science.gov (United States)

    Correia, João; Formisano, Elia; Valente, Giancarlo; Hausfeld, Lars; Jansma, Bernadette; Bonte, Milene

    2014-01-01

    Bilinguals derive the same semantic concepts from equivalent, but acoustically different, words in their first and second languages. The neural mechanisms underlying the representation of language-independent concepts in the brain remain unclear. Here, we measured fMRI in human bilingual listeners and reveal that response patterns to individual spoken nouns in one language (e.g., "horse" in English) accurately predict the response patterns to equivalent nouns in the other language (e.g., "paard" in Dutch). Stimuli were four monosyllabic words in both languages, all from the category of "animal" nouns. For each word, pronunciations from three different speakers were included, allowing the investigation of speaker-independent representations of individual words. We used multivariate classifiers and a searchlight method to map the informative fMRI response patterns that enable decoding spoken words within languages (within-language discrimination) and across languages (across-language generalization). Response patterns discriminative of spoken words within language were distributed in multiple cortical regions, reflecting the complexity of the neural networks recruited during speech and language processing. Response patterns discriminative of spoken words across language were limited to localized clusters in the left anterior temporal lobe, the left angular gyrus and the posterior bank of the left postcentral gyrus, the right posterior superior temporal sulcus/superior temporal gyrus, the right medial anterior temporal lobe, the right anterior insula, and bilateral occipital cortex. These results corroborate the existence of "hub" regions organizing semantic-conceptual knowledge in abstract form at the fine-grained level of within semantic category discriminations.

  17. Quantitative meta-analysis of fMRI and PET studies reveals consistent activation in fronto-striatal-parietal regions and cerebellum during antisaccades and prosaccades

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    Sharna eJamadar

    2013-10-01

    Full Text Available The antisaccade task is a classic task of oculomotor control that requires participants to inhibit a saccade to a target and instead make a voluntary saccade to the mirror opposite location. By comparison, the prosaccade task requires participants to make a visually-guided saccade to the target. These tasks have been studied extensively using behavioural oculomotor, electrophysiological and neuroimaging in both non-human primates and humans. In humans, the antisaccade task is under active investigation as a potential endophenotype or biomarker for multiple psychiatric and neurological disorders. A large and growing body of literature has used functional magnetic resonance imaging (fMRI and positron emission tomography (PET to study the neural correlates of the antisaccade and prosaccade tasks. We present a quantitative meta-analysis of all published voxel-wise fMRI and PET studies (18 of the antisaccade task and show that consistent activation for antisaccades and prosaccades is obtained in a fronto-subcortical-parietal network encompassing frontal and supplementary eye fields, thalamus, striatum and intraparietal cortex. This network is strongly linked to oculomotor control and was activated to a greater extent for antisaccade than prosaccade trials. Antisaccade but not prosaccade trials additionally activated dorsolateral and ventrolateral prefrontal cortices. We also found that a number of additional regions not classically linked to oculomotor control were activated to a greater extent for antisaccade versus prosaccade trials; these regions are often reported in antisaccade studies but rarely commented upon. While the number of studies eligible to be included in this meta-analysis was small, the results of this systematic review reveal that antisaccade and prosaccade trials consistently activate a distributed network of regions both within and outside the classic definition of the oculomotor network.

  18. Resting state fMRI reveals a default mode dissociation between retrosplenial and medial prefrontal subnetworks in ASD despite motion scrubbing

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    Tuomo eStarck

    2013-11-01

    Full Text Available In resting state fMRI studies of autism spectrum disorders (ASDs decreased frontal-posterior functional connectivity is a persistent finding. However, the picture of the default mode network hypoconnectivity remains incomplete. In addition, the functional connectivity analyses have been shown to be susceptible even to subtle motion. Default mode network (DMN hypoconnectivity in ASD has been specifically called for re-evaluation with stringent motion correction, which we aimed to conduct by so-called scrubbing. A rich set of default mode subnetworks can be obtained with high dimensional group independent component analysis (ICA which can potentially provide more detailed view of the connectivity alterations. We compared the DMN connectivity in high-functioning adolescents with ASDs to typically developing controls using ICA dual-regression with decompositions from typical to high dimensionality. Dual-regression analysis within DMN subnetworks did not reveal alterations but connectivity between anterior and posterior DMN subnetworks was decreased in ASD. The results were very similar with and without motion scrubbing thus indicating the efficacy of the conventional motion correction methods combined with ICA dual-regression. Specific dissociation between DMN subnetworks was revealed on high ICA dimensionality, where networks centered at the medial prefrontal cortex and retrosplenial cortex showed weakened coupling in adolescents with ASDs compared to typically developing control participants. Generally the results speak for disruption in the anterior-posterior DMN interplay on the network level whereas local functional connectivity in DMN seems relatively unaltered.

  19. [Does the individual adaptation of standardized speech paradigmas for clinical functional magnetic resonance imaging (fMRI) effect the localization of the language-dominant hemisphere and of Broca's and Wernicke's areas].

    Science.gov (United States)

    Konrad, F; Nennig, E; Ochmann, H; Kress, B; Sartor, K; Stippich, C

    2005-03-01

    Functional magnetic resonance imaging (fMRI) localizes Broca's area (B) and Wernicke's area (W) and the hemisphere dominant for language. In clinical fMRI, adapting the stimulation paradigms to each patient's individual cognitive capacity is crucial for diagnostic success. To interpret clinical fMRI findings correctly, we studied the effect of varying frequency and number of stimuli on functional localization, determination of language dominance and BOLD signals. Ten volunteers (VP) were investigated at 1.5 Tesla during visually triggered sentence generation using a standardized block design. In four different measurements, the stimuli were presented to each VP with frequencies of 1/1 s, (1/2) s, (1/3) s and (1/6) s. The functional localizations and the correlations of the measured BOLD signals to the applied hemodynamic reference function (r) were almost independent from frequency and number of the stimuli in both hemispheres, whereas the relative BOLD signal changes (DeltaS) in B and W increased with the stimulation rate, which also changed the lateralization indices. The strongest BOLD activations were achieved with the highest stimulation rate or with the maximum language production task, respectively. The adaptation of language paradigms necessary in clinical fMRI does not alter the functional localizations but changes the BOLD signals and language lateralization which should not be attributed to the underlying brain pathology.

  20. Genomic signatures reveal geographic adaption and human selection in cattle

    Science.gov (United States)

    We investigated geographic adaptation and human selection using high-density SNP data of five diverse cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-k...

  1. Distinct loading conditions reveal various patterns of right ventricular adaptation

    NARCIS (Netherlands)

    Borgdorff, Marinus A. J.; Bartelds, Beatrijs; Dickinson, Michael G.; Steendijk, Paul; de Vroomen, Maartje; Berger, Rolf M. F.

    2013-01-01

    Right ventricular (RV) failure due to chronically abnormal loading is a main determinant of outcome in pulmonary hypertension (PH) and congenital heart disease. However, distinct types of RV loading have been associated with different outcomes. To determine whether the adaptive RV response depends o

  2. Disrupted effective connectivity between the amygdala and orbitofrontal cortex in social anxiety disorder during emotion discrimination revealed by dynamic causal modeling for FMRI.

    Science.gov (United States)

    Sladky, Ronald; Höflich, Anna; Küblböck, Martin; Kraus, Christoph; Baldinger, Pia; Moser, Ewald; Lanzenberger, Rupert; Windischberger, Christian

    2015-04-01

    Social anxiety disorder (SAD) is characterized by over-reactivity of fear-related circuits in social or performance situations and associated with marked social impairment. We used dynamic causal modeling (DCM), a method to evaluate effective connectivity, to test our hypothesis that SAD patients would exhibit dysfunctions in the amygdala-prefrontal emotion regulation network. Thirteen unmedicated SAD patients and 13 matched healthy controls performed a series of facial emotion and object discrimination tasks while undergoing fMRI. The emotion-processing network was identified by a task-related contrast and motivated the selection of the right amygdala, OFC, and DLPFC for DCM analysis. Bayesian model averaging for DCM revealed abnormal connectivity between the OFC and the amygdala in SAD patients. In healthy controls, this network represents a negative feedback loop. In patients, however, positive connectivity from OFC to amygdala was observed, indicating an excitatory connection. As we did not observe a group difference of the modulatory influence of the FACE condition on the OFC to amygdala connection, we assume a context-independent reduction of prefrontal control over amygdalar activation in SAD patients. Using DCM, it was possible to highlight not only the neuronal dysfunction of isolated brain regions, but also the dysbalance of a distributed functional network.

  3. Orchestrating Proactive and Reactive Mechanisms for Filtering Distracting Information: Brain-Behavior Relationships Revealed by a Mixed-Design fMRI Study.

    Science.gov (United States)

    Marini, Francesco; Demeter, Elise; Roberts, Kenneth C; Chelazzi, Leonardo; Woldorff, Marty G

    2016-01-20

    Given the information overload often imparted to human cognitive-processing systems, suppression of irrelevant and distracting information is essential for successful behavior. Using a hybrid block/event-related fMRI design, we characterized proactive and reactive brain mechanisms for filtering distracting stimuli. Participants performed a flanker task, discriminating the direction of a target arrow in the presence versus absence of congruent or incongruent flanking distracting arrows during either Pure blocks (distracters always absent) or Mixed blocks (distracters on 80% of trials). Each Mixed block had either 20% or 60% incongruent trials. Activations in the dorsal frontoparietal attention network during Mixed versus Pure blocks evidenced proactive (blockwise) recruitment of a distraction-filtering mechanism. Sustained activations in right middle frontal gyrus during 60% Incongruent blocks correlated positively with behavioral indices of distraction-filtering (slowing when distracters might occur) and negatively with distraction-related behavioral costs (incongruent vs congruent trials), suggesting a role in coordinating proactive filtering of potential distracters. Event-related analyses showed that incongruent trials elicited greater reactive activations in 20% (vs 60%) Incongruent blocks for counteracting distraction and conflict, including in the insula and anterior cingulate. Context-related effects in occipitoparietal cortex consisted of greater target-evoked activations for distracter-absent trials (central-target-only) in Mixed versus Pure blocks, suggesting enhanced attentional engagement. Functional-localizer analyses in V1/V2/V3 revealed less distracter-processing activity in 60% (vs 20%) Incongruent blocks, presumably reflecting tonic suppression by proactive filtering mechanisms. These results delineate brain mechanisms underlying proactive and reactive filtering of distraction and conflict, and how they are orchestrated depending on distraction

  4. Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales.

    Science.gov (United States)

    Bird, Jordan T; Baker, Brett J; Probst, Alexander J; Podar, Mircea; Lloyd, Karen G

    2016-01-01

    The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, USA, we sequenced a single cell amplified genome (SAG), WOR_SM1_SCG, and used it to identify and refine two high-quality genomes from metagenomes, WOR_SM1_79 and WOR_SM1_86-2, from the same site. These three genomic reconstructions form a monophyletic group, which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, caused the protein to be encoded as two subunits at non-adjacent loci. Consistent with the terrestrial spring clades, our estuarine genomes contained a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identified two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which was more widespread, diverse, and not associated with visible mats. The core Alti-1 genome suggested Alti-1 is adapted for the stream environment with lipopolysaccharide production capacity and extracellular hami structures. The core Alti-2 genome suggested members of this clade are free-living with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These data

  5. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales

    Directory of Open Access Journals (Sweden)

    Jordan T Bird

    2016-08-01

    Full Text Available The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus (Ca. Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, we sequenced a single cell amplified genome (SAG, WOR_SCG_SM1, and used it to identify and refine two high-quality genomes from metagenomes, WOR_79 and WOR_86-2, from the same site in a different year. These three genomic reconstructions form a monophyletic group which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, causes the protein to be encoded as two subunits at distant loci. Consistent with the terrestrial spring clades, our estuarine genomes contain a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identify two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which is more widespread, diverse, and not associated with visible mats. The core Alti-1 genome supports Alti-1 as adapted for the stream environment, with lipopolysaccharide production capacity, extracellular hami structures. The core Alti-2 genome members of this clade are free-living, with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These

  6. Adaptive Optics Reveals Photoreceptor Abnormalities in Diabetic Macular Ischemia

    Science.gov (United States)

    Nesper, Peter L.; Scarinci, Fabio

    2017-01-01

    Diabetic macular ischemia (DMI) is a phenotype of diabetic retinopathy (DR) associated with chronic hypoxia of retinal tissue. The goal of this prospective observational study was to report evidence of photoreceptor abnormalities using adaptive optics scanning laser ophthalmoscopy (AOSLO) in eyes with DR in the setting of deep capillary plexus (DCP) non-perfusion. Eleven eyes from 11 patients (6 women, age 31–68), diagnosed with DR without macular edema, underwent optical coherence tomography angiography (OCTA) and AOSLO imaging. One patient without OCTA imaging underwent fluorescein angiography to characterize the enlargement of the foveal avascular zone. The parameters studied included photoreceptor heterogeneity packing index (HPi) on AOSLO, as well as DCP non-perfusion and vessel density on OCTA. Using AOSLO, OCTA and spectral domain (SD)-OCT, we observed that photoreceptor abnormalities on AOSLO and SD-OCT were found in eyes with non-perfusion of the DCP on OCTA. All eight eyes with DCP non-flow on OCTA showed photoreceptor abnormalities on AOSLO. Six of the eight eyes also had outer retinal abnormalities on SD-OCT. Three eyes with DR and robust capillary perfusion of the DCP had normal photoreceptors on SD-OCT and AOSLO. Compared to eyes with DR without DCP non-flow, the eight eyes with DCP non-flow had significantly lower HPi (P = 0.013) and parafoveal DCP vessel density (P = 0.016). We found a significant correlation between cone HPi and parafoveal DCP vessel density (r = 0.681, P = 0.030). Using a novel approach with AOSLO and OCTA, this study shows an association between capillary non-perfusion of the DCP and abnormalities in the photoreceptor layer in eyes with DR. This observation is important in confirming the significant contribution of the DCP to oxygen requirements of photoreceptors in DMI, while highlighting the ability of AOSLO to detect subtle photoreceptor changes not always visible on SD-OCT. PMID:28068435

  7. The genome of Tetranychus urticae reveals herbivorous pest adaptations

    Science.gov (United States)

    Grbić, Miodrag; Van Leeuwen, Thomas; Clark, Richard M.; Rombauts, Stephane; Rouzé, Pierre; Grbić, Vojislava; Osborne, Edward J.; Dermauw, Wannes; Ngoc, Phuong Cao Thi; Ortego, Félix; Hernández-Crespo, Pedro; Diaz, Isabel; Martinez, Manuel; Navajas, Maria; Sucena, Élio; Magalhães, Sara; Nagy, Lisa; Pace, Ryan M.; Djuranović, Sergej; Smagghe, Guy; Iga, Masatoshi; Christiaens, Olivier; Veenstra, Jan A.; Ewer, John; Villalobos, Rodrigo Mancilla; Hutter, Jeffrey L.; Hudson, Stephen D.; Velez, Marisela; Yi, Soojin V.; Zeng, Jia; Pires-daSilva, Andre; Roch, Fernando; Cazaux, Marc; Navarro, Marie; Zhurov, Vladimir; Acevedo, Gustavo; Bjelica, Anica; Fawcett, Jeffrey A.; Bonnet, Eric; Martens, Cindy; Baele, Guy; Wissler, Lothar; Sanchez-Rodriguez, Aminael; Tirry, Luc; Blais, Catherine; Demeestere, Kristof; Henz, Stefan R.; Gregory, T. Ryan; Mathieu, Johannes; Verdon, Lou; Farinelli, Laurent; Schmutz, Jeremy; Lindquist, Erika; Feyereisen, René; Van de Peer, Yves

    2016-01-01

    The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant–herbivore interactions, and provides unique opportunities for developing novel plant protection strategies. PMID:22113690

  8. Control over the Strength of Connections Between Modules: A Double Dissociation Between Stimulus Format and Task Revealed by Granger Causality Mapping in fMRI

    Directory of Open Access Journals (Sweden)

    Britt eAnderson

    2015-03-01

    Full Text Available Drawing on theoretical and computational work with the localist Dual Route reading model and results from behavioral studies, Besner, Moroz, and O'Malley (2011 proposed that the ability to perform tasks that require overriding stimulus-specific defaults (e.g., semantics when naming Arabic numerals, and phonology when evaluating the parity of number words necessitate the ability to modulate the strength of connections between cognitive modules for lexical representation, semantics, and phonology on a task- and stimulus-specific basis. We used fMRI to evaluate this account by assessing changes in functional connectivity while participants performed tasks that did and did not require such stimulus-task default overrides. The occipital region showing the greatest modulation of BOLD signal strength for the two stimulus types was used as the seed region for Granger Causality Mapping (GCM. Our GCM analysis revealed a region of rostromedial frontal cortex with a crossover interaction. When participants performed tasks that required overriding stimulus type defaults (i.e., parity judgments of number words and naming Arabic numerals functional connectivity between the occipital region and rostromedial frontal cortex was present. Statistically significant functional connectivity was absent when the tasks were the default for the stimulus type (i.e., parity judgments of Arabic numerals and reading number words. This frontal region (BA 10 has previously been shown to be involved in goal-directed behaviour and maintenance of a specific task-set. We conclude that overriding stimulus-task defaults requires a modulation of connection strengths between cognitive modules and that the override mechanism predicted from cognitive theory is instantiated by frontal modulation of neural activity of brain regions specialized for sensory processing.

  9. Line scanning fMRI reveals earlier onset of optogenetically evoked BOLD response in rat somatosensory cortex as compared to sensory stimulation.

    Science.gov (United States)

    Albers, Franziska; Schmid, Florian; Wachsmuth, Lydia; Faber, Cornelius

    2016-12-21

    The combination of optogenetic control and fMRI readout in the brain is increasingly used to assess neuronal networks and underlying signal processing. However, how exactly optogenetic activation or inhibition reproduces normal physiological input has not been fully unraveled. To assess details of temporal dynamics of the hemodynamic response, temporal resolution in rodent fMRI is often not sufficient. Recent advances in human fMRI using faster acquisition schemes cannot be easily translated to small animals due to smaller dimensions, fast physiological motion, and higher sensitivity to artefacts. Here, we applied a one dimensional line scanning acquisition with 50ms temporal resolution in rat somatosensory cortex. We observed that optogenetic activation reproduces the hemodynamic response upon sensory stimulation, but shows a 160 to 340ms earlier onset of the response. This difference is explained by direct activation of all opsin-expressing and illuminated cortical layers, while hemodynamic response to sensory stimulation is delayed during intracortical transmission between cortical layers. Our results confirm that optogenetic activation is a valid model for physiological neuronal input, and that differences in temporal behavior of only a few hundred milliseconds can be resolved in rodent fMRI.

  10. Multi-voxel pattern analysis (MVPA) reveals abnormal fMRI activity in both the 'core' and 'extended' face network in congenital prosopagnosia

    OpenAIRE

    Rivolta, Davide; Woolgar, Alexandra; Palermo, Romina; Butko, Marina; Schmalzl, Laura; Williams, Mark A.

    2014-01-01

    The ability to identify faces is mediated by a network of cortical and subcortical brain regions in humans. It is still a matter of debate which regions represent the functional substrate of congenital prosopagnosia (CP), a condition characterized by a lifelong impairment in face recognition, and affecting around 2.5% of the general population. Here, we used functional Magnetic Resonance Imaging (fMRI) to measure neural responses to faces, objects, bodies, and body-parts in a group of seven C...

  11. Parametric merging of MEG and fMRI reveals spatiotemporal differences in cortical processing of spoken words and environmental sounds in background noise.

    Science.gov (United States)

    Renvall, Hanna; Formisano, Elia; Parviainen, Tiina; Bonte, Milene; Vihla, Minna; Salmelin, Riitta

    2012-01-01

    There is an increasing interest to integrate electrophysiological and hemodynamic measures for characterizing spatial and temporal aspects of cortical processing. However, an informative combination of responses that have markedly different sensitivities to the underlying neural activity is not straightforward, especially in complex cognitive tasks. Here, we used parametric stimulus manipulation in magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) recordings on the same subjects, to study effects of noise on processing of spoken words and environmental sounds. The added noise influenced MEG response strengths in the bilateral supratemporal auditory cortex, at different times for the different stimulus types. Specifically for spoken words, the effect of noise on the electrophysiological response was remarkably nonlinear. Therefore, we used the single-subject MEG responses to construct parametrization for fMRI data analysis and obtained notably higher sensitivity than with conventional stimulus-based parametrization. fMRI results showed that partly different temporal areas were involved in noise-sensitive processing of words and environmental sounds. These results indicate that cortical processing of sounds in background noise is stimulus specific in both timing and location and provide a new functionally meaningful platform for combining information obtained with electrophysiological and hemodynamic measures of brain function.

  12. Resting-state fMRI revealed different brain activities responding to valproic acid and levetiracetam in benign epilepsy with central-temporal spikes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qirui; Zhang, Zhiqiang; Xu, Qiang; Wu, Han; Li, Zhipeng; Lu, Guangming [Nanjing University School of Medicine, Department of Medical Imaging, Jinling Hospital, Nanjing (China); Yang, Fang; Li, Qian [Nanjing University School of Medicine, Department of Neurology, Jinling Hospital, Nanjing (China); Hu, Zheng [Nanjing Children' s Hospital, Department of Neurology, Nanjing (China); Dante, Mantini [Faculty of Kinesiology and Rehabilitation Sciences, KU Leuven (Belgium); Li, Kai [Suzhou University, Laboratory of Molecular Medicine, Suzhou (China)

    2017-05-15

    Our aim was to investigate regional difference in brain activities in response to antiepileptic drug (AED) medications in benign epilepsy with central-temporal spikes (BECTS) using resting-state functional magnetic resonance imaging (fMRI). Fifty-seven patients with BECTS underwent resting-state fMRI scans after receiving either valproic acid (VPA) (n = 15), levetiracetam (LEV) (n = 21), or no medication (n = 21). fMRI regional homogeneity (ReHo) parameter among the three groups of patients were compared and were correlated with total doses of AED in the two medicated groups. Compared with patients on no-medication, patients receiving either VPA or LEV showed decreased ReHo in the central-temporal region, frontal cortex, and thalamus. In particular, the VPA group showed greater ReHo decrease in the thalamus and milder in cortices and caudate heads compared with the LEV group. In addition, the VPA group demonstrated a negative correlation between ReHo values in the central-temporal region and medication dose. Both VPA and LEV inhibit resting-state neural activity in the central-temporal region, which is the main epileptogenic focus of BECTS. VPA reduced brain activity in the cortical epileptogenic regions and thalamus evenly, whereas LEV reduced brain activity predominantly in the cortices. Interestingly, VPA showed a cumulative effect on inhibiting brain activity in the epileptogenic regions in BECTS. (orig.)

  13. S3-3: Misbinding of Color and Motion in Human V2 Revealed by Color-Contingent Motion Adaptation

    Directory of Open Access Journals (Sweden)

    Fang Fang

    2012-10-01

    Full Text Available Wu, Kanai, & Shimojo (2004 Nature 429 262 described a compelling illusion demonstrating a steady-state misbinding of color and motion. Here, we took advantage of the illusion and performed psychophysical and fMRI adaptation experiments to explore the neural mechanism of color-motion misbinding. The stimulus subtended 20 deg by 14 deg of visual angle and contained two sheets of random dots, one sheet moving up and the other moving down. On the upward-moving sheet, dots in the right-end area (4 deg by 14 deg were red, and the rest of the dots were green. On the downward-moving sheet, dots in the right-end area were green, and the rest of the dots were red. When subjects fixated at the center of the stimulus, they bound the color and motion of the dots in the right-end area erroneously–the red dots appeared to move downwards and the green dots appeared to move upwards. In the psychophysical experiment, we measured the color-contingent motion aftereffect in the right-end area after adaptation to the illusory stimulus. A significant aftereffect was observed as if subjects had adapted to the perceived binding of color and motion, rather than the physical binding. For example, after adaptation, stationary red dots appeared to move upwards, and stationary green dots appeared to move downwards. In the fMRI experiment, we measured direction-selective motion adaptation effects in V1, V2, V3, V4, V3A/B, and V5. Relative to other cortical areas, V2 showed a much stronger adaptation effect to the perceived motion direction (rather than the physical direction for both the red and green dots. Significantly, the fMRI adaptation effect in V2 correlated with the color-contingent motion aftereffect across twelve subjects. This study provides the first human evidence that color and motion could be misbound at a very early stage of visual processing.

  14. fMRI Neuroinformatics

    DEFF Research Database (Denmark)

    Nielsen, Finn Årup; Christensen, Mark Schram; Madsen, Kristoffer M.

    2006-01-01

    Functional magnetic resonance imaging (fMRI) generates vast amounts of data. The handling, processing, and analysis of fMRI data would be inconceivable without computer-based methods. fMRI neuroinformatics is concerned with research, development, and operation of these methods. Reconstruction...

  15. Multi-voxel pattern analysis (MVPA) reveals abnormal fMRI activity in both the “core” and “extended” face network in congenital prosopagnosia

    Science.gov (United States)

    Rivolta, Davide; Woolgar, Alexandra; Palermo, Romina; Butko, Marina; Schmalzl, Laura; Williams, Mark A.

    2014-01-01

    The ability to identify faces is mediated by a network of cortical and subcortical brain regions in humans. It is still a matter of debate which regions represent the functional substrate of congenital prosopagnosia (CP), a condition characterized by a lifelong impairment in face recognition, and affecting around 2.5% of the general population. Here, we used functional Magnetic Resonance Imaging (fMRI) to measure neural responses to faces, objects, bodies, and body-parts in a group of seven CPs and ten healthy control participants. Using multi-voxel pattern analysis (MVPA) of the fMRI data we demonstrate that neural activity within the “core” (i.e., occipital face area and fusiform face area) and “extended” (i.e., anterior temporal cortex) face regions in CPs showed reduced discriminability between faces and objects. Reduced differentiation between faces and objects in CP was also seen in the right parahippocampal cortex. In contrast, discriminability between faces and bodies/body-parts and objects and bodies/body-parts across the ventral visual system was typical in CPs. In addition to MVPA analysis, we also ran traditional mass-univariate analysis, which failed to show any group differences in face and object discriminability. In sum, these findings demonstrate (i) face-object representations impairments in CP which encompass both the “core” and “extended” face regions, and (ii) superior power of MVPA in detecting group differences. PMID:25431556

  16. Multi-voxel pattern analysis (MVPA reveals abnormal fMRI activity in both the core and extended face network in congenital prosopagnosia

    Directory of Open Access Journals (Sweden)

    Davide eRivolta

    2014-11-01

    Full Text Available The ability to identify faces is mediated by a network of cortical and subcortical brain regions in humans. It is still a matter of debate which regions represent the functional substrate of congenital prosopagnosia (CP, a condition characterized by a lifelong impairment in face recognition, and affecting around 2.5% of the general population. Here, we used functional Magnetic Resonance Imaging (fMRI to measure neural responses to faces, objects, bodies and body-parts in a group of seven CPs and ten healthy control participants. Using multi-voxel pattern analysis (MVPA of the fMRI data we demonstrate that neural activity within the core (i.e., occipital face area and fusiform face area and extended (i.e., anterior temporal cortex face regions in CPs showed reduced discriminability between faces and objects. Reduced differentiation between faces and objects in CP was also seen in the right parahippocampal cortex. In contrast, discriminability between faces and bodies/body-parts and objects and bodies/body-parts across the ventral visual system was typical in CPs. In addition to MVPA analysis, we also ran traditional mass-univariate analysis, which failed to show any group differences in face and object discriminability. In sum, these findings demonstrate (i face-object representations impairments in CP which encompass both the core and extended face regions, and (ii superior power of MVPA in detecting group differences.

  17. Multi-voxel pattern analysis (MVPA) reveals abnormal fMRI activity in both the "core" and "extended" face network in congenital prosopagnosia.

    Science.gov (United States)

    Rivolta, Davide; Woolgar, Alexandra; Palermo, Romina; Butko, Marina; Schmalzl, Laura; Williams, Mark A

    2014-01-01

    The ability to identify faces is mediated by a network of cortical and subcortical brain regions in humans. It is still a matter of debate which regions represent the functional substrate of congenital prosopagnosia (CP), a condition characterized by a lifelong impairment in face recognition, and affecting around 2.5% of the general population. Here, we used functional Magnetic Resonance Imaging (fMRI) to measure neural responses to faces, objects, bodies, and body-parts in a group of seven CPs and ten healthy control participants. Using multi-voxel pattern analysis (MVPA) of the fMRI data we demonstrate that neural activity within the "core" (i.e., occipital face area and fusiform face area) and "extended" (i.e., anterior temporal cortex) face regions in CPs showed reduced discriminability between faces and objects. Reduced differentiation between faces and objects in CP was also seen in the right parahippocampal cortex. In contrast, discriminability between faces and bodies/body-parts and objects and bodies/body-parts across the ventral visual system was typical in CPs. In addition to MVPA analysis, we also ran traditional mass-univariate analysis, which failed to show any group differences in face and object discriminability. In sum, these findings demonstrate (i) face-object representations impairments in CP which encompass both the "core" and "extended" face regions, and (ii) superior power of MVPA in detecting group differences.

  18. Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Feizi, Amir; Bisschops, Markus M. M.

    2017-01-01

    Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions....... Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether...... sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid...

  19. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations

    OpenAIRE

    Frank Förster; Daniela Beisser; Grohme, Markus A.; Chunguang Liang; Brahim Mali; Alexander Matthias Siegl; Engelmann, Julia C.; Shkumatov, Alexander V; Elham Schokraie; Tobias Müller; Martina Schnölzer; Schill, Ralph O.; Marcus Frohme; Thomas Dandekar

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade \\(Milnesium\\) \\(tardigradum\\) were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from \\(Hypsibius\\) \\(dujardini\\), revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardig...

  20. Single-trial EEG-informed fMRI reveals spatial dependency of BOLD signal on early and late IC-ERP amplitudes during face recognition.

    Science.gov (United States)

    Wirsich, Jonathan; Bénar, Christian; Ranjeva, Jean-Philippe; Descoins, Médéric; Soulier, Elisabeth; Le Troter, Arnaud; Confort-Gouny, Sylviane; Liégeois-Chauvel, Catherine; Guye, Maxime

    2014-10-15

    Simultaneous EEG-fMRI has opened up new avenues for improving the spatio-temporal resolution of functional brain studies. However, this method usually suffers from poor EEG quality, especially for evoked potentials (ERPs), due to specific artifacts. As such, the use of EEG-informed fMRI analysis in the context of cognitive studies has particularly focused on optimizing narrow ERP time windows of interest, which ignores the rich diverse temporal information of the EEG signal. Here, we propose to use simultaneous EEG-fMRI to investigate the neural cascade occurring during face recognition in 14 healthy volunteers by using the successive ERP peaks recorded during the cognitive part of this process. N170, N400 and P600 peaks, commonly associated with face recognition, were successfully and reproducibly identified for each trial and each subject by using a group independent component analysis (ICA). For the first time we use this group ICA to extract several independent components (IC) corresponding to the sequence of activation and used single-trial peaks as modulation parameters in a general linear model (GLM) of fMRI data. We obtained an occipital-temporal-frontal stream of BOLD signal modulation, in accordance with the three successive IC-ERPs providing an unprecedented spatio-temporal characterization of the whole cognitive process as defined by BOLD signal modulation. By using this approach, the pattern of EEG-informed BOLD modulation provided improved characterization of the network involved than the fMRI-only analysis or the source reconstruction of the three ERPs; the latter techniques showing only two regions in common localized in the occipital lobe.

  1. Functional Network Overlap as Revealed by fMRI Using sICA and Its Potential Relationships with Functional Heterogeneity, Balanced Excitation and Inhibition, and Sparseness of Neuron Activity

    Science.gov (United States)

    Xu, Jiansong; Calhoun, Vince D.; Worhunsky, Patrick D.; Xiang, Hui; Li, Jian; Wall, John T.; Pearlson, Godfrey D.; Potenza, Marc N.

    2015-01-01

    Functional magnetic resonance imaging (fMRI) studies traditionally use general linear model-based analysis (GLM-BA) and regularly report task-related activation, deactivation, or no change in activation in separate brain regions. However, several recent fMRI studies using spatial independent component analysis (sICA) find extensive overlap of functional networks (FNs), each exhibiting different task-related modulation (e.g., activation vs. deactivation), different from the dominant findings of GLM-BA. This study used sICA to assess overlap of FNs extracted from four datasets, each related to a different cognitive task. FNs extracted from each dataset overlapped with each other extensively across most or all brain regions and showed task-related concurrent increases, decreases, or no changes in activity. These findings indicate that neural substrates showing task-related concurrent but different modulations in activity intermix with each other and distribute across most of the brain. Furthermore, spatial correlation analyses found that most FNs were highly consistent in spatial patterns across different datasets. This finding indicates that these FNs probably reflect large-scale patterns of task-related brain activity. We hypothesize that FN overlaps as revealed by sICA might relate to functional heterogeneity, balanced excitation and inhibition, and population sparseness of neuron activity, three fundamental properties of the brain. These possibilities deserve further investigation. PMID:25714362

  2. Functional network overlap as revealed by fMRI using sICA and its potential relationships with functional heterogeneity, balanced excitation and inhibition, and sparseness of neuron activity.

    Science.gov (United States)

    Xu, Jiansong; Calhoun, Vince D; Worhunsky, Patrick D; Xiang, Hui; Li, Jian; Wall, John T; Pearlson, Godfrey D; Potenza, Marc N

    2015-01-01

    Functional magnetic resonance imaging (fMRI) studies traditionally use general linear model-based analysis (GLM-BA) and regularly report task-related activation, deactivation, or no change in activation in separate brain regions. However, several recent fMRI studies using spatial independent component analysis (sICA) find extensive overlap of functional networks (FNs), each exhibiting different task-related modulation (e.g., activation vs. deactivation), different from the dominant findings of GLM-BA. This study used sICA to assess overlap of FNs extracted from four datasets, each related to a different cognitive task. FNs extracted from each dataset overlapped with each other extensively across most or all brain regions and showed task-related concurrent increases, decreases, or no changes in activity. These findings indicate that neural substrates showing task-related concurrent but different modulations in activity intermix with each other and distribute across most of the brain. Furthermore, spatial correlation analyses found that most FNs were highly consistent in spatial patterns across different datasets. This finding indicates that these FNs probably reflect large-scale patterns of task-related brain activity. We hypothesize that FN overlaps as revealed by sICA might relate to functional heterogeneity, balanced excitation and inhibition, and population sparseness of neuron activity, three fundamental properties of the brain. These possibilities deserve further investigation.

  3. Secretome analysis revealed adaptive and non-adaptive responses of the Staphylococcus carnosus femB mutant.

    Science.gov (United States)

    Nega, Mulugeta; Dube, Linda; Kull, Melanie; Ziebandt, Anne-Kathrin; Ebner, Patrick; Albrecht, Dirk; Krismer, Bernhard; Rosenstein, Ralf; Hecker, Michael; Götz, Friedrich

    2015-04-01

    FemABX peptidyl transferases are involved in non-ribosomal pentaglycine interpeptide bridge biosynthesis. Here, we characterized the phenotype of a Staphylococcus carnosus femB deletion mutant, which was affected in growth and showed pleiotropic effects such as enhanced methicillin sensitivity, lysostaphin resistance, cell clustering, and decreased peptidoglycan cross-linking. However, comparative secretome analysis revealed a most striking difference in the massive secretion or release of proteins into the culture supernatant in the femB mutant than the wild type. The secreted proteins can be categorized into typical cytosolic proteins and various murein hydrolases. As the transcription of the murein hydrolase genes was up-regulated in the mutant, they most likely represent an adaption response to the life threatening mutation. Even though the transcription of the cytosolic protein genes was unaltered, their high abundance in the supernatant of the mutant is most likely due to membrane leakage triggered by the weakened murein sacculus and enhanced autolysins.

  4. Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid.

    Science.gov (United States)

    Koczula, Anna; Jarek, Michael; Visscher, Christian; Valentin-Weigand, Peter; Goethe, Ralph; Willenborg, Jörg

    2017-02-15

    Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids. On the other hand, they suggested differences in the de novo amino acid biosynthesis. This prompted us to further dissect S. suis adaptation to porcine blood and CSF by RNA deep sequencing (RNA-seq). In blood, the majority of differentially expressed genes were associated with transport of alternative carbohydrate sources and the carbohydrate metabolism (pentose phosphate pathway, glycogen metabolism). In CSF, predominantly genes involved in the biosynthesis of branched-chain and aromatic amino acids were differentially expressed. Especially, isoleucine biosynthesis seems to be of major importance for S. suis in CSF because several related biosynthetic genes were more highly expressed. In conclusion, our data revealed niche-specific metabolic gene activity which emphasizes a selective adaptation of S. suis to host environments.

  5. Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid

    Directory of Open Access Journals (Sweden)

    Anna Koczula

    2017-02-01

    Full Text Available Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF revealed conserved activities of central carbon metabolism in both body fluids. On the other hand, they suggested differences in the de novo amino acid biosynthesis. This prompted us to further dissect S. suis adaptation to porcine blood and CSF by RNA deep sequencing (RNA-seq. In blood, the majority of differentially expressed genes were associated with transport of alternative carbohydrate sources and the carbohydrate metabolism (pentose phosphate pathway, glycogen metabolism. In CSF, predominantly genes involved in the biosynthesis of branched-chain and aromatic amino acids were differentially expressed. Especially, isoleucine biosynthesis seems to be of major importance for S. suis in CSF because several related biosynthetic genes were more highly expressed. In conclusion, our data revealed niche-specific metabolic gene activity which emphasizes a selective adaptation of S. suis to host environments.

  6. fMRI reveals a lower visual field preference for hand actions in human superior parieto-occipital cortex (SPOC) and precuneus.

    Science.gov (United States)

    Rossit, Stéphanie; McAdam, Teresa; McLean, D Adam; Goodale, Melvyn A; Culham, Jody C

    2013-10-01

    Humans are more efficient when performing actions towards objects presented in the lower visual field (VF) than in the upper VF. The present study used slow event-related functional magnetic resonance imaging (fMRI) to examine whether human brain areas implicated in action would show such VF preferences. Participants were asked to fixate one of four different positions allowing objects to be presented in the upper left, upper right, lower left or lower right VF. In some trials they reached to grasp the object with the right hand while in others they passively viewed the object. Crucially, by manipulating the fixation position, rather than the position of the objects, the biomechanics of the movements did not differ across conditions. The superior parieto-occipital cortex (SPOC) and the left precuneus, brain areas implicated in the control of reaching, were significantly more activated when participants grasped objects presented in the lower VF relative to the upper VF. Importantly, no such VF preferences were observed in these regions during passive viewing. This finding fits well with evidence from the macaque neurophysiology that neurons within visuomotor regions over-represent the lower VF relative to the upper VF and indicate that the neural responses within these regions may reflect a functional lower VF advantage during visually-guided actions.

  7. A penny for your thoughts! patterns of fMRI activity reveal the content and the spatial topography of visual mental images.

    Science.gov (United States)

    Boccia, Maddalena; Piccardi, Laura; Palermo, Liana; Nemmi, Federico; Sulpizio, Valentina; Galati, Gaspare; Guariglia, Cecilia

    2015-03-01

    Visual mental imagery is a complex process that may be influenced by the content of mental images. Neuropsychological evidence from patients with hemineglect suggests that in the imagery domain environments and objects may be represented separately and may be selectively affected by brain lesions. In the present study, we used functional magnetic resonance imaging (fMRI) to assess the possibility of neural segregation among mental images depicting parts of an object, of an environment (imagined from a first-person perspective), and of a geographical map, using both a mass univariate and a multivariate approach. Data show that different brain areas are involved in different types of mental images. Imagining an environment relies mainly on regions known to be involved in navigational skills, such as the retrosplenial complex and parahippocampal gyrus, whereas imagining a geographical map mainly requires activation of the left angular gyrus, known to be involved in the representation of categorical relations. Imagining a familiar object mainly requires activation of parietal areas involved in visual space analysis in both the imagery and the perceptual domain. We also found that the pattern of activity in most of these areas specifically codes for the spatial arrangement of the parts of the mental image. Our results clearly demonstrate a functional neural segregation for different contents of mental images and suggest that visuospatial information is coded by different patterns of activity in brain areas involved in visual mental imagery. © 2014 Wiley Periodicals, Inc.

  8. Functional and anatomical dissociation between the orthographic lexicon and the orthographic buffer revealed in reading and writing Chinese characters by fMRI.

    Science.gov (United States)

    Chen, Hsiang-Yu; Chang, Erik C; Chen, Sinead H Y; Lin, Yi-Chen; Wu, Denise H

    2016-04-01

    The contribution of orthographic representations to reading and writing has been intensively investigated in the literature. However, the distinction between neuronal correlates of the orthographic lexicon and the orthographic (graphemic) buffer has rarely been examined in alphabetic languages and never been explored in non-alphabetic languages. To determine whether the neural networks associated with the orthographic lexicon and buffer of logographic materials are comparable to those reported in the literature, the present fMRI experiment manipulated frequency and the stroke number of Chinese characters in the tasks of form judgment and stroke judgment, which emphasized the processing of character recognition and writing, respectively. It was found that the left fusiform gyrus exhibited higher activation when encountering low-frequency than high-frequency characters in both tasks, which suggested this region to be the locus of the orthographic lexicon that represents the knowledge of character forms. On the other hand, the activations in the posterior part of the left middle frontal gyrus and in the left angular gyrus were parametrically modulated by the stroke number of target characters only in the stroke judgment task, which suggested these regions to be the locus of the orthographic buffer that represents the processing of stroke sequence in writing. These results provide the first evidence for the functional and anatomical dissociation between the orthographic lexicon and buffer in reading and writing Chinese characters. They also demonstrate the critical roles of the left fusiform area and the frontoparietal network to the long-term and short-term representations of orthographic knowledge, respectively, across different orthographies.

  9. The evolution of annelids reveals two adaptive routes to the interstitial realm.

    Science.gov (United States)

    Struck, Torsten Hugo; Golombek, Anja; Weigert, Anne; Franke, Franziska Anni; Westheide, Wilfried; Purschke, Günter; Bleidorn, Christoph; Halanych, Kenneth Michael

    2015-08-03

    Many animals permanently inhabit the marine interstitium, the space between sand grains [1, 2]. Different evolutionary scenarios may explain the existence of interstitial animals [3, 4]. These scenarios include (1) that the interstitial realm is the ancestral habitat of bilaterians [5, 6], (2) that interstitial taxa evolved from larger ancestors by miniaturization, or (3) progenesis [3]. The first view mirrors the former hypothesis that interstitial annelids, called archiannelids, were at the base of the annelid radiation [7]. Based on morphological data, however, progenesis is generally favored for interstitial annelids today [3, 4, 8]. Herein, our phylogenomic approach revealed that interstitial archiannelids are robustly placed into two groups nested within the annelid tree. Evolution of the first group comprising among others Dinophilidae is best explained by progenesis. In contrast, the second group comprising Protodrilida and Polygordiidae appears to have evolved by stepwise miniaturization adapting from coarser to finer sediments. Thus, in addition to progenesis [3, 4], miniaturization, thought to be too slow for an adaptation to the interstitium [3], is an important second route allowing adaptation to interstitial environments. Both progenesis and miniaturization should be considered when investigating evolution of interstitial taxa [1, 3].

  10. A resurrection study reveals rapid adaptive evolution within populations of an invasive plant.

    Science.gov (United States)

    Sultan, Sonia E; Horgan-Kobelski, Tim; Nichols, Lauren M; Riggs, Charlotte E; Waples, Ryan K

    2013-02-01

    The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11-year period, the evolution of increased reproductive output as well as greater physiological and root-allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically-important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics.

  11. Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization.

    Science.gov (United States)

    Müller, Daniel B; Schubert, Olga T; Röst, Hannes; Aebersold, Ruedi; Vorholt, Julia A

    2016-10-01

    Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals species-specific adaptations to the host environment and provide evidence for niche separation within the plant microbiota.

  12. The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal

    Science.gov (United States)

    Seim, Inge; Ma, Siming; Zhou, Xuming; Gerashchenko, Maxim V.; Lee, Sang-Goo; Suydam, Robert; George, John C.; Bickham, John W.; Gladyshev, Vadim N.

    2014-01-01

    Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases. PMID:25411232

  13. The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal.

    Science.gov (United States)

    Seim, Inge; Ma, Siming; Zhou, Xuming; Gerashchenko, Maxim V; Lee, Sang-Goo; Suydam, Robert; George, John C; Bickham, John W; Gladyshev, Vadim N

    2014-10-01

    Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases.

  14. Adaptations to a Subterranean Environment and Longevity Revealed by the Analysis of Mole Rat Genomes

    Directory of Open Access Journals (Sweden)

    Xiaodong Fang

    2014-09-01

    Full Text Available Subterranean mammals spend their lives in dark, unventilated environments that are rich in carbon dioxide and ammonia and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber. Comparative genome analyses, along with the transcriptomes of related subterranean rodents, revealed candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, an aberrant melatonin system, pain insensitivity, and unique processing of 28S rRNA. Together, these genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance, and longevity.

  15. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.

    Science.gov (United States)

    Förster, Frank; Beisser, Daniela; Grohme, Markus A; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C; Shkumatov, Alexander V; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.

  16. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic

    Energy Technology Data Exchange (ETDEWEB)

    Saunders, Neil F.W.; Thomas, Torsten; Curmi, Paul M.G.; Mattick, John S.; Kuczek, Elizabeth; Slade, Rob; Davis, John; Franzmann, Peter; Boone, David; Rusterholtz, Karl; Feldman, Robert; Gates, Chris; Bench, Shellie; Sowers, Kevin; Kadner, Kristen; Aerts, Andrea; Dehal, Paramvir; Detter, Chris; Glavina, Tijana; Lucas, Susan; Richardson, Paul; Larimer, Frank; Hauser , Frank; Hauser, Loren; Land, Miriam; Cavicchioli, Richard

    2003-03-01

    We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of non-charged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15-98 C) was used to generate 1 111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent accessible area for more Gln, Thr an hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles.

  17. Does the individual adaption of standardized speech paradigmas for clinical functional Magnetic Resonance Imaging (fMRI) effect the localization of the language-dominant hemisphere and of Broca's and Wernicke's areas; Beeinflusst die individuelle Anpassung standardisierter Sprachparadigmen fuer die klinische funktionelle Magnetresonanztomographie (fMRT) die Lokalisation der sprachdominanten Hemisphaere, des Broca- und des Wernicke-Sprachzentrums?

    Energy Technology Data Exchange (ETDEWEB)

    Konrad, F.; Nennig, E.; Kress, B.; Sartor, K.; Stippich, C. [Abteilung Neuroradiologie, Neurologische Klinik, Universitaetsklinikum Heidelberg (Germany); Ochmann, H. [Neurochirurgische Klinik, Universitaetsklinikum Heidelberg (Germany)

    2005-03-01

    Purpose: Functional magnetic resonance imaging (fMRI) localizes Broca's area (B) and Wernicke's area (W) and the hemisphere dominant for language. In clinical fMRI, adapting the stimulation paradigms to each patient's individual cognitive capacity is crucial for diagnostic success. To interpret clinical fMRI findings correctly, we studied the effect of varying frequency and number of stimuli on functional localization, determination of language dominance and BOLD signals. Materials and Methods: Ten volunteers (VP) were investigated at 1.5 Tesla during visually triggered sentence generation using a standardized block design. In four different measurements, the stimuli were presented to each VP with frequencies of (1/1)s, (1/2)s,(1/3)s and (1/6)s. Results: The functional localizations and the correlations of the measured BOLD signals to the applied hemodynamic reference function (r) were almost independent from frequency and number of the stimuli in both hemispheres, whereas the relative BOLD signal changes ({delta}S) in B and W increased with the stimulation rate, which also changed the lateralization indices. The strongest BOLD activations were achieved with the highest stimulation rate or with the maximum language production task, respectively. Conclusion: The adaptation of language paradigms necessary in clinical fMRI does not alter the functional localizations but changes the BOLD signals and language lateralization which should not be attributed to the underlying brain pathology. (orig.)

  18. Revealing the Organization of Complex Adaptive Systems through Multivariate Time Series Modeling

    Directory of Open Access Journals (Sweden)

    David G. Angeler

    2011-09-01

    Full Text Available Revealing the adaptive responses of ecological, social, and economic systems to a transforming biosphere is crucial for understanding system resilience and preventing collapse. However, testing the theory that underpins complex adaptive system organization (e.g., panarchy theory is challenging. We used multivariate time series modeling to identify scale-specific system organization and, by extension, apparent resilience mechanisms. We used a 20-year time series of invertebrates and phytoplankton from 26 Swedish lakes to test the proposition that a few key-structuring environmental variables at specific scales create discontinuities in community dynamics. Cross-scale structure was manifested in two independent species groups within both communities across lakes. The first species group showed patterns of directional temporal change, which was related to environmental variables that acted at broad spatiotemporal scales (reduced sulfate deposition, North Atlantic Oscillation. The second species group showed fluctuation patterns, which often could not be explained by environmental variables. However, when significant relationships were found, species-group trends were predicted by variables (total organic carbon, nutrients that acted at narrower spatial scales (i.e., catchment and lake. Although the sets of environmental variables that predicted the species groups differed between phytoplankton and invertebrates, the scale-specific imprints of keystone environmental variables for creating cross-scale structure were clear for both communities. Temporal trends of functional groups did not track the observed structural changes, suggesting functional stability despite structural change. Our approach allows for identifying scale-specific patterns and processes, thus providing opportunities for better characterization of complex adaptive systems organization and dynamics. This, in turn, holds potential for more accurate evaluation of resilience in

  19. The Evolution of Two-Component Systems in Bacteria RevealsDifferent Strategies for Niche Adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Alm, Eric; Huang, Katherine; Arkin, Adam

    2006-09-13

    Two-component systems including histidine protein kinasesrepresent the primary signal transduction paradigm in prokaryoticorganisms. To understand how these systems adapt to allow organisms todetect niche-specific signals, we analyzed the phylogenetic distributionof nearly 5000 histidine protein kinases from 207 sequenced prokaryoticgenomes. We found that many genomes carry a large repertoire of recentlyevolved signaling genes, which may reflect selective pressure to adapt tonew environmental conditions. Both lineage-specific gene family expansionand horizontal gene transfer play major roles in the introduction of newhistidine kinases into genomes; however, there are differences in howthese two evolutionary forces act. Genes imported via horizontal transferare more likely to retain their original functionality as inferred from asimilar complement of signaling domains, while gene family expansionaccompanied by domain shuffling appears to be a major source of novelgenetic diversity. Family expansion is the dominantsource of newhistidine kinase genes in the genomes most enriched in signalingproteins, and detailed analysis reveals that divergence in domainstructure and changes in expression patterns are hallmarks of recentexpansions. Finally, while these two modes of gene acquisition arewidespread across bacterial taxa, there are clear species-specificpreferences for which mode is used.

  20. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

    Science.gov (United States)

    Olsen, Jeanine L; Rouzé, Pierre; Verhelst, Bram; Lin, Yao-Cheng; Bayer, Till; Collen, Jonas; Dattolo, Emanuela; De Paoli, Emanuele; Dittami, Simon; Maumus, Florian; Michel, Gurvan; Kersting, Anna; Lauritano, Chiara; Lohaus, Rolf; Töpel, Mats; Tonon, Thierry; Vanneste, Kevin; Amirebrahimi, Mojgan; Brakel, Janina; Boström, Christoffer; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry W; Jueterbock, Alexander; Mraz, Amy; Stam, Wytze T; Tice, Hope; Bornberg-Bauer, Erich; Green, Pamela J; Pearson, Gareth A; Procaccini, Gabriele; Duarte, Carlos M; Schmutz, Jeremy; Reusch, Thorsten B H; Van de Peer, Yves

    2016-02-18

    Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.

  1. Comparison of Models for Bubonic Plague Reveals Unique Pathogen Adaptations to the Dermis.

    Science.gov (United States)

    Gonzalez, Rodrigo J; Weening, Eric H; Lane, M Chelsea; Miller, Virginia L

    2015-07-01

    Vector-borne pathogens are inoculated in the skin of mammals, most likely in the dermis. Despite this, subcutaneous (s.c.) models of infection are broadly used in many fields, including Yersinia pestis pathogenesis. We expand on a previous report where we implemented intradermal (i.d.) inoculations to study bacterial dissemination during bubonic plague and compare this model with an s.c. We found that i.d. inoculations result in faster kinetics of infection and that bacterial dose influenced mouse survival after i.d. but not s.c. inoculation. Moreover, a deletion mutant of rovA, previously shown to be moderately attenuated in the s.c. model, was severely attenuated in the i.d. Lastly, based on previous observations where a population bottleneck from the skin to lymph nodes was observed after i.d., but not after s.c., inoculations, we used the latter model as a strategy to identify an additional bottleneck in bacterial dissemination from lymph nodes to the bloodstream. Our data indicate that the more biologically relevant i.d. model of bubonic plague differs significantly from the s.c. model in multiple aspects of infection. These findings reveal adaptations of Y. pestis to the dermis and how these adaptations can define the progression of disease. They also emphasize the importance of using a relevant route of infection when addressing host-pathogen interactions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  2. Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast.

    Science.gov (United States)

    Hope, Elyse A; Amorosi, Clara J; Miller, Aaron W; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J

    2017-06-01

    Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. Copyright © 2017 Hope et al.

  3. RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose.

    Science.gov (United States)

    Brown, Neil Andrew; Ries, Laure N A; Reis, Thaila F; Rajendran, Ranjith; Corrêa Dos Santos, Renato Augusto; Ramage, Gordon; Riaño-Pachón, Diego Mauricio; Goldman, Gustavo H

    2016-01-01

    Sugarcane is one of the world's most profitable crops. Waste steam-exploded sugarcane bagasse (SEB) is a cheap, abundant, and renewable lignocellulosic feedstock for the next-generation biofuels. In nature, fungi seldom exist as planktonic cells, similar to those found in the nutrient-rich environment created within an industrial fermenter. Instead, fungi predominantly form biofilms that allow them to thrive in hostile environments. In turn, we adopted an RNA-sequencing approach to interrogate how the model fungus, Aspergillus nidulans, adapts to SEB, revealing the induction of carbon starvation responses and the lignocellulolytic machinery, in addition to morphological adaptations. Genetic analyses showed the importance of hydrophobins for growth on SEB. The major hydrophobin, RodA, was retained within the fungal biofilm on SEB fibres. The StuA transcription factor that regulates fungal morphology was up-regulated during growth on SEB and controlled hydrophobin gene induction. The absence of the RodA or DewC hydrophobins reduced biofilm formation. The loss of a RodA or a functional StuA reduced the retention of the hydrolytic enzymes within the vicinity of the fungus. Hence, hydrophobins promote biofilm formation on SEB, and may enhance lignocellulose utilisation via promoting a compact substrate-enzyme-fungus structure. This novel study highlights the importance of hydrophobins to the formation of biofilms and the efficient deconstruction of lignocellulose.

  4. Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation

    Directory of Open Access Journals (Sweden)

    Xian Zhang

    2016-08-01

    Full Text Available Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.

  5. Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation.

    Science.gov (United States)

    Zhang, Xian; Feng, Xue; Tao, Jiemeng; Ma, Liyuan; Xiao, Yunhua; Liang, Yili; Liu, Xueduan; Yin, Huaqun

    2016-08-19

    Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.

  6. The evolution of two-component systems in bacteria reveals different strategies for niche adaptation.

    Directory of Open Access Journals (Sweden)

    Eric Alm

    2006-11-01

    Full Text Available Two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. To understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. We found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions. Both lineage-specific gene family expansion and horizontal gene transfer play major roles in the introduction of new histidine kinases into genomes; however, there are differences in how these two evolutionary forces act. Genes imported via horizontal transfer are more likely to retain their original functionality as inferred from a similar complement of signaling domains, while gene family expansion accompanied by domain shuffling appears to be a major source of novel genetic diversity. Family expansion is the dominant source of new histidine kinase genes in the genomes most enriched in signaling proteins, and detailed analysis reveals that divergence in domain structure and changes in expression patterns are hallmarks of recent expansions. Finally, while these two modes of gene acquisition are widespread across bacterial taxa, there are clear species-specific preferences for which mode is used.

  7. Comparative Proteomic Analysis of Flag Leaves Reveals New Insight into Wheat Heat Adaptation

    Directory of Open Access Journals (Sweden)

    Yunze Lu

    2017-06-01

    Full Text Available Hexaploid wheat (Triticum aestivum L. is an important food crop but it is vulnerable to heat. The heat-responsive proteome of wheat remains to be fully elucidated because of previous technical and genomic limitations, and this has hindered our understanding of the mechanisms of wheat heat adaptation and advances in improving thermotolerance. Here, flag leaves of wheat during grain filling stage were subjected to high daytime temperature stress, and 258 heat-responsive proteins (HRPs were identified with iTRAQ analysis. Enrichment analysis revealed that chlorophyll synthesis, carbon fixation, protein turnover, and redox regulation were the most remarkable heat-responsive processes. The HRPs involved in chlorophyll synthesis and carbon fixation were significantly decreased, together with severe membrane damage, demonstrating the specific effects of heat on photosynthesis of wheat leaves. In addition, the decrease in chlorophyll content may result from the decrease in HRPs involved in chlorophyll precursor synthesis. Further analysis showed that the accumulated effect of heat stress played a critical role in photosynthesis reduction, suggested that improvement in heat tolerance of photosynthesis, and extending heat tolerant period would be major research targets. The significantly accumulation of GSTs and Trxs in response to heat suggested their important roles in redox regulation, and they could be the promising candidates for improving wheat thermotolerance. In summary, our results provide new insight into wheat heat adaption and provide new perspectives on thermotolerance improvement.

  8. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

    KAUST Repository

    Olsen, Jeanine L.

    2016-01-27

    Seagrasses colonized the sea1 on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet2. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes3, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae4 and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming5, 6, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants7.

  9. Legume adaptation to sulfur deficiency revealed by comparing nutrient allocation and seed traits in Medicago truncatula.

    Science.gov (United States)

    Zuber, Hélène; Poignavent, Germain; Le Signor, Christine; Aimé, Delphine; Vieren, Eric; Tadla, Charlène; Lugan, Raphaël; Belghazi, Maya; Labas, Valérie; Santoni, Anne-Lise; Wipf, Daniel; Buitink, Julia; Avice, Jean-Christophe; Salon, Christophe; Gallardo, Karine

    2013-12-01

    Reductions in sulfur dioxide emissions and the use of sulfur-free mineral fertilizers are decreasing soil sulfur levels and threaten the adequate fertilization of most crops. To provide knowledge regarding legume adaptation to sulfur restriction, we subjected Medicago truncatula, a model legume species, to sulfur deficiency at various developmental stages, and compared the yield, nutrient allocation and seed traits. This comparative analysis revealed that sulfur deficiency at the mid-vegetative stage decreased yield and altered the allocation of nitrogen and carbon to seeds, leading to reduced levels of major oligosaccharides in mature seeds, whose germination was dramatically affected. In contrast, during the reproductive period, sulfur deficiency had little influence on yield and nutrient allocation, but the seeds germinated slowly and were characterized by low levels of a biotinylated protein, a putative indicator of germination vigor that has not been previously related to sulfur nutrition. Significantly, plants deprived of sulfur at an intermediary stage (flowering) adapted well by remobilizing nutrients from source organs to seeds, ensuring adequate quantities of carbon and nitrogen in seeds. This efficient remobilization of photosynthates may be explained by vacuolar sulfate efflux to maintain leaf metabolism throughout reproductive growth, as suggested by transcript and metabolite profiling. The seeds from these plants, deprived of sulfur at the floral transition, contained normal levels of major oligosaccharides but their germination was delayed, consistent with low levels of sucrose and the glycolytic enzymes required to restart seed metabolism during imbibition. Overall, our findings provide an integrative view of the legume response to sulfur deficiency.

  10. Functional photoreceptor loss revealed with adaptive optics: an alternate cause of color blindness.

    Science.gov (United States)

    Carroll, Joseph; Neitz, Maureen; Hofer, Heidi; Neitz, Jay; Williams, David R

    2004-06-01

    There is enormous variation in the X-linked L/M (long/middle wavelength sensitive) gene array underlying "normal" color vision in humans. This variability has been shown to underlie individual variation in color matching behavior. Recently, red-green color blindness has also been shown to be associated with distinctly different genotypes. This has opened the possibility that there may be important phenotypic differences within classically defined groups of color blind individuals. Here, adaptive optics retinal imaging has revealed a mechanism for producing dichromatic color vision in which the expression of a mutant cone photopigment gene leads to the loss of the entire corresponding class of cone photoreceptor cells. Previously, the theory that common forms of inherited color blindness could be caused by the loss of photoreceptor cells had been discounted. We confirm that remarkably, this loss of one-third of the cones does not impair any aspect of vision other than color.

  11. Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host

    Science.gov (United States)

    Wang, Shuai; Wang, Sen; Luo, Yingfeng; Xiao, Lihua; Luo, Xuenong; Gao, Shenghan; Dou, Yongxi; Zhang, Huangkai; Guo, Aijiang; Meng, Qingshu; Hou, Junling; Zhang, Bing; Zhang, Shaohua; Yang, Meng; Meng, Xuelian; Mei, Hailiang; Li, Hui; He, Zilong; Zhu, Xueliang; Tan, Xinyu; Zhu, Xing-quan; Yu, Jun; Cai, Jianping; Zhu, Guan; Hu, Songnian; Cai, Xuepeng

    2016-01-01

    Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica. PMID:27653464

  12. High-Resolution Mapping of Protein Concentration Reveals Principles of Proteome Architecture and Adaptation

    Directory of Open Access Journals (Sweden)

    Emmanuel D. Levy

    2014-05-01

    Full Text Available A single yeast cell contains a hundred million protein molecules. How these proteins are organized to orchestrate living processes is a central question in biology. To probe this organization in vivo, we measured the local concentration of proteins based on the strength of their nonspecific interactions with a neutral reporter protein. We first used a cytosolic reporter and measured local concentrations for ∼2,000 proteins in S. cerevisiae, with accuracy comparable to that of mass spectrometry. Localizing the reporter to membranes specifically increased the local concentration measured for membrane proteins. Comparing the concentrations measured by both reporters revealed that encounter frequencies between proteins are primarily dictated by their abundances. However, to change these encounter frequencies and restructure the proteome, as in adaptation, we find that changes in localization have more impact than changes in abundance. These results highlight how protein abundance and localization contribute to proteome organization and reorganization.

  13. Vibrotactile cuing revisited to reveal a possible challenge to sensorimotor adaptation.

    Science.gov (United States)

    Lee, Beom-Chan; Thrasher, Timothy A; Layne, Charles S; Martin, Bernard J

    2016-12-01

    Motor responses to unexpected external perturbations require the adjustment of the motor commands driving the ongoing activity. Strategies can be learned with practice to compensate for these unpredictable perturbations (e.g., externally induced slips and trips). It has been hypothesized that response improvements reflect the adaptation of motor commands through updates of an internal model. This hypothesis may be nuanced when a pre-existing motor response could be used. In that case, since a relatively adequate response is known, only the timing of the command needs to be determined. If so, then it could be inferred that the timing of movement initiation and the specific sequence of motor commands can be dissociated. Previously, we quantified the benefits of cuing vs. learning on recovery motor responses resulting from a trip induced by the abrupt stop of one side of a split belt treadmill. Trip occurrence was randomized within a series of strides. Two groups of young adults participated to two distinct experiments (learning, cuing). In the learning experiment, trip recovery improved progressively from the 4th to the 8th trial to reach an "adapted response". In the cuing experiment, trip recovery was immediate (from 1st trial). Expanding from these results, the aim of the present work was to differentiate the processes underlying the generation of motor compensation strategies in response to an external perturbation under time uncertainty. A supplementary analysis revealed that "cued" responses were kinematically similar to the "adapted response" and remained invariant regardless of cue lead time (250, 500 ms before trip) and application location of the cue (arm, trunk, lower leg). It is posited that all responses (cued and non-cued) are the expression of a pre-existing motor program derived from life experiences. Here, the cue significantly reduces time uncertainty and adaptation consists primarily in resolving time uncertainty based on the trial

  14. Talaromyces marneffei Genomic, Transcriptomic, Proteomic and Metabolomic Studies Reveal Mechanisms for Environmental Adaptations and Virulence

    Directory of Open Access Journals (Sweden)

    Susanna K. P. Lau

    2017-06-01

    Full Text Available Talaromyces marneffei is a thermally dimorphic fungus causing systemic infections in patients positive for HIV or other immunocompromised statuses. Analysis of its ~28.9 Mb draft genome and additional transcriptomic, proteomic and metabolomic studies revealed mechanisms for environmental adaptations and virulence. Meiotic genes and genes for pheromone receptors, enzymes which process pheromones, and proteins involved in pheromone response pathway are present, indicating its possibility as a heterothallic fungus. Among the 14 Mp1p homologs, only Mp1p is a virulence factor binding a variety of host proteins, fatty acids and lipids. There are 23 polyketide synthase genes, one for melanin and two for mitorubrinic acid/mitorubrinol biosynthesis, which are virulence factors. Another polyketide synthase is for biogenesis of the diffusible red pigment, which consists of amino acid conjugates of monascorubin and rubropunctatin. Novel microRNA-like RNAs (milRNAs and processing proteins are present. The dicer protein, dcl-2, is required for biogenesis of two milRNAs, PM-milR-M1 and PM-milR-M2, which are more highly expressed in hyphal cells. Comparative transcriptomics showed that tandem repeat-containing genes were overexpressed in yeast phase, generating protein polymorphism among cells, evading host’s immunity. Comparative proteomics between yeast and hyphal cells revealed that glyceraldehyde-3-phosphate dehydrogenase, up-regulated in hyphal cells, is an adhesion factor for conidial attachment.

  15. The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese.

    Directory of Open Access Journals (Sweden)

    Christophe Monnet

    Full Text Available Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.

  16. Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure.

    Science.gov (United States)

    Galinsky, Kevin J; Loh, Po-Ru; Mallick, Swapan; Patterson, Nick J; Price, Alkes L

    2016-11-03

    Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for using population differentiation to detect selection and enables an analysis of the UK population structure at fine resolution. In this study, analyses of 113,851 UK Biobank samples showed that population structure in the UK is dominated by five principal components (PCs) spanning six clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses of ancient Eurasians revealed that populations in the northern UK have higher levels of Steppe ancestry and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along the top PCs identified a genome-wide-significant signal of selection at the coding variant rs601338 in FUT2 (p = 9.16 × 10(-9)). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified genome-wide-significant (p = 5 × 10(-8)) signals of recent selection at two additional loci: CYP1A2-CSK and F12. We detected strong associations between diastolic blood pressure in the UK Biobank and both the variants with selection signals at CYP1A2-CSK (p = 1.10 × 10(-19)) and the variants with ancient Eurasian selection signals at the ATXN2-SH2B3 locus (p = 8.00 × 10(-33)), implicating recent adaptation related to blood pressure.

  17. RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize.

    Science.gov (United States)

    Arora, Kanika; Panda, Kusuma Kumari; Mittal, Shikha; Mallikarjuna, Mallana Gowdra; Rao, Atmakuri Ramakrishna; Dash, Prasanta Kumar; Thirunavukkarasu, Nepolean

    2017-09-08

    Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis of the roots of a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These 21,364 DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation of invertase (49-fold) and hexokinase (36-fold) in roots explained the ATP requirement in waterlogging condition. Also, high up-regulation of expansins (42-fold), plant aspartic protease A3 (19-fold), polygalacturonases (16-fold), respiratory burst oxidase homolog (12-fold), and hydrolases (11-fold) explained the PCD of root cortical cells followed by the formation of aerenchyma tissue during waterlogging stress. We hypothesized that the oxygen transfer in waterlogged roots is promoted by a cross-talk of fermentative, metabolic, and glycolytic pathways that generate ATPs for PCD and aerenchyma formation in root cortical cells. SNPs were mapped to the DEGs regulating aerenchyma formation (12), ethylene-responsive factors (11), and glycolysis (4) under stress. RNAseq derived SNPs can be used in selection approaches to breed tolerant hybrids. Overall, this investigation provided significant evidence of genes operating in the adaptive traits such as ethylene production and aerenchyma formation to cope-up the waterlogging stress.

  18. Learning theories reveal loss of pancreatic electrical connectivity in diabetes as an adaptive response.

    Directory of Open Access Journals (Sweden)

    Pranay Goel

    Full Text Available Cells of almost all solid tissues are connected with gap junctions which permit the direct transfer of ions and small molecules, integral to regulating coordinated function in the tissue. The pancreatic islets of Langerhans are responsible for secreting the hormone insulin in response to glucose stimulation. Gap junctions are the only electrical contacts between the beta-cells in the tissue of these excitable islets. It is generally believed that they are responsible for synchrony of the membrane voltage oscillations among beta-cells, and thereby pulsatility of insulin secretion. Most attempts to understand connectivity in islets are often interpreted, bottom-up, in terms of measurements of gap junctional conductance. This does not, however, explain systematic changes, such as a diminished junctional conductance in type 2 diabetes. We attempt to address this deficit via the model presented here, which is a learning theory of gap junctional adaptation derived with analogy to neural systems. Here, gap junctions are modelled as bonds in a beta-cell network, that are altered according to homeostatic rules of plasticity. Our analysis reveals that it is nearly impossible to view gap junctions as homogeneous across a tissue. A modified view that accommodates heterogeneity of junction strengths in the islet can explain why, for example, a loss of gap junction conductance in diabetes is necessary for an increase in plasma insulin levels following hyperglycemia.

  19. Functional connectivity-based signatures of schizophrenia revealed by multiclass pattern analysis of resting-state fMRI from schizophrenic patients and their healthy siblings

    Directory of Open Access Journals (Sweden)

    Yu Yang

    2013-02-01

    Full Text Available Abstract Background Recently, a growing number of neuroimaging studies have begun to investigate the brains of schizophrenic patients and their healthy siblings to identify heritable biomarkers of this complex disorder. The objective of this study was to use multiclass pattern analysis to investigate the inheritable characters of schizophrenia at the individual level, by comparing whole-brain resting-state functional connectivity of patients with schizophrenia to their healthy siblings. Methods Twenty-four schizophrenic patients, twenty-five healthy siblings and twenty-two matched healthy controls underwent the resting-state functional Magnetic Resonance Imaging (rs-fMRI scanning. A linear support vector machine along with principal component analysis was used to solve the multi-classification problem. By reconstructing the functional connectivities with high discriminative power, three types of functional connectivity-based signatures were identified: (i state connectivity patterns, which characterize the nature of disruption in the brain network of patients with schizophrenia; (ii trait connectivity patterns, reflecting shared connectivities of dysfunction in patients with schizophrenia and their healthy siblings, thereby providing a possible neuroendophenotype and revealing the genetic vulnerability to develop schizophrenia; and (iii compensatory connectivity patterns, which underlie special brain connectivities by which healthy siblings might compensate for an increased genetic risk for developing schizophrenia. Results Our multiclass pattern analysis achieved 62.0% accuracy via leave-one-out cross-validation (p  Conclusions Based on our experimental results, we saw some indication of differences in functional connectivity patterns in the healthy siblings of schizophrenic patients compared to other healthy individuals who have no relations with the patients. Our preliminary investigation suggested that the use of resting-state functional

  20. Control over the strength of connections between modules: a double dissociation between stimulus format and task revealed by Granger causality mapping in fMRI

    Science.gov (United States)

    Anderson, Britt; Soliman, Sherif; O’Malley, Shannon; Danckert, James; Besner, Derek

    2015-01-01

    Drawing on theoretical and computational work with the localist dual route reading model and results from behavioral studies, Besner et al. (2011) proposed that the ability to perform tasks that require overriding stimulus-specific defaults (e.g., semantics when naming Arabic numerals, and phonology when evaluating the parity of number words) necessitate the ability to modulate the strength of connections between cognitive modules for lexical representation, semantics, and phonology on a task- and stimulus-specific basis. We used functional magnetic resonance imaging to evaluate this account by assessing changes in functional connectivity while participants performed tasks that did and did not require such stimulus-task default overrides. The occipital region showing the greatest modulation of BOLD signal strength for the two stimulus types was used as the seed region for Granger causality mapping (GCM). Our GCM analysis revealed a region of rostromedial frontal cortex with a crossover interaction. When participants performed tasks that required overriding stimulus type defaults (i.e., parity judgments of number words and naming Arabic numerals) functional connectivity between the occipital region and rostromedial frontal cortex was present. Statistically significant functional connectivity was absent when the tasks were the default for the stimulus type (i.e., parity judgments of Arabic numerals and reading number words). This frontal region (BA 10) has previously been shown to be involved in goal-directed behavior and maintenance of a specific task set. We conclude that overriding stimulus-task defaults requires a modulation of connection strengths between cognitive modules and that the override mechanism predicted from cognitive theory is instantiated by frontal modulation of neural activity of brain regions specialized for sensory processing. PMID:25870571

  1. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle.

    Science.gov (United States)

    Załuga, Joanna; Stragier, Pieter; Baeyen, Steve; Haegeman, Annelies; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

    2014-05-22

    The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as pathogenic Cmm hampers a clear judgment on the seed quality and health. To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2 and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG 26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes. The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and

  2. Differential molecular responses of rapeseed cotyledons to light and dark reveal metabolic adaptations towards autotrophy establishment

    Directory of Open Access Journals (Sweden)

    Dongli He

    2016-07-01

    Full Text Available Photosynthesis competent autotrophy should be established during the postgerminative stage of plant growth. Among the multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark condition, the rapeseed hypocotyl extends quickly with an apical hook, and the cotyledon is yellow and folded, and maintains high level of the isocitrate lyase (ICL. By contrast, in the light, the hypocotyl extends slowly, the cotyledon unfolds and turns green, the ICL content changes in parallel with the cotyledon greening. To reveal metabolic adaptations during the establishment of postgerminative autotrophy in rapeseed, we conducted comparative proteomic and metabolomic analyses of the cotyledons of seedlings grown under light versus dark conditions. Under both conditions, the increase of the protease, fatty acids β-oxidation and glyoxylate-cycle related proteins was accompanied with rapid degradation of the stored proteins and lipids with an accumulation of the amino acids, while light condition partially retarded these conversions. Light significantly induced the expression of chlorophyll-binding and photorespiration related proteins, resulting in an increase of the reducing-sugar. However, the levels of some chlide conversion, Calvin-cycle and photorespiration related proteins also accumulated in dark grown cotyledons, implying that the transition from heterotrophy to autotrophy is programmed in the seed rather than induced by light. Various anti-stress systems, e.g., redox related proteins, salicylic acid, proline and chaperones, were employed to release the oxidative stress, which was mainly derived from lipid oxidation or photorespiration, under both conditions. This study provides a comprehensive understanding of the differential molecular responses of rapeseed cotyledons to light and dark conditions, which will facilitate further study on the complex mechanism underlying the transition from heterotrophy to

  3. Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data

    DEFF Research Database (Denmark)

    Yang, Lei; Rau, Martin Holm; Yang, Liang

    2011-01-01

    features from the transcriptomic dataset and improve clustering patterns of CF isolates. Decomposition of the transcriptomic dataset by ICA also facilitates gene identification and gene ontology enrichment. Conclusions: Our results show that P. aeruginosa employs multiple patient-specific adaption...

  4. Phylogenomic Analyses Reveal Convergent Patterns of Adaptive Evolution in Elephant and Human Ancestries

    National Research Council Canada - National Science Library

    Morris Goodman; Kirstin N. Sterner; Munirul Islam; Monica Uddin; Chet C. Sherwood; Patrick R. Hof; Zhuo-Cheng Hou; Leonard Lipovich; Hui Jia; Lawrence I. Grossman; Derek E. Wildman

    2009-01-01

    .... Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages...

  5. Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

    Science.gov (United States)

    Gossmann, Toni I.; Song, Bao-Hua; Windsor, Aaron J.; Mitchell-Olds, Thomas; Dixon, Christopher J.; Kapralov, Maxim V.; Filatov, Dmitry A.; Eyre-Walker, Adam

    2010-01-01

    The relative contribution of advantageous and neutral mutations to the evolutionary process is a central problem in evolutionary biology. Current estimates suggest that whereas Drosophila, mice, and bacteria have undergone extensive adaptive evolution, hominids show little or no evidence of adaptive evolution in protein-coding sequences. This may be a consequence of differences in effective population size. To study the matter further, we have investigated whether plants show evidence of adaptive evolution using an extension of the McDonald–Kreitman test that explicitly models slightly deleterious mutations by estimating the distribution of fitness effects of new mutations. We apply this method to data from nine pairs of species. Altogether more than 2,400 loci with an average length of ≈280 nucleotides were analyzed. We observe very similar results in all species; we find little evidence of adaptive amino acid substitution in any comparison except sunflowers. This may be because many plant species have modest effective population sizes. PMID:20299543

  6. New insight into motor adaptation to pain revealed by a combination of modelling and empirical approaches.

    Science.gov (United States)

    Hodges, P W; Coppieters, M W; MacDonald, D; Cholewicki, J

    2013-09-01

    Movement changes in pain. Unlike the somewhat stereotypical response of limb muscles to pain, trunk muscle responses are highly variable when challenged by pain in that region. This has led many to question the existence of a common underlying theory to explain the adaptation. Here, we tested the hypotheses that (1) adaptation in muscle activation in acute pain leads to enhanced spine stability, despite variation in the pattern of muscle activation changes; and (2) individuals would use a similar 'signature' pattern for tasks with different mechanical demands. In 17 healthy individuals, electromyography recordings were made from a broad array of anterior and posterior trunk muscles while participants moved slowly between trunk flexion and extension with and without experimentally induced back pain. Hypotheses were tested by estimating spine stability (Stability Index) with an electromyography-driven spine model and analysis of individual and overall (net) adaptations in muscle activation. The Stability Index (P muscle activity (P muscle activity. For most, the adaptation was similar between movement directions despite opposite movement demands. These data provide the first empirical confirmation that, in most individuals, acute back pain leads to increased spinal stability and that the pattern of muscle activity is not stereotypical, but instead involves an individual-specific response to pain. This adaptation is likely to provide short-term benefit to enhance spinal protection, but could have long-term consequences for spinal health. © 2013 European Federation of International Association for the Study of Pain Chapters.

  7. Adaptive responses reveal contemporary and future ecotypes in a desert shrub.

    Science.gov (United States)

    Richardson, Bryce A; Kitchen, Stanley G; Pendleton, Rosemary L; Pendleton, Burton K; Germino, Matthew J; Rehfeldt, Gerald E; Meyer, Susan E

    2014-03-01

    Interacting threats to ecosystem function, including climate change, wildfire, and invasive species necessitate native plant restoration in desert ecosystems. However, native plant restoration efforts often remain unguided by ecological genetic information. Given that many ecosystems are in flux from climate change, restoration plans need to account for both contemporary and future climates when choosing seed sources. In this study we analyze vegetative responses, including mortality, growth, and carbon isotope ratios in two blackbrush (Coleogyne ramosissima) common gardens that included 26 populations from a range-wide collection. This shrub occupies ecotones between the warm and cold deserts of Mojave and Colorado Plateau ecoregions in western North America. The variation observed in the vegetative responses of blackbrush populations was principally explained by grouping populations by ecoregions and by regression with site-specific climate variables. Aridity weighted by winter minimum temperatures best explained vegetative responses; Colorado Plateau sites were usually colder and drier than Mojave sites. The relationship between climate and vegetative response was mapped within the boundaries of the species-climate space projected for the contemporary climate and for the decade surrounding 2060. The mapped ecological genetic pattern showed that genetic variation could be classified into cool-adapted and warm-adapted ecotypes, with populations often separated by steep dines. These transitions are predicted to occur in both the Mojave Desert and Colorado Plateau ecoregions. While under contemporary conditions the warm-adapted ecotype occupies the majority of climate space, climate projections predict that the cool-adapted ecotype could prevail as the dominant ecotype as the climate space of blackbrush expands into higher elevations and latitudes. This study provides the framework for delineating climate change-responsive seed transfer guidelines, which are needed

  8. Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries.

    Science.gov (United States)

    Goodman, Morris; Sterner, Kirstin N; Islam, Munirul; Uddin, Monica; Sherwood, Chet C; Hof, Patrick R; Hou, Zhuo-Cheng; Lipovich, Leonard; Jia, Hui; Grossman, Lawrence I; Wildman, Derek E

    2009-12-08

    Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains and short life spans. Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages, and whether aerobic energy metabolism genes are especially well represented in the elephant and human patterns. Our analyses encompassed approximately 6,000 genes in each of these lineages with each gene yielding extensive coding sequence matches in interordinal comparisons. Each gene's nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined. Then, from gene ontology information on genes with the higher dN/dS ratios, we identified the more prevalent sets of genes that belong to specific functional categories and that evolved adaptively. Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes. In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage.

  9. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

    Science.gov (United States)

    Castoe, Todd A; de Koning, A P Jason; Hall, Kathryn T; Card, Daren C; Schield, Drew R; Fujita, Matthew K; Ruggiero, Robert P; Degner, Jack F; Daza, Juan M; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J; Castoe, Jill M; Fox, Samuel E; Poole, Alex W; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W; Li, Qing; Schott, Ryan K; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A; Hoffmann, Federico G; Bogden, Robert; Smith, Eric N; Chang, Belinda S W; Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Richardson, Michael K; Mackessy, Stephen P; Bronikowski, Anne M; Bronikowsi, Anne M; Yandell, Mark; Warren, Wesley C; Secor, Stephen M; Pollock, David D

    2013-12-17

    Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

  10. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

    Science.gov (United States)

    Castoe, Todd A.; de Koning, A. P. Jason; Hall, Kathryn T.; Card, Daren C.; Schield, Drew R.; Fujita, Matthew K.; Ruggiero, Robert P.; Degner, Jack F.; Daza, Juan M.; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J.; Castoe, Jill M.; Fox, Samuel E.; Poole, Alex W.; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W.; Li, Qing; Schott, Ryan K.; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A.; Hoffmann, Federico G.; Bogden, Robert; Smith, Eric N.; Chang, Belinda S. W.; Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Richardson, Michael K.; Mackessy, Stephen P.; Bronikowski, Anne M.; Yandell, Mark; Warren, Wesley C.; Secor, Stephen M.; Pollock, David D.

    2013-01-01

    Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome. PMID:24297902

  11. Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions.

    Science.gov (United States)

    Artemov, Artem V; Mugue, Nikolai S; Rastorguev, Sergey M; Zhenilo, Svetlana; Mazur, Alexander M; Tsygankova, Svetlana V; Boulygina, Eugenia S; Kaplun, Daria; Nedoluzhko, Artem V; Medvedeva, Yulia A; Prokhortchouk, Egor B

    2017-09-01

    The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution-adaptation to a freshwater environment. Although genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, and ATP4A were differentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities

    DEFF Research Database (Denmark)

    Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.

    2013-01-01

    versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs...... compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides...

  13. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane; Kuo, Alan; Brueggeman, Andrew; Dunigan, David D.; Gurnon, James; Ladunga, Istvan; Lindquist, Erika; Lucas, Susan; Pangilinan, Jasmyn; Proschold, Thomas; Salamov, Asaf; Schmutz, Jeremy; Weeks, Donald; Tamada, Takashi; Lomsadze, Alexandre; Borodovsky, Mark; Claverie, Jean-Michel; Grigoriev, Igor V.; Van Etten, James L.

    2012-02-13

    Background Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. Results The 48.8 Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes is highly reshuffled within synteny blocks, suggesting that intra-chromosomal rearrangements were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C-169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN). Conclusions We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.

  14. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

    DEFF Research Database (Denmark)

    Liu, Shiping; Lorenzen, Eline D.; Fumagalli, Matteo

    2014-01-01

    Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyperlipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show...

  15. Multi-task connectivity reveals flexible hubs for adaptive task control

    Science.gov (United States)

    Cole, Michael W.; Reynolds, Jeremy R.; Power, Jonathan D.; Repovs, Grega; Anticevic, Alan; Braver, Todd S.

    2013-01-01

    Extensive evidence suggests the human ability to adaptively implement a wide variety of tasks is preferentially due to the operation of a fronto-parietal brain network. We hypothesized that this network’s adaptability is made possible by ‘flexible hubs’ – brain regions that rapidly update their pattern of global functional connectivity according to task demands. We utilized recent advances in characterizing brain network organization and dynamics to identify mechanisms consistent with the flexible hub theory. We found that the fronto-parietal network’s brain-wide functional connectivity pattern shifted more than other networks’ across a variety of task states, and that these connectivity patterns could be used to identify the current task. Further, these patterns were consistent across practiced and novel tasks, suggesting reuse of flexible hub connectivity patterns facilitates adaptive (novel) task performance. Together, these findings support a central role for fronto-parietal flexible hubs in cognitive control and adaptive implementation of task demands generally. PMID:23892552

  16. Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    Full Text Available Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low CaratioMg ratio in A. lyrata.

  17. A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

    Science.gov (United States)

    Modulating days to flowering is a key mechanism in plants for adapting to new environments, and variation in days to flowering drives population structure by limiting mating. To elucidate the genetic architecture of flowering across maize, a quantitative trait, we mapped flowering in five global pop...

  18. Asynchrony adaptation reveals neural population code for audio-visual timing.

    Science.gov (United States)

    Roach, Neil W; Heron, James; Whitaker, David; McGraw, Paul V

    2011-05-01

    The relative timing of auditory and visual stimuli is a critical cue for determining whether sensory signals relate to a common source and for making inferences about causality. However, the way in which the brain represents temporal relationships remains poorly understood. Recent studies indicate that our perception of multisensory timing is flexible--adaptation to a regular inter-modal delay alters the point at which subsequent stimuli are judged to be simultaneous. Here, we measure the effect of audio-visual asynchrony adaptation on the perception of a wide range of sub-second temporal relationships. We find distinctive patterns of induced biases that are inconsistent with the previous explanations based on changes in perceptual latency. Instead, our results can be well accounted for by a neural population coding model in which: (i) relative audio-visual timing is represented by the distributed activity across a relatively small number of neurons tuned to different delays; (ii) the algorithm for reading out this population code is efficient, but subject to biases owing to under-sampling; and (iii) the effect of adaptation is to modify neuronal response gain. These results suggest that multisensory timing information is represented by a dedicated population code and that shifts in perceived simultaneity following asynchrony adaptation arise from analogous neural processes to well-known perceptual after-effects.

  19. Adaptation to real motion reveals direction-selective interactions between real and implied motion processing.

    Science.gov (United States)

    Lorteije, Jeannette A M; Kenemans, J Leon; Jellema, Tjeerd; van der Lubbe, Rob H J; Lommers, Marjolein W; van Wezel, Richard J A

    2007-08-01

    Viewing static pictures of running humans evokes neural activity in the dorsal motion-sensitive cortex. To establish whether this response arises from direction-selective neurons that are also involved in real motion processing, we measured the visually evoked potential to implied motion following adaptation to static or moving random dot patterns. The implied motion response was defined as the difference between evoked potentials to pictures with and without implied motion. Interaction between real and implied motion was found as a modulation of this difference response by the preceding motion adaptation. The amplitude of the implied motion response was significantly reduced after adaptation to motion in the same direction as the implied motion, compared to motion in the opposite direction. At 280 msec after stimulus onset, the average difference in amplitude reduction between opposite and same adapted direction was 0.5 muV on an average implied motion amplitude of 2.0 muV. These results indicate that the response to implied motion arises from direction-selective motion-sensitive neurons. This is consistent with interactions between real and implied motion processing at a neuronal level.

  20. Starvation stress during larval development reveals predictive adaptive response in adult worker honey bees (Apis mellifera)

    Science.gov (United States)

    A variety of organisms exhibit developmental plasticity that results in differences in adult morphology, physiology or behavior. This variation in the phenotype, called “Predictive Adaptive Response (PAR),” gives a selective advantage in an adult's environment if the adult experiences environments s...

  1. Comparative population genomics of Fusarium graminearum reveals adaptive divergence among cereal head blight pathogens

    Science.gov (United States)

    In this study we sequenced the genomes of 60 Fusarium graminearum, the major fungal pathogen responsible for Fusarium head blight (FHB) in cereal crops world-wide. To investigate adaptive evolution of FHB pathogens, we performed population-level analyses to characterize genomic structure, signatures...

  2. Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis.

    Directory of Open Access Journals (Sweden)

    Le Wang

    Full Text Available The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.

  3. Complex adaptive responses during antagonistic coevolution between Tribolium castaneum and its natural parasite Nosema whitei revealed by multiple fitness components

    Directory of Open Access Journals (Sweden)

    Bérénos Camillo

    2012-01-01

    Full Text Available Abstract Background Host-parasite coevolution can lead to local adaptation of either parasite or host if there is specificity (GxG interactions and asymmetric evolutionary potential between host and parasite. This has been demonstrated both experimentally and in field studies, but a substantial proportion of studies fail to detect such clear-cut patterns. One explanation for this is that adaptation can be masked by counter-adaptation by the antagonist. Additionally, genetic architecture underlying the interaction is often highly complex thus preventing specific adaptive responses. Here, we have employed a reciprocal cross-infection experiment to unravel the adaptive responses of two components of fitness affecting both parties with different complexities of the underlying genetic architecture (i.e. mortality and spore load. Furthermore, our experimental coevolution of hosts (Tribolium castaneum and parasites (Nosema whitei included paired replicates of naive hosts from identical genetic backgrounds to allow separation between host- and parasite-specific responses. Results In hosts, coevolution led to higher resistance and altered resistance profiles compared to paired control lines. Host genotype × parasite genotype interactions (GH × GP were observed for spore load (the trait of lower genetic complexity, but not for mortality. Overall parasite performance correlated with resistance of its matching host coevolution background reflecting a directional and unspecific response to strength of selection during coevolution. Despite high selective pressures exerted by the obligatory killing parasite, and host- and parasite-specific mortality profiles, no general pattern of local adaptation was observed, but one case of parasite maladaptation was consistently observed on both coevolved and control host populations. In addition, the use of replicate control host populations in the assay revealed one case of host maladaptation and one case of parasite

  4. Physiologically informed dynamic causal modeling of fMRI data.

    Science.gov (United States)

    Havlicek, Martin; Roebroeck, Alard; Friston, Karl; Gardumi, Anna; Ivanov, Dimo; Uludag, Kamil

    2015-11-15

    The functional MRI (fMRI) signal is an indirect measure of neuronal activity. In order to deconvolve the neuronal activity from the experimental fMRI data, biophysical generative models have been proposed describing the link between neuronal activity and the cerebral blood flow (the neurovascular coupling), and further the hemodynamic response and the BOLD signal equation. These generative models have been employed both for single brain area deconvolution and to infer effective connectivity in networks of multiple brain areas. In the current paper, we introduce a new fMRI model inspired by experimental observations about the physiological underpinnings of the BOLD signal and compare it with the generative models currently used in dynamic causal modeling (DCM), a widely used framework to study effective connectivity in the brain. We consider three fundamental aspects of such generative models for fMRI: (i) an adaptive two-state neuronal model that accounts for a wide repertoire of neuronal responses during and after stimulation; (ii) feedforward neurovascular coupling that links neuronal activity to blood flow; and (iii) a balloon model that can account for vascular uncoupling between the blood flow and the blood volume. Finally, we adjust the parameterization of the BOLD signal equation for different magnetic field strengths. This paper focuses on the form, motivation and phenomenology of DCMs for fMRI and the characteristics of the various models are demonstrated using simulations. These simulations emphasize a more accurate modeling of the transient BOLD responses - such as adaptive decreases to sustained inputs during stimulation and the post-stimulus undershoot. In addition, we demonstrate using experimental data that it is necessary to take into account both neuronal and vascular transients to accurately model the signal dynamics of fMRI data. By refining the models of the transient responses, we provide a more informed perspective on the underlying neuronal

  5. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.

    Science.gov (United States)

    Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

    2012-10-01

    The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects.

  6. Preparatory EMG activity reveals a rapid adaptation pattern in humans performing landing movements in blindfolded condition.

    Science.gov (United States)

    Magalhães, Fernando Henrique; Goroso, Daniel Gustavo

    2009-10-01

    The main questions addressed in this work were whether and how adaptation to suppression of visual information occurs in a free-fall paradigm, and the extent to which vision availability influences the control of landing movements. The prelanding modulation of EMG timing and amplitude of four lower-limb muscles was investigated. Participants performed six consecutive drop-landings from four different heights in two experimental conditions: with and without vision. Experimental design precluded participants from estimating the height of the drop. Since cues provided by proprioceptive and vestibular information acquired during the first trials were processed, the nervous system rapidly adapted to the lack of visual information, and hence produced a motor output (i.e., prelanding EMG modulation) similar to that observed when performing the activity with vision available.

  7. Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus.

    Science.gov (United States)

    Altwasser, Robert; Baldin, Clara; Weber, Jakob; Guthke, Reinhard; Kniemeyer, Olaf; Brakhage, Axel A; Linde, Jörg; Valiante, Vito

    2015-01-01

    Mitogen activated protein kinases (MAPKs) are highly conserved in eukaryotic organisms. In pathogenic fungi, their activities were assigned to different physiological functions including drug adaptation and resistance. Aspergillus fumigatus is a human pathogenic fungus, which causes life-threatening invasive infections. Therapeutic options against invasive mycoses are still limited. One of the clinically used drugs is caspofungin, which specifically targets the fungal cell wall biosynthesis. A systems biology approach, based on comprehensive transcriptome data sets and mathematical modeling, was employed to infer a regulatory network and identify key interactions during adaptation to caspofungin stress in A. fumigatus. Mathematical modeling and experimental validations confirmed an intimate cross talk occurring between the cell wall-integrity and the high osmolarity-glycerol signaling pathways. Specifically, increased concentrations of caspofungin promoted activation of these signalings. Moreover, caspofungin affected the intracellular transport, which caused an additional osmotic stress that is independent of glucan inhibition. High concentrations of caspofungin reduced this osmotic stress, and thus decreased its toxic activity. Our results demonstrated that MAPK signaling pathways play a key role during caspofungin adaptation and are contributing to the paradoxical effect exerted by this drug.

  8. Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature

    Science.gov (United States)

    Kong, Hoi-Kuan; Law, Hon-Wai; Liu, Xuan; Law, Carmen O. K.; Pan, Qing; Gao, Lin; Xiong, Lifeng; Lau, Susanna K. P.; Woo, Patrick C. Y.; Lau, Terrence chi kong

    2017-01-01

    Bacterial adaptation to different hosts requires transcriptomic alteration in response to the environmental conditions. Laribacter hongkongensis is a gram-negative, facultative anaerobic, urease-positive bacillus caused infections in liver cirrhosis patients and community-acquired gastroenteritis. It was also found in intestine from commonly consumed freshwater fishes and drinking water reservoirs. Since L. hongkongensis could survive as either fish or human pathogens, their survival mechanisms in two different habitats should be temperature-regulated and highly complex. Therefore, we performed transcriptomic analysis of L. hongkongensis at body temperatures of fish and human in order to elucidate the versatile adaptation mechanisms coupled with the temperatures. We identified numerous novel temperature-induced pathways involved in host pathogenesis, in addition to the shift of metabolic equilibriums and overexpression of stress-related proteins. Moreover, these pathways form a network that can be activated at a particular temperature, and change the physiology of the bacteria to adapt to the environments. In summary, the dynamic of transcriptomes in L. hongkongensis provides versatile strategies for the bacterial survival at different habitats and this alteration prepares the bacterium for the challenge of host immunity. PMID:28085929

  9. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

    Directory of Open Access Journals (Sweden)

    James B Pease

    2016-02-01

    Full Text Available Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon, we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

  10. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

    Science.gov (United States)

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

  11. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.

    Science.gov (United States)

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.

  12. Functional magnetic resonance adaptation reveals the involvement of the dorsomedial stream in hand orientation for grasping.

    Science.gov (United States)

    Monaco, Simona; Cavina-Pratesi, Cristiana; Sedda, Anna; Fattori, Patrizia; Galletti, Claudio; Culham, Jody C

    2011-11-01

    Reach-to-grasp actions require coordination of different segments of the upper limbs. Previous studies have examined the neural substrates of arm transport and hand grip components of such actions; however, a third component has been largely neglected: the orientation of the wrist and hand appropriately for the object. Here we used functional magnetic resonance imaging adaptation (fMRA) to investigate human brain areas involved in processing hand orientation during grasping movements. Participants used the dominant right hand to grasp a rod with the four fingers opposing the thumb or to reach and touch the rod with the knuckles without visual feedback. In a control condition, participants passively viewed the rod. Trials in a slow event-related design consisted of two sequential stimuli in which the rod orientation changed (requiring a change in wrist posture while grasping but not reaching or looking) or remained the same. We found reduced activation, that is, adaptation, in superior parieto-occipital cortex (SPOC) when the object was repeatedly grasped with the same orientation. In contrast, there was no adaptation when reaching or looking at an object in the same orientation, suggesting that hand orientation, rather than object orientation, was the critical factor. These results agree with recent neurophysiological research showing that a parieto-occipital area of macaque (V6A) is modulated by hand orientation during reach-to-grasp movements. We suggest that the human dorsomedial stream, like that in the macaque, plays a key role in processing hand orientation in reach-to-grasp movements.

  13. Contrast discrimination at high contrasts reveals the influence of local light adaptation on contrast processing.

    Science.gov (United States)

    Kingdom, F A; Whittle, P

    1996-03-01

    Previous measurements of contrast discrimination threshold, delta C, as a function of pedestal contrast, C, for sine-wave gratings have shown a power law relationship between delta C and C at suprathreshold levels of C. However, these studies have rarely used contrasts greater than 50%. Whittle (1986), using incremental and decremental patches, found that delta C increased with C only up to about 50%. At higher contrasts it decreased. Since a periodic stimulus can be considered to be composed of increments and decrements, we thought we might find such an inverse U-shaped function for gratings if we used contrasts up to 100%. We tested this for both sine-wave and square-wave stimuli at spatial frequencies from 0.0625 to 8.0 c/deg. We found that for frequencies up to 0.5 c/deg, delta C in nearly all cases 'dipped down' after about C = 50% contrast. At 4.0 and 8.0 c/deg, however, no dip-down occurred. Additional experiments showed that the dip-down was unlikely to be due to cortical long-term adaptation and most likely an effect of localized light adaptation to the dark bars. We argue that the absence of dip-down at high spatial frequencies was mainly due to the attenuation of contrast by the optics of the eye. As for the results of Whittle (1986), a Weber's Law in W = (Lmax-Lmin)/Lmin describes the inverse U-shaped contrast discrimination function well. Two other contrast expressions also linearize the data on log-log plots. We show how some familiar notions about the physiological operation of localized light adaptation can easily account for the form of the contrast discrimination function. Finally we estimate the number of discriminable steps in contrast from detection threshold to maximum contrast for the various spatial frequencies tested.

  14. Molecular characterization of insulin from squamate reptiles reveals sequence diversity and possible adaptive evolution.

    Science.gov (United States)

    Yamagishi, Genki; Yoshida, Ayaka; Kobayashi, Aya; Park, Min Kyun

    2016-01-01

    The Squamata are the most adaptive and prosperous group among ectothermic amniotes, reptiles, due to their species-richness and geographically wide habitat. Although the molecular mechanisms underlying their prosperity remain largely unknown, unique features have been reported from hormones that regulate energy metabolism. Insulin, a central anabolic hormone, is one such hormone, as its roles and effectiveness in regulation of blood glucose levels remain to be examined in squamates. In the present study, cDNAs coding for insulin were isolated from multiple species that represent various groups of squamates. The deduced amino acid sequences showed a high degree of divergence, with four lineages showing obviously higher number of amino acid substitutions than most of vertebrates, from teleosts to mammals. Among 18 sites presented to comprise the two receptor binding surfaces (one with 12 sites and the other with 6 sites), substitutions were observed in 13 sites. Among them was the substitution of HisB10, which results in the loss of the ability to hexamerize. Furthermore, three of these substitutions were reported to increase mitogenicity in human analogues. These substitutions were also reported from insulin of hystricomorph rodents and agnathan fishes, whose mitogenic potency have been shown to be increased. The estimated value of the non-synonymous-to-synonymous substitution ratio (ω) for the Squamata clade was larger than those of the other reptiles and aves. Even higher values were estimated for several lineages among squamates. These results, together with the regulatory mechanisms of digestion and nutrient assimilation in squamates, suggested a possible adaptive process through the molecular evolution of squamate INS. Further studies on the roles of insulin, in relation to the physiological and ecological traits of squamate species, will provide an insight into the molecular mechanisms that have led to the adaptivity and prosperity of squamates.

  15. The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal

    OpenAIRE

    Seim, Inge; Ma, Siming; Zhou, Xuming; Gerashchenko, Maxim V.; Lee, Sang-Goo; Suydam, Robert; George, John C.; Bickham, John W.; Gladyshev, Vadim N.

    2014-01-01

    Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its t...

  16. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

    Science.gov (United States)

    Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

    2012-01-01

    The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects. PMID:22726122

  17. Transcriptomic analysis reveals adaptive responses of an Enterobacteriaceae strain LSJC7 to arsenic exposure

    Directory of Open Access Journals (Sweden)

    Yingjiao eZhang

    2016-05-01

    Full Text Available Arsenic (As resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V uptake were down-regulated, those involved in As(V reduction and As(III efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO were induced, which caused cellular damages including DNA, proteins, and Fe-S clusters damages in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V stressed LSJC7 cells, including reactive species scavenging and repairing the damages of DNA, proteins, and Fe-S clusters. Therefore, besides As uptake, reduction, and efflux, oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V stress.

  18. Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure.

    Science.gov (United States)

    Zhang, Yingjiao; Chen, Songcan; Hao, Xiuli; Su, Jian-Qiang; Xue, Ximei; Yan, Yu; Zhu, Yong-Guan; Ye, Jun

    2016-01-01

    Arsenic (As) resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V) resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V) stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V) stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V) uptake were down-regulated, those involved in As(V) reduction and As(III) efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO) were induced, which caused cellular damages including DNA, protein, and Fe-S cluster damage in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V) stressed LSJC7 cells, including reactive species scavenging and repairing damaged DNA, proteins, and Fe-S clusters. Therefore, besides As uptake, reduction, and efflux; oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V) stress.

  19. Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

    Directory of Open Access Journals (Sweden)

    Carolina M. Voloch

    2014-11-01

    Full Text Available Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G, RNA-dependent RNA polymerase (L and polymerase (P genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

  20. Fortune Favours the Bold: An Agent-Based Model Reveals Adaptive Advantages of Overconfidence in War

    Science.gov (United States)

    Johnson, Dominic D. P.; Weidmann, Nils B.; Cederman, Lars-Erik

    2011-01-01

    Overconfidence has long been considered a cause of war. Like other decision-making biases, overconfidence seems detrimental because it increases the frequency and costs of fighting. However, evolutionary biologists have proposed that overconfidence may also confer adaptive advantages: increasing ambition, resolve, persistence, bluffing opponents, and winning net payoffs from risky opportunities despite occasional failures. We report the results of an agent-based model of inter-state conflict, which allows us to evaluate the performance of different strategies in competition with each other. Counter-intuitively, we find that overconfident states predominate in the population at the expense of unbiased or underconfident states. Overconfident states win because: (1) they are more likely to accumulate resources from frequent attempts at conquest; (2) they are more likely to gang up on weak states, forcing victims to split their defences; and (3) when the decision threshold for attacking requires an overwhelming asymmetry of power, unbiased and underconfident states shirk many conflicts they are actually likely to win. These “adaptive advantages” of overconfidence may, via selection effects, learning, or evolved psychology, have spread and become entrenched among modern states, organizations and decision-makers. This would help to explain the frequent association of overconfidence and war, even if it no longer brings benefits today. PMID:21731627

  1. Multi-omic profiling of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    2015-01-01

    the existence of production bottlenecks in energy metabolism (i.e., glycolytic metabolites, NAD(P)H/NAD(P)+ and ANPs) in batch culture or in the secretory protein production pathway (i.e., gene dosage, transcription and post-translational processing of EPO) in chemostat culture at specific productivities up...... to 5 pg/cell/day. Time-course analysis of high- and low-producing clones in chemostat culture revealed rapid adaptation of transcription levels of amino acid catabolic genes in favor of EPO production within nine generations. Interestingly, the adaptation was followed by an increase in specific EPO......Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied...

  2. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

    NARCIS (Netherlands)

    Olsen, Jeanine; Rouzé, Pierre; Verhelst, Bram; Lin, Yao-Cheng; Bayer, Till; Collen, Jonas; Dattolo, Emanuela; De Paoli, Emanuele; Dittami, Simon; Maumus, Florian; Michel, Gurvan; Kersting, Anna; Lauritano, Chiara; Lohaus, Rolf; Töpel, Mats; Tonon, Thierry; Vanneste, Kevin; Amirebrahimi, Mojgan; Brakel, Janina; Boström, Christoffer; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry W; Jueterbock, Alexander; Mraz, Amy; Stam, Wytze T; Tice, Hope; Bornberg-Bauer, Erich; Green, Pamela J; Pearson, Gareth A; Procaccini, Gabriele; Duarte, Carlos M; Schmutz, Jeremy; Reusch, Thorsten B H; Van de Peer, Yves

    2016-01-01

    Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals u

  3. Comparative transcriptomic analysis of roots of contrasting Gossypium herbaceum genotypes revealing adaptation to drought

    Directory of Open Access Journals (Sweden)

    Ranjan Alok

    2012-11-01

    Full Text Available Abstract Background Root length and its architecture govern the adaptability of plants to various stress conditions, including drought stress. Genetic variations in root growth, length, and architecture are genotypes dependent. In this study, we compared the drought-induced transcriptome of four genotypes of Gossypium herbaceum that differed in their drought tolerance adaptability. Three different methodologies, namely, microarray, pyrosequencing, and qRT–PCR, were used for transcriptome analysis and validation. Results The variations in root length and growth were found among four genotypes of G.herbaceum when exposed to mannitol-induced osmotic stress. Under osmotic stress, the drought tolerant genotypes Vagad and GujCot-21 showed a longer root length than did by drought sensitive RAHS-14 and RAHS-IPS-187. Further, the gene expression patterns in the root tissue of all genotypes were analyzed. We obtained a total of 794 differentially expressed genes by microarray and 104928 high-quality reads representing 53195 unigenes from the root transcriptome. The Vagad and GujCot-21 respond to water stress by inducing various genes and pathways such as response to stresses, response to water deprivation, and flavonoid pathways. Some key regulatory genes involved in abiotic stress such as AP2 EREBP, MYB, WRKY, ERF, ERD9, and LEA were highly expressed in Vagad and GujCot-21. The genes RHD3, NAP1, LBD, and transcription factor WRKY75, known for root development under various stress conditions, were expressed specifically in Vagad and GujCot-21. The genes related to peroxidases, transporters, cell wall-modifying enzymes, and compatible solutes (amino acids, amino sugars, betaine, sugars, or sugar alcohols were also highly expressed in Vagad and Gujcot-21. Conclusion Our analysis highlights changes in the expression pattern of genes and depicts a small but highly specific set of drought responsive genes induced in response to drought stress. Some of these

  4. Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.

    Directory of Open Access Journals (Sweden)

    Minjun Yang

    Full Text Available Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC. Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

  5. Learning theories reveal loss of pancreatic electrical connectivity in diabetes as an adaptive response

    CERN Document Server

    Goel, Pranay

    2013-01-01

    Cells of almost all solid tissues are connected with gap junctions which permit the direct transfer of ions and small molecules, integral to regulating coordinated function in the tissue. The pancreatic islets of Langerhans are responsible for secreting the hormone insulin in response to glucose stimulation. Gap junctions are the only electrical contacts between the beta-cells in the tissue of these excitable islets. It is generally believed that they are responsible for synchrony of the membrane voltage oscillations among beta-cells, and thereby pulsatility of insulin secretion. Most attempts to understand connectivity in islets are often interpreted, bottom-up, in terms of measurements of gap junctional conductance. This does not, however explain systematic changes, such as a diminished junctional conductance in type 2 diabetes. We attempt to address this deficit via the model presented here, which is a learning theory of gap junctional adaptation derived with analogy to neural systems. Here, gap junctions ...

  6. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic

    Directory of Open Access Journals (Sweden)

    Vincent J. Lynch

    2015-07-01

    Full Text Available Woolly mammoths and living elephants are characterized by major phenotypic differences that have allowed them to live in very different environments. To identify the genetic changes that underlie the suite of woolly mammoth adaptations to extreme cold, we sequenced the nuclear genome from three Asian elephants and two woolly mammoths, and we identified and functionally annotated genetic changes unique to woolly mammoths. We found that genes with mammoth-specific amino acid changes are enriched in functions related to circadian biology, skin and hair development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. Finally, we resurrected and functionally tested the mammoth and ancestral elephant TRPV3 gene, which encodes a temperature-sensitive transient receptor potential (thermoTRP channel involved in thermal sensation and hair growth, and we show that a single mammoth-specific amino acid substitution in an otherwise highly conserved region of the TRPV3 channel strongly affects its temperature sensitivity.

  7. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts

    KAUST Repository

    Otto, Thomas D.

    2014-09-09

    Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis of P. falciparum adaptation to human hosts by fully sequencing the genome of the closely related chimpanzee parasite species P. reichenowi, and obtaining partial sequence data from a more distantly related chimpanzee parasite (P. gaboni). The close relationship between P. reichenowi and P. falciparum is emphasized by almost complete conservation of genomic synteny, but against this strikingly conserved background we observe major differences at loci involved in erythrocyte invasion. The organization of most virulence-associated multigene families, including the hypervariable var genes, is broadly conserved, but P. falciparum has a smaller subset of rif and stevor genes whose products are expressed on the infected erythrocyte surface. Genome-wide analysis identifies other loci under recent positive selection, but a limited number of changes at the host–parasite interface may have mediated host switching.

  8. Adjustments with running speed reveal neuromuscular adaptations during landing associated with high mileage running training.

    Science.gov (United States)

    Verheul, Jasper; Clansey, Adam C; Lake, Mark J

    2016-12-08

    It remains to be determined whether running training influences the amplitude of lower limb muscle activations prior to and during the first half of stance, and whether such changes are associated with joint stiffness regulation and usage of stored energy from tendons. Therefore, the aim of this study was to investigate neuromuscular and movement adaptations before and during landing in response to running training across a range of speeds. Two groups of high mileage (HM; >45 km/wk, n=13) and low mileage (LM; muscular activations before landing. Estimated elastic work about the ankle was found to be higher in the HM runners which might play a role in reducing weight acceptance phase muscle activation levels and improve muscle activation efficiency with running training.

  9. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

    Science.gov (United States)

    Otto, Thomas D; Rayner, Julian C; Böhme, Ulrike; Pain, Arnab; Spottiswoode, Natasha; Sanders, Mandy; Quail, Michael; Ollomo, Benjamin; Renaud, François; Thomas, Alan W; Prugnolle, Franck; Conway, David J; Newbold, Chris; Berriman, Matthew

    2014-09-09

    Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis of P. falciparum adaptation to human hosts by fully sequencing the genome of the closely related chimpanzee parasite species P. reichenowi, and obtaining partial sequence data from a more distantly related chimpanzee parasite (P. gaboni). The close relationship between P. reichenowi and P. falciparum is emphasized by almost complete conservation of genomic synteny, but against this strikingly conserved background we observe major differences at loci involved in erythrocyte invasion. The organization of most virulence-associated multigene families, including the hypervariable var genes, is broadly conserved, but P. falciparum has a smaller subset of rif and stevor genes whose products are expressed on the infected erythrocyte surface. Genome-wide analysis identifies other loci under recent positive selection, but a limited number of changes at the host-parasite interface may have mediated host switching.

  10. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    DEFF Research Database (Denmark)

    Thøgersen, Juliane Charlotte; Mørup, Morten; Pedersen, Søren Damkiær;

    2013-01-01

    BACKGROUND: Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data.The aim of this study...... is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas...... expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates...

  11. Adaptive adjustment of connectivity in the inferior colliculus revealed by focal pharmacological inactivation.

    Science.gov (United States)

    Gold, J I; Knudsen, E I

    2001-04-01

    In the midbrain sound localization pathway of the barn owl, a map of auditory space is synthesized in the external nucleus of the inferior colliculus (ICX) and transmitted to the optic tectum. Early auditory experience shapes these maps of auditory space in part by modifying the tuning of the constituent neurons for interaural time difference (ITD), a primary cue for sound-source azimuth. Here we show that these adaptive modifications in ITD tuning correspond to changes in the pattern of connectivity within the inferior colliculus. We raised owls with an acoustic filtering device in one ear that caused frequency-dependent changes in sound timing and level. As reported previously, device rearing shifted the representation of ITD in the ICX and tectum but not in the primary source of input to the ICX, the central nucleus of the inferior colliculus (ICC). We applied the local anesthetic lidocaine (QX-314) iontophoretically in the ICC to inactivate small populations of neurons that represented particular values of frequency and ITD. We measured the effect of this inactivation in the optic tecta of a normal owl and owls raised with the device. In the normal owl, inactivation at a critical site in the ICC eliminated responses in the tectum to the frequency-specific ITD value represented at the site of inactivation in the ICC. The location of this site was consistent with the known pattern of ICC-ICX-tectum connectivity. In the device-reared owls, adaptive changes in the representation of ITD in the tectum corresponded to dramatic and predictable changes in the locations of the critical sites of inactivation in the ICC. Given that the abnormal representation of ITD in the tectum depended on frequency and was likely conveyed directly from the ICX, these results suggest that experience causes large-scale, frequency-specific adjustments in the pattern of connectivity between the ICC and the ICX.

  12. Within-host evolution of Pseudomonas aeruginosa reveals adaptation toward iron acquisition from hemoglobin

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Pedersen, Søren Damkiær; Khademi, Seyed Mohammad Hossein

    2014-01-01

    Pseudomonas aeruginosa airway infections are a major cause of mortality and morbidity of cystic fibrosis (CF) patients. In order to persist, P. aeruginosa depends on acquiring iron from its host, and multiple different iron acquisition systems may be active during infection. This includes the pyo...... iron-scavenging mechanisms and/or an increase in the availability of hemoglobin at the site of infection. This information is relevant to the design of novel CF therapeutics and the development of models of chronic CF infections.......Pseudomonas aeruginosa airway infections are a major cause of mortality and morbidity of cystic fibrosis (CF) patients. In order to persist, P. aeruginosa depends on acquiring iron from its host, and multiple different iron acquisition systems may be active during infection. This includes...... the pyoverdine siderophore and the Pseudomonas heme utilization (phu) system. While the regulation and mechanisms of several iron-scavenging systems are well described, it is not clear whether such systems are targets for selection during adaptation of P. aeruginosa to the host environment. Here we investigated...

  13. The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

    Science.gov (United States)

    Axelsson, Erik; Ratnakumar, Abhirami; Arendt, Maja-Louise; Maqbool, Khurram; Webster, Matthew T; Perloski, Michele; Liberg, Olof; Arnemo, Jon M; Hedhammar, Ake; Lindblad-Toh, Kerstin

    2013-03-21

    The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.

  14. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.

    Science.gov (United States)

    Davies, Kalina T J; Bennett, Nigel C; Tsagkogeorga, Georgia; Rossiter, Stephen J; Faulkes, Christopher G

    2015-12-01

    During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein-protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group.

  15. Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum.

    Science.gov (United States)

    Subramanian, Abhishek; Sarkar, Ram Rup

    2017-08-31

    Human macrophage phagolysosome and sandfly midgut provide antagonistic ecological niches for Leishmania parasites to survive and proliferate. Parasites optimize their metabolism to utilize the available inadequate resources by adapting to those environments. Lately, a number of metabolomics studies have revived the interest to understand metabolic strategies utilized by the Leishmania parasite for optimal survival within its hosts. For the first time, we propose a reconstructed genome-scale metabolic model for Leishmania infantum JPCM5, the analyses of which not only captures observations reported by metabolomics studies in other Leishmania species but also divulges novel features of the L. infantum metabolome. Our results indicate that Leishmania metabolism is organized in such a way that the parasite can select appropriate alternatives to compensate for limited external substrates. A dynamic non-essential amino acid motif exists within the network that promotes a restricted redistribution of resources to yield required essential metabolites. Further, subcellular compartments regulate this metabolic re-routing by reinforcing the physiological coupling of specific reactions. This unique metabolic organization is robust against accidental errors and provides a wide array of choices for the parasite to achieve optimal survival.

  16. Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification

    KAUST Repository

    Dineshram, R.

    2015-10-28

    © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Decreasing pH due to anthropogenic CO2 inputs, called ocean acidification (OA), can make coastal environments unfavorable for oysters. This is a serious socioeconomical issue for China which supplies >70% of the world\\'s edible oysters. Here, we present an iTRAQ-based protein profiling approach for the detection and quantification of proteome changes under OA in the early life stage of a commercially important oyster, Crassostrea hongkongensis. Availability of complete genome sequence for the pacific oyster (Crassostrea gigas) enabled us to confidently quantify over 1500 proteins in larval oysters. Over 7% of the proteome was altered in response to OA at pHNBS 7.6. Analysis of differentially expressed proteins and their associated functional pathways showed an upregulation of proteins involved in calcification, metabolic processes, and oxidative stress, each of which may be important in physiological adaptation of this species to OA. The downregulation of cytoskeletal and signal transduction proteins, on the other hand, might have impaired cellular dynamics and organelle development under OA. However, there were no significant detrimental effects in developmental processes such as metamorphic success. Implications of the differentially expressed proteins and metabolic pathways in the development of OA resistance in oyster larvae are discussed. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD002138 (http://proteomecentral.proteomexchange.org/dataset/PXD002138).

  17. Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles.

    Science.gov (United States)

    Mu, Dashuai; Yu, Xiuxia; Xu, Zhenxing; Du, Zongjun; Chen, Guanjun

    2016-07-21

    An increasing number of studies have investigated the effects of nanoparticles (NPs) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against NPs. Whether secondary metabolism biosynthesis is a response to NP stress and contributes to the adaption of bacteria to NPs is unclear. Here, a significant induction in the surfactin production and biofilm formation were detected by adding Al2O3 NPs to the B. subtilis fermentation broth. Physiological analysis showed that Al2O3 NP stress could also affect the cell and colony morphogenesis and inhibit the motility and sporulation. Exogenously adding commercial surfactin restored the swarming motility. Additionally, a suite of toxicity assays analyzing membrane damage, cellular ROS generation, electron transport activity and membrane potential was used to determine the molecular mechanisms of toxicity of Al2O3 NPs. Furthermore, whole transcriptomic analysis was used to elucidate the mechanisms of B. subtilis adaption to Al2O3 NPs. These results revealed several mechanisms by which marine B. subtilis C01 adapt to Al2O3 NPs. Additionally, this study broadens the applications of nanomaterials and describes the important effects on secondary metabolism and multicellularity regulation by using Al2O3 NPs or other nano-products.

  18. Comparative system identification of flower tracking performance in three hawkmoth species reveals adaptations for dim light vision.

    Science.gov (United States)

    Stöckl, Anna L; Kihlström, Klara; Chandler, Steven; Sponberg, Simon

    2017-04-05

    Flight control in insects is heavily dependent on vision. Thus, in dim light, the decreased reliability of visual signal detection also prompts consequences for insect flight. We have an emerging understanding of the neural mechanisms that different species employ to adapt the visual system to low light. However, much less explored are comparative analyses of how low light affects the flight behaviour of insect species, and the corresponding links between physiological adaptations and behaviour. We investigated whether the flower tracking behaviour of three hawkmoth species with different diel activity patterns revealed luminance-dependent adaptations, using a system identification approach. We found clear luminance-dependent differences in flower tracking in all three species, which were explained by a simple luminance-dependent delay model, which generalized across species. We discuss physiological and anatomical explanations for the variance in tracking responses, which could not be explained by such simple models. Differences between species could not be explained by the simple delay model. However, in several cases, they could be explained through the addition on a second model parameter, a simple scaling term, that captures the responsiveness of each species to flower movements. Thus, we demonstrate here that much of the variance in the luminance-dependent flower tracking responses of hawkmoths with different diel activity patterns can be captured by simple models of neural processing.This article is part of the themed issue 'Vision in dim light'.

  19. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

    Directory of Open Access Journals (Sweden)

    Patrick C Y Woo

    2009-03-01

    Full Text Available Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature and 20 degrees C (freshwater habitat temperature showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be

  20. The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood.

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    Heidi C Vebø

    Full Text Available BACKGROUND: Enterococcus faecalis plays a dual role in human ecology, predominantly existing as a commensal in the alimentary canal, but also as an opportunistic pathogen that frequently causes nosocomial infections like bacteremia. A number of virulence factors that contribute to the pathogenic potential of E. faecalis have been established. However, the process in which E. faecalis gains access to the bloodstream and establishes a persistent infection is not well understood. METHODOLOGY/PRINCIPAL FINDINGS: To enhance our understanding of how this commensal bacterium adapts during a bloodstream infection and to examine the interplay between genes we designed an in vitro experiment using genome-wide microarrays to investigate what effects the presence of and growth in blood have on the transcriptome of E. faecalis strain V583. We showed that growth in both 2xYT supplemented with 10% blood and in 100% blood had a great impact on the transcription of many genes in the V583 genome. We identified several immediate changes signifying cellular processes that might contribute to adaptation and growth in blood. These include modulation of membrane fatty acid composition, oxidative and lytic stress protection, acquisition of new available substrates, transport functions including heme/iron transporters and genes associated with virulence in E. faecalis. CONCLUSIONS/SIGNIFICANCE: The results presented here reveal that cultivation of E. faecalis in blood in vitro has a profound impact on its transcriptome, which includes a number of virulence traits. Observed regulation of genes and pathways revealed new insight into physiological features and metabolic capacities which enable E. faecalis to adapt and grow in blood. A number of the regulated genes might potentially be useful candidates for development of new therapeutic approaches for treatment of E. faecalis infections.

  1. Perceptual suppression revealed by adaptive multi-scale entropy analysis of local field potential in monkey visual cortex.

    Science.gov (United States)

    Hu, Meng; Liang, Hualou

    2013-04-01

    Generalized flash suppression (GFS), in which a salient visual stimulus can be rendered invisible despite continuous retinal input, provides a rare opportunity to directly study the neural mechanism of visual perception. Previous work based on linear methods, such as spectral analysis, on local field potential (LFP) during GFS has shown that the LFP power at distinctive frequency bands are differentially modulated by perceptual suppression. Yet, the linear method alone may be insufficient for the full assessment of neural dynamic due to the fundamentally nonlinear nature of neural signals. In this study, we set forth to analyze the LFP data collected from multiple visual areas in V1, V2 and V4 of macaque monkeys while performing the GFS task using a nonlinear method - adaptive multi-scale entropy (AME) - to reveal the neural dynamic of perceptual suppression. In addition, we propose a new cross-entropy measure at multiple scales, namely adaptive multi-scale cross-entropy (AMCE), to assess the nonlinear functional connectivity between two cortical areas. We show that: (1) multi-scale entropy exhibits percept-related changes in all three areas, with higher entropy observed during perceptual suppression; (2) the magnitude of the perception-related entropy changes increases systematically over successive hierarchical stages (i.e. from lower areas V1 to V2, up to higher area V4); and (3) cross-entropy between any two cortical areas reveals higher degree of asynchrony or dissimilarity during perceptual suppression, indicating a decreased functional connectivity between cortical areas. These results, taken together, suggest that perceptual suppression is related to a reduced functional connectivity and increased uncertainty of neural responses, and the modulation of perceptual suppression is more effective at higher visual cortical areas. AME is demonstrated to be a useful technique in revealing the underlying dynamic of nonlinear/nonstationary neural signal.

  2. Bone Microstructure of the Stereospondyl Lydekkerina Huxleyi Reveals Adaptive Strategies to the Harsh Post Permian-Extinction Environment.

    Science.gov (United States)

    Canoville, Aurore; Chinsamy, Anusuya

    2015-07-01

    The small-bodied stereospondyl Lydekkerina huxleyi, dominated the amphibian fauna of the South African Lower Triassic. Even though the anatomy of this amphibian has been well described, its growth strategies and lifestyle habits have remained controversial. Previous studies attributed the relative uniformity in skull sizes to a predominance of subadult and adult specimens recovered in the fossil record. Anatomical and taphonomic data suggested that the relatively small body-size of this genus, as compared to its Permo-Triassic relatives, could be linked to a shortened, rapid developmental period as an adaptation to maintain successful breeding populations under harsh environmental conditions. Moreover, Lydekkerina's habitat has been hypothesized to be either aquatic or mainly terrestrial. The current study, utilizes bone microstructure to reassess previous hypotheses pertaining to the biology and ecology of Lydekkerina. Various skeletal elements of different-sized specimens are analyzed to understand its growth dynamics, intraskeletal variability, and lifestyle adaptations. Bone histology revealed that our sample comprises individuals at different ontogenetic stages i.e., juveniles to mature individuals. Our results show that these amphibians, despite exhibiting plasticity in growth, experienced an overall faster growth during early ontogeny (thereby attaining sexual maturity sooner), as compared to most other temnospondyls. The microanatomy of the long bones with their thick bone walls and distinctive medullary cavity suggests that Lydekkerina may have been amphibious with a tendency to be more terrestrial. Our study concludes that Lydekkerina employed a peculiar growth strategy and lifestyle adaptations, which enabled it to endure the harsh, dry conditions of the Early Triassic.

  3. Immunohistochemical characterization of the chemosensory pulmonary neuroepithelial bodies in the naked mole-rat reveals a unique adaptive phenotype.

    Directory of Open Access Journals (Sweden)

    Jie Pan

    Full Text Available The pulmonary neuroepithelial bodies (NEBs constitute polymodal airway chemosensors for monitoring and signaling ambient gas concentrations (pO2, pCO2/H+ via complex innervation to the brain stem controlling breathing. NEBs produce the bioactive amine, serotonin (5-HT, and a variety of peptides with multiple effects on lung physiology and other organ systems. NEBs in mammals appear prominent and numerous during fetal and neonatal periods, and decline in the post-natal period suggesting an important role during perinatal adaptation. The naked mole-rat (NMR, Heterocephalus glaber, has adapted to the extreme environmental conditions of living in subterranean burrows in large colonies (up to 300 colony mates. The crowded, unventilated burrows are environments of severe hypoxia and hypercapnia. However, NMRs adjust readily to above ground conditions. The chemosensory NEBs of this species were characterized and compared to those of the conventional Wistar rat (WR to identify similarities and differences that could explain the NMR's adaptability to environments. A multilabel immunohistochemical analysis combined with confocal microscopy revealed that the expression patterns of amine, peptide, neuroendocrine, innervation markers and chemosensor component proteins in NEBs of NMR were similar to that of WR. However, we found the following differences: 1 NEBs in both neonatal and adult NMR lungs were significantly larger and more numerous as compared to WR; 2 NEBs in NMR had a more variable compact cell organization and exhibited significant differences in the expression of adhesion proteins; 3 NMR NEBs showed a significantly greater ratio of 5-HT positive cells with an abundance of 5-HT; 4 NEBs in NMR expressed the proliferating cell nuclear antigen (PCNA and the neurogenic gene (MASH1 indicating active proliferation and a state of persistent differentiation. Taken together our findings suggest that NEBs in lungs of NMR are in a hyperactive, functional

  4. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

    Energy Technology Data Exchange (ETDEWEB)

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finely, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Sotrey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2012-02-07

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

  5. Comparative genomic analyses reveal a lack of a substantial signature of host adaptation in Rhodococcus equi ('Prescottella equi').

    Science.gov (United States)

    Sangal, Vartul; Jones, Amanda L; Goodfellow, Michael; Sutcliffe, Iain C; Hoskisson, Paul A

    2014-08-01

    Rhodococcus equi ('Prescottella equi') is a pathogenic actinomycete primarily infecting horses but has emerged as an opportunistic human pathogen. We have sequenced the genome of the type strain of this species, R. equi strain C7(T) , and compared the genome with that of another foal isolate 103S and of a human isolate ATCC 33707. The R. equi strains are closely related to each other and yet distantly related to other rhodococci and Nocardia brasiliensis. The comparison of gene contents among R. equi strains revealed minor differences that could be associated with host adaptation from foals to humans, including the presence of a paa operon in the human isolate, which is potentially involved in pathogenesis. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  6. Convolution power spectrum analysis for FMRI data based on prior image signal.

    Science.gov (United States)

    Zhang, Jiang; Chen, Huafu; Fang, Fang; Liao, Wei

    2010-02-01

    Functional MRI (fMRI) data-processing methods based on changes in the time domain involve, among other things, correlation analysis and use of the general linear model with statistical parametric mapping (SPM). Unlike conventional fMRI data analysis methods, which aim to model the blood-oxygen-level-dependent (BOLD) response of voxels as a function of time, the theory of power spectrum (PS) analysis focuses completely on understanding the dynamic energy change of interacting systems. We propose a new convolution PS (CPS) analysis of fMRI data, based on the theory of matched filtering, to detect brain functional activation for fMRI data. First, convolution signals are computed between the measured fMRI signals and the image signal of prior experimental pattern to suppress noise in the fMRI data. Then, the PS density analysis of the convolution signal is specified as the quantitative analysis energy index of BOLD signal change. The data from simulation studies and in vivo fMRI studies, including block-design experiments, reveal that the CPS method enables a more effective detection of some aspects of brain functional activation, as compared with the canonical PS SPM and the support vector machine methods. Our results demonstrate that the CPS method is useful as a complementary analysis in revealing brain functional information regarding the complex nature of fMRI time series.

  7. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

    Energy Technology Data Exchange (ETDEWEB)

    Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hilden, Kristiina; Kues, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wosten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis

    2012-04-27

    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

  8. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.

    Science.gov (United States)

    Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G; Ohm, Robin A; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L; Bailey, Andrew M; Billette, Christophe; Coutinho, Pedro M; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hildén, Kristiina; Kües, Ursula; Labutti, Kurt M; Lapidus, Alla; Lindquist, Erika A; Lucas, Susan M; Murat, Claude; Riley, Robert W; Salamov, Asaf A; Schmutz, Jeremy; Subramanian, Venkataramanan; Wösten, Han A B; Xu, Jianping; Eastwood, Daniel C; Foster, Gary D; Sonnenberg, Anton S M; Cullen, Dan; de Vries, Ronald P; Lundell, Taina; Hibbett, David S; Henrissat, Bernard; Burton, Kerry S; Kerrigan, Richard W; Challen, Michael P; Grigoriev, Igor V; Martin, Francis

    2012-10-23

    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

  9. Biomarker Analysis Revealed Distinct Profiles of Innate and Adaptive Immunity in Infants with Ocular Lesions of Congenital Toxoplasmosis

    Science.gov (United States)

    Machado, Anderson Silva; Carneiro, Ana Carolina Aguiar Vasconcelos; Béla, Samantha Ribeiro; Andrade, Gláucia Manzan Queiroz; Vasconcelos-Santos, Daniel Vitor; Januário, José Nélio; Coelho-dos-Reis, Jordana G.; Ferro, Eloisa Amália Vieira; Teixeira-Carvalho, Andréa; Vitor, Ricardo Wagner Almeida; Martins-Filho, Olindo Assis; —UFMG-CTBG, UFMG Congenital Toxoplasmosis Brazilian Group

    2014-01-01

    Toxoplasma gondii is the main infectious cause of human posterior retinochoroiditis, the most frequent clinical manifestation of congenital toxoplasmosis. This investigation was performed after neonatal screening to identify biomarkers of immunity associated with immunopathological features of the disease by flow cytometry. The study included infected infants without NRL and with retinochoroidal lesions (ARL, ACRL, and CRL) as well as noninfected individuals (NI). Our data demonstrated that leukocytosis, with increased monocytes and lymphocytes, was a relevant hematological biomarker of ARL. Immunophenotypic analysis also revealed expansion of CD14+CD16+HLA-DRhigh monocytes and CD56dim cytotoxic NK-cells in ARL. Moreover, augmented TCRγδ+ and CD8+ T-cell counts were apparently good biomarkers of morbidity. Biomarker network analysis revealed that complex and intricated networks underscored the negative correlation of monocytes with NK- and B-cells in NRL. The remarkable lack of connections involving B-cells and a relevant shift of NK-cell connections from B-cells toward T-cells observed in ARL were outstanding. A tightly connected biomarker network was observed in CRL, with relevant connections of NK- and CD8+ T-cells with a broad range of cell subsets. Our findings add novel elements to the current knowledge on the innate and adaptive immune responses in congenital toxoplasmosis. PMID:25328286

  10. Biomarker Analysis Revealed Distinct Profiles of Innate and Adaptive Immunity in Infants with Ocular Lesions of Congenital Toxoplasmosis

    Directory of Open Access Journals (Sweden)

    Anderson Silva Machado

    2014-01-01

    Full Text Available Toxoplasma gondii is the main infectious cause of human posterior retinochoroiditis, the most frequent clinical manifestation of congenital toxoplasmosis. This investigation was performed after neonatal screening to identify biomarkers of immunity associated with immunopathological features of the disease by flow cytometry. The study included infected infants without NRL and with retinochoroidal lesions (ARL, ACRL, and CRL as well as noninfected individuals (NI. Our data demonstrated that leukocytosis, with increased monocytes and lymphocytes, was a relevant hematological biomarker of ARL. Immunophenotypic analysis also revealed expansion of CD14+CD16+HLA-DRhigh monocytes and CD56dim cytotoxic NK-cells in ARL. Moreover, augmented TCRγδ+ and CD8+ T-cell counts were apparently good biomarkers of morbidity. Biomarker network analysis revealed that complex and intricated networks underscored the negative correlation of monocytes with NK- and B-cells in NRL. The remarkable lack of connections involving B-cells and a relevant shift of NK-cell connections from B-cells toward T-cells observed in ARL were outstanding. A tightly connected biomarker network was observed in CRL, with relevant connections of NK- and CD8+ T-cells with a broad range of cell subsets. Our findings add novel elements to the current knowledge on the innate and adaptive immune responses in congenital toxoplasmosis.

  11. Multi-omic profiling -of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production.

    Science.gov (United States)

    Ley, Daniel; Seresht, Ali Kazemi; Engmark, Mikael; Magdenoska, Olivera; Nielsen, Kristian Fog; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

    2015-11-01

    Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied to study the production of erythropoietin (EPO) in a panel of CHO-K1 cells under growth-limited and unlimited conditions in batch and chemostat cultures. Physiological characterization of the EPO-producing cells included global transcriptome analysis, targeted metabolome analysis, including intracellular pools of glycolytic intermediates, NAD(P)H/NAD(P)(+) , adenine nucleotide phosphates (ANP), and extracellular concentrations of sugars, organic acids, and amino acids. Potential impact of EPO expression on the protein secretory pathway was assessed at multiple stages using quantitative PCR (qPCR), reverse transcription PCR (qRT-PCR), Western blots (WB), and global gene expression analysis to assess EPO gene copy numbers, EPO gene expression, intracellular EPO retention, and differentially expressed genes functionally related to secretory protein processing, respectively. We found no evidence supporting the existence of production bottlenecks in energy metabolism (i.e., glycolytic metabolites, NAD(P)H/NAD(P)(+) and ANPs) in batch culture or in the secretory protein production pathway (i.e., gene dosage, transcription and post-translational processing of EPO) in chemostat culture at specific productivities up to 5 pg/cell/day. Time-course analysis of high- and low-producing clones in chemostat culture revealed rapid adaptation of transcription levels of amino acid catabolic genes in favor of EPO production within nine generations. Interestingly, the adaptation was followed by an increase in specific EPO productivity.

  12. Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue

    Institute of Scientific and Technical Information of China (English)

    LI Mei; ZHAO ChunJiang

    2009-01-01

    Oxygen concentration is essential for appropriate metabolism. Hypoxia can exert a significant impact on physiological alteration of the cell and organism. Tibetan Chicken (Gallus gallus) is a Chinese in-digenous breed inhabiting in Tibetan areas, which is also a chicken breed living at high altitude for the longest time in the world. It has developed an adaptive mechanism to hypoxia, which is demonstrated by that Tibetan Chicken has much higher hatchability than low-land chicken breeds in high-altitude areas of Tibet. In the present study, Tibetan Chicken fertilized full sib eggs were incubated up to Ham-burger-Hamilton stage 43 under 13% and 21% oxygen concentration, respectively. Shouguang Chicken and Dwarf Recessive White Chicken were used as control groups. The hearts in all of the 3 chicken breeds under hypoxic and normoxic conditions were isolated and hybridized to GeneChip Chicken Genome Array to study molecular mechanisms underlying the adaptation to high altitude of Tibetan Chicken. As a result, 50 transcripts highly expressed in hypoxia are screened out. Among up-regulated genes, some are involved in the gone ontology (GO) such as cell growth, cell difference, muscle con-traction and signal transduction. However, the expression levels of 21 transcripts are lower in hypoxia than those in normoxia. Some down-regulated genes take part in cell communication, ion transport, protein amino acid phosphorylation and signal transduction. Interestingly, gene enrichment analyses of these differential gone expressions are mainly associated with immune system response and ion channel activity in response to stimulus. Moreover, the transcriptional expression profiles analyzed by hierarchical clustering and CPP-SOM software in all of the 3 different chicken breeds revealed that TI-betan Chicken is much closely related to Shouguang Chicken rather than Dwarf Recessive White Chicken. In addition, 12 transcripts of Tibetan Chicken breed-specific expressed genes were

  13. Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Oxygen concentration is essential for appropriate metabolism.Hypoxia can exert a significant impact on physiological alteration of the cell and organism.Tibetan Chicken(Gallus gallus) is a Chinese indigenous breed inhabiting in Tibetan areas,which is also a chicken breed living at high altitude for the longest time in the world.It has developed an adaptive mechanism to hypoxia,which is demonstrated by that Tibetan Chicken has much higher hatchability than low-land chicken breeds in high-altitude areas of Tibet.In the present study,Tibetan Chicken fertilized full sib eggs were incubated up to Hamburger-Hamilton stage 43 under 13% and 21% oxygen concentration,respectively.Shouguang Chicken and Dwarf Recessive White Chicken were used as control groups.The hearts in all of the 3 chicken breeds under hypoxic and normoxic conditions were isolated and hybridized to Genechip Chicken Genome Array to study molecular mechanisms underlying the adaptation to high altitude of Tibetan Chicken.As a result,50 transcripts highly expressed in hypoxia are screened out.Among up-regulated genes,some are involved in the gene ontology(GO) such as cell growth,cell difference,muscle contraction and signal transduction.However,the expression levels of 21 transcripts are lower in hypoxia than those in normoxia.Some down-regulated genes take part in cell communication,ion transport,protein amino acid phosphorylation and signal transduction.Interestingly,gene enrichment analyses of these differential gene expressions are mainly associated with immune system response and ion channel activity in response to stimulus.Moreover,the transcriptional expression profiles analyzed by hierarchical clustering and CPP-SOM software in all of the 3 different chicken breeds revealed that Tibetan Chicken is much closely related to Shouguang Chicken rather than Dwarf Recessive White Chicken.In addition,12 transcripts of Tibetan Chicken breed-specific expressed genes were identified,which seem to result in a

  14. Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms.

    Directory of Open Access Journals (Sweden)

    Juliana Durack

    Full Text Available The ability of Listeria monocytogenes to adapt to various food and food- processing environments has been attributed to its robustness, persistence and prevalence in the food supply chain. To improve the present understanding of molecular mechanisms involved in hyperosmotic and low-temperature stress adaptation of L. monocytogenes, we undertook transcriptomics analysis on three strains adapted to sub-lethal levels of these stress stimuli and assessed functional gene response. Adaptation to hyperosmotic and cold-temperature stress has revealed many parallels in terms of gene expression profiles in strains possessing different levels of stress tolerance. Gene sets associated with ribosomes and translation, transcription, cell division as well as fatty acid biosynthesis and peptide transport showed activation in cells adapted to either cold or hyperosmotic stress. Repression of genes associated with carbohydrate metabolism and transport as well as flagella was evident in stressed cells, likely linked to activation of CodY regulon and consequential cellular energy conservation.

  15. Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications.

    Directory of Open Access Journals (Sweden)

    Weibing Shi

    Full Text Available Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host

  16. The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

    Energy Technology Data Exchange (ETDEWEB)

    Blanc, Guillaume; Duncan, Garry A.; Agarakova, Irina; Borodovsky, Mark; Gurnon, James; Kuo, Alan; Lindquist, Erika; Lucas, Susan; Pangailinan, Jasmyn; Polle, Juergen; Salamov, Asaf; Terry, Astrid; Yamada, Takashi; Dunigan, David D.; Grigoriev, Igor V.; Claverie, Jean-Michel; Etten, James L. Van

    2010-05-06

    Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.

  17. Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance

    Directory of Open Access Journals (Sweden)

    Gil M Penuliar

    2015-05-01

    Full Text Available Antimicrobial chemotherapy is critical in the fight against infectious diseases caused by Entamoeba histolytica. Among the drugs available for the treatment of amebiasis, metronidazole (MTZ is considered the drug of choice. Recently, in vitro studies have described MTZ resistance and the potential mechanisms involved. Costs to fitness and adaptive responses associated with resistance, however, have not been investigated. In this study we generated an HM-1 derived strain resistant to 12 µM MTZ (MTZR. We examined its phenotypic and transcriptional profile to determine the consequences and mRNA level changes associated with MTZ resistance. Our results indicated increased cell size and granularity, and decreased rates in cell division, adhesion, phagocytosis, cytopathogenicity, and glucose consumption. Transcriptome analysis revealed 142 differentially expressed genes in MTZR. In contrast to other MTZ resistant parasites, MTZR did not down-regulate pyruvate:ferredoxin oxidoreductase, but showed increased expression of genes for a hypothetical protein (HP1 and several iron-sulfur flavoproteins, and downregulation of genes for leucine-rich proteins. Fisher’s exact test showed 24 significantly enriched GO terms in MTZR, and a 3-way comparison of modulated genes in MTZR against those of MTZR cultured without MTZ and HM-1 cultured with MTZ, showed that 88 genes were specific to MTZR. Overall, our findings suggested that MTZ resistance is associated with specific transcriptional changes and decreased parasite virulence.

  18. Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance

    Science.gov (United States)

    Penuliar, Gil M.; Nakada-Tsukui, Kumiko; Nozaki, Tomoyoshi

    2015-01-01

    Antimicrobial chemotherapy is critical in the fight against infectious diseases caused by Entamoeba histolytica. Among the drugs available for the treatment of amebiasis, metronidazole (MTZ) is considered the drug of choice. Recently, in vitro studies have described MTZ resistance and the potential mechanisms involved. Costs to fitness and adaptive responses associated with resistance, however, have not been investigated. In this study we generated an HM-1 derived strain resistant to 12 μM MTZ (MTZR). We examined its phenotypic and transcriptional profile to determine the consequences and mRNA level changes associated with MTZ resistance. Our results indicated increased cell size and granularity, and decreased rates in cell division, adhesion, phagocytosis, cytopathogenicity, and glucose consumption. Transcriptome analysis revealed 142 differentially expressed genes in MTZR. In contrast to other MTZ resistant parasites, MTZR did not down-regulate pyruvate:ferredoxin oxidoreductase, but showed increased expression of genes for a hypothetical protein (HP1) and several iron-sulfur flavoproteins, and downregulation of genes for leucine-rich proteins. Fisher's exact test showed 24 significantly enriched GO terms in MTZR, and a 3-way comparison of modulated genes in MTZR against those of MTZR cultured without MTZ and HM-1 cultured with MTZ, showed that 88 genes were specific to MTZR. Overall, our findings suggested that MTZ resistance is associated with specific transcriptional changes and decreased parasite virulence. PMID:25999919

  19. Transcriptomes reveal alterations in gravity impact circadian clocks and activate mechanotransduction pathways with adaptation through epigenetic change.

    Science.gov (United States)

    Casey, Theresa; Patel, Osman V; Plaut, Karen

    2015-04-01

    Few studies have investigated the impact of alterations in gravity on mammalian transcriptomes. Here, we describe the impact of spaceflight on mammary transcriptome of late pregnant rats and the effect of hypergravity exposure on mammary, liver, and adipose transcriptomes in late pregnancy and at the onset of lactation. RNA was isolated from mammary collected on pregnancy day 20 from rats exposed to spaceflight from days 11 to 20 of gestation. To measure the impact of hypergravity on mammary, liver, and adipose transcriptomes we isolated RNA from tissues collected on P20 and lactation day 1 from rats exposed to hypergravity beginning on pregnancy day 9. Gene expression was measured with Affymetrix GeneChips. Microarray analysis of variance revealed alterations in gravity affected the expression of genes that regulate circadian clocks and activate mechanotransduction pathways. Changes in these systems may explain global gene expression changes in immune response, metabolism, and cell proliferation. Expression of genes that modify chromatin structure and methylation was affected, suggesting adaptation to gravity alterations may proceed through epigenetic change. Altered gravity experiments offer insights into the role of forces omnipresent on Earth that shape genomes in heritable ways. Our study is the first to analyze the impact of alterations in gravity on transcriptomes of pregnant and lactating mammals. Findings provide insight into systems that sense gravity and the way in which they affect phenotype, as well as the possibility of sustaining life beyond Earth's orbit.

  20. Metabolic profiling reveals ethylene mediated metabolic changes and a coordinated adaptive mechanism of 'Jonagold' apple to low oxygen stress.

    Science.gov (United States)

    Bekele, Elias A; Beshir, Wasiye F; Hertog, Maarten L A T M; Nicolai, Bart M; Geeraerd, Annemie H

    2015-11-01

    Apples are predominantly stored in controlled atmosphere (CA) storage to delay ripening and prolong their storage life. Profiling the dynamics of metabolic changes during ripening and CA storage is vital for understanding the governing molecular mechanism. In this study, the dynamics of the primary metabolism of 'Jonagold' apples during ripening in regular air (RA) storage and initiation of CA storage was profiled. 1-Methylcyclopropene (1-MCP) was exploited to block ethylene receptors and to get insight into ethylene mediated metabolic changes during ripening of the fruit and in response to hypoxic stress. Metabolic changes were quantified in glycolysis, the tricarboxylic acid (TCA) cycle, the Yang cycle and synthesis of the main amino acids branching from these metabolic pathways. Partial least square discriminant analysis of the metabolic profiles of 1-MCP treated and control apples revealed a metabolic divergence in ethylene, organic acid, sugar and amino acid metabolism. During RA storage at 18°C, most amino acids were higher in 1-MCP treated apples, whereas 1-aminocyclopropane-1-carboxylic acid (ACC) was higher in the control apples. The initial response of the fruit to CA initiation was accompanied by an increase of alanine, succinate and glutamate, but a decline in aspartate. Furthermore, alanine and succinate accumulated to higher levels in control apples than 1-MCP treated apples. The observed metabolic changes in these interlinked metabolites may indicate a coordinated adaptive strategy to maximize energy production.

  1. Neuroendocrine transcriptional programs adapt dynamically to the supply and demand for neuropeptides as revealed in NSF mutant zebrafish

    Directory of Open Access Journals (Sweden)

    Baier Herwig

    2009-06-01

    reveal an unexpected role for NSF in hypothalamic development, with mutant 5 days post-fertilization larvae exhibiting a stage-dependent loss of neuroendocrine transcripts and a corresponding accumulation of neuropeptides in the soma. Based on our collective findings, we speculate that neuroendocrine transcriptional programs adapt dynamically to both the supply and demand for neuropeptides to ensure adequate homeostatic responses.

  2. Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood).

    Science.gov (United States)

    Suarez-Gonzalez, Adriana; Hefer, Charles A; Christe, Camille; Corea, Oliver; Lexer, Christian; Cronk, Quentin C B; Douglas, Carl J

    2016-06-01

    Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species Populus balsamifera and identified candidate genes for local adaptation. Here, we explored the patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or subfunctionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.

  3. [Radiation-induced "bystander effect" revealed by means of adaptive response in cocultured lymphocytes from humans of different genders].

    Science.gov (United States)

    Kolesnikova, I S; Vorobtsova, I E

    2011-01-01

    The "bystander effect" was investigated in mixed cultures of lymphocytes from humans of opposite genders. Development of the adaptive response (AR) in non-irradiated female/male cells was estimated after adaptive pretreatment of opposite gender lymphocytes, chromosome aberrations being evaluated. Experiments were performed using two schedules of adaptive (0.05 Gy) and challenging (1 Gy) irradiations: G0-G1 and G1-G1. The results obtained indicate the development of a mediated adaptive response ("bystander effect") in the lymphocytes neighboring pre-irradiated cells, as well as the influence of a time scheme of adapting and challenging irradiations on the amount of induced chromosome aberrations in mixed cultures and a possible dependence of the adaptive response intensity on the donor gender.

  4. Comparative genomic analysis ofLactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles

    Institute of Scientific and Technical Information of China (English)

    Ping LI; Xuan LI; Qing GU; Xiu-yu LOU; Xiao-mei ZHANG; Da-feng SONG; Chen ZHANG

    2016-01-01

    题目:比较基因组学揭示植物乳杆菌ZJ316的生境适应性及潜在益生特性目的:前期研究发现植物乳杆菌ZJ316能显著抑制病原菌,促进仔猪生长,提高猪肉质量等,本研究拟在ZJ316全基因组测序的基础上,运用比较基因组学手段揭示与其生境适应性及益生特性相关基因。创新点:首次从基因水平上分析与植物乳杆菌ZJ316的生境适应性、抑菌活性及益生特性等相关的基因,为进一步揭示其生理功能打下基础。方法:运用BLASTN、Mauve和MUMmer等将植物乳杆菌ZJ316全基因组序列与已测序的8个植物乳杆菌全基因组序列进行比对及分析;用CRISPRFinder寻找CRISPR重复序列。结论:植物乳杆菌ZJ316包含碳水化合物的运输和代谢、蛋白水解酶系统和氨基酸的生物合成等相关基因,具有CRISPR、应激反应、耐胆盐、粘附宿主肠壁、胞外多糖、生物合成和细菌素生物合成等相关基因。这些基因的功能是其作为益生菌的重要特征和基础。%Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as an-timicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentialy related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence ofL. plantarumZJ316 was compared with those of eightL. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palin-dromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and pro-biotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid bio-synthesis, CRISPR adaptive

  5. Sports-related testing protocols are required to reveal trunk stability adaptations in high-level athletes.

    Science.gov (United States)

    Barbado, David; Barbado, Luis C; Elvira, Jose L L; Dieën, Jaap H van; Vera-Garcia, Francisco J

    2016-09-01

    Trunk/core stability is considered a key component of training programs, because it could contribute to prevention of low-back and lower-limb injuries and to sports performance. Based on the specificity principle, sports-related trunk stability tests would be required in elite sports performance. However, there may be some generic qualities underlying trunk stability that can be assessed with nonspecific protocols, which are broadly used in sport and rehabilitation. To assess whether specific tests are needed in a high-performance context, we analyzed the influence of specialization in sports with large but qualitatively different balance control demands (judo and kayaking) on trunk stability and compared high-performance athletes with recreational athletes without a specific training history. Twenty-five judokas, sixteen kayakers and thirty-seven recreational athletes performed two trunk stability protocols: sudden loading, to assess trunk responses to external and unexpected perturbations; stable and unstable sitting, to assess the participant's ability to control trunk while sitting. Within-session test-retest reliability analyses were performed to support the between-groups comparison. Judokas showed lower angular displacement (0.199rad) against posterior loading than kayakers (0.221rad) probably because they are frequently challenged by higher sudden loads while they are pushed or pulled. Kayakers showed lower error (7.33mm), probably because they train and compete seated on unstable surfaces. Importantly, judokas and kayakers obtained better results than recreational athletes only in those tests designed according to the specific demands of each sport (psport training induces specific trunk stability adaptations, which are not revealed through nonspecific tests.

  6. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

    KAUST Repository

    Ngugi, David

    2014-08-08

    The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate \\'switch\\' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

  7. ALV-J GP37 molecular analysis reveals novel virus-adapted sites and three tyrosine-based Env species.

    Directory of Open Access Journals (Sweden)

    Jianqiang Ye

    Full Text Available Compared to other avian leukosis viruses (ALV, ALV-J primarily induces myeloid leukemia and hemangioma and causes significant economic loss for the poultry industry. The ALV-J Env protein is hypothesized to be related to its unique pathogenesis. However, the molecular determinants of Env for ALV-J pathogenesis are unclear. In this study, we compared and analyzed GP37 of ALV-J Env and the EAV-HP sequence, which has high homology to that of ALV-J Env. Phylogenetic analysis revealed five groups of ALV-J GP37 and two novel ALV-J Envs with endemic GP85 and EAV-HP-like GP37. Furthermore, at least 15 virus-adapted mutations were detected in GP37 compared to the EAV-HP sequence. Further analysis demonstrated that three tyrosine-based motifs (YxxM, ITIM (immune tyrosine-based inhibitory motif and ITAM-like (immune tyrosine-based active motif like associated with immune disease and oncogenesis were found in the cytoplasmic tail of GP37. Based on the potential function and distribution of these motifs in GP37, ALV-J Env was grouped into three species, inhibitory Env, bifunctional Env and active Env. Accordingly, 36.91%, 61.74% and 1.34% of ALV-J Env sequences from GenBank are classified as inhibitory, bifunctional and active Env, respectively. Additionally, the Env of the ALV-J prototype strain, HPRS-103, and 17 of 18 EAV-HP sequences belong to the inhibitory Env. And models for signal transduction of the three ALV-J Env species were predicted. Our findings and models provide novel insights for identifying the roles and molecular mechanism of ALV-J Env in the unique pathogenesis of ALV-J.

  8. ALV-J GP37 molecular analysis reveals novel virus-adapted sites and three tyrosine-based Env species.

    Science.gov (United States)

    Ye, Jianqiang; Fan, Zhonglei; Shang, Jianjun; Tian, Xiaoyan; Yang, Jialiang; Chen, Hongjun; Shao, Hongxia; Qin, Aijian

    2015-01-01

    Compared to other avian leukosis viruses (ALV), ALV-J primarily induces myeloid leukemia and hemangioma and causes significant economic loss for the poultry industry. The ALV-J Env protein is hypothesized to be related to its unique pathogenesis. However, the molecular determinants of Env for ALV-J pathogenesis are unclear. In this study, we compared and analyzed GP37 of ALV-J Env and the EAV-HP sequence, which has high homology to that of ALV-J Env. Phylogenetic analysis revealed five groups of ALV-J GP37 and two novel ALV-J Envs with endemic GP85 and EAV-HP-like GP37. Furthermore, at least 15 virus-adapted mutations were detected in GP37 compared to the EAV-HP sequence. Further analysis demonstrated that three tyrosine-based motifs (YxxM, ITIM (immune tyrosine-based inhibitory motif) and ITAM-like (immune tyrosine-based active motif like)) associated with immune disease and oncogenesis were found in the cytoplasmic tail of GP37. Based on the potential function and distribution of these motifs in GP37, ALV-J Env was grouped into three species, inhibitory Env, bifunctional Env and active Env. Accordingly, 36.91%, 61.74% and 1.34% of ALV-J Env sequences from GenBank are classified as inhibitory, bifunctional and active Env, respectively. Additionally, the Env of the ALV-J prototype strain, HPRS-103, and 17 of 18 EAV-HP sequences belong to the inhibitory Env. And models for signal transduction of the three ALV-J Env species were predicted. Our findings and models provide novel insights for identifying the roles and molecular mechanism of ALV-J Env in the unique pathogenesis of ALV-J.

  9. Transcriptome profile of yeast reveals the essential role of PMA2 and uncharacterized gene YBR056W-A (MNC1) in adaptation to toxic manganese concentration.

    Science.gov (United States)

    Andreeva, N; Kulakovskaya, E; Zvonarev, A; Penin, A; Eliseeva, I; Teterina, A; Lando, A; Kulakovskiy, I V; Kulakovskaya, T

    2017-02-22

    Adaptation of S. cerevisiae to toxic concentrations of manganese provides a physiological model of heavy metal homeostasis. Transcriptome analysis of adapted yeast cells reveals upregulation of cell wall and plasma membrane proteins including membrane transporters. The gene expression in adapted cells differs from that of cells under short-term toxic metal stress. Among the most significantly upregulated genes are PMA2, encoding an ortholog of Pma1 H(+)-ATPase of the plasma membrane, and YBR056W-A, encoding a putative membrane protein Mnc1 that belongs to the CYSTM family and presumably chelates manganese at the cell surface. We demonstrate that these genes are essential for the adaptation to toxic manganese concentration and propose an extended scheme of manganese detoxification in yeast.

  10. Pseudomonas lini Strain ZBG1 Revealed Carboxylic Acid Utilization and Copper Resistance Features Required for Adaptation to Vineyard Soil Environment: A Draft Genome Analysis

    Science.gov (United States)

    Chan, Kok-Gan; Chong, Teik-Min; Adrian, Tan-Guan-Sheng; Kher, Heng Leong; Grandclément, Catherine; Faure, Denis; Yin, Wai-Fong; Dessaux, Yves; Hong, Kar-Wai

    2016-01-01

    Pseudomonas lini strain ZBG1 was isolated from the soil of vineyard in Zellenberg, France and the draft genome was reported in this study. Bioinformatics analyses of the genome revealed presence of genes encoding tartaric and malic acid utilization as well as copper resistance that correspond to the adaptation this strain in vineyard soil environment. PMID:27512520

  11. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians.

    Science.gov (United States)

    Yang, Xinwang; Wang, Ying; Zhang, Yue; Lee, Wen-Hui; Zhang, Yun

    2016-01-27

    Elucidating the mechanisms of high-altitude adaptation is an important research area in modern biology. To date, however, knowledge has been limited to the genetic mechanisms of adaptation to the lower oxygen and temperature levels prevalent at high altitudes, with adaptation to UV radiation largely neglected. Furthermore, few proteomic or peptidomic analyses of these factors have been performed. In this study, the molecular adaptation of high-altitude Odorrana andersonii and cavernicolous O. wuchuanensis to elevated UV radiation was investigated. Compared with O. wuchuanensis, O. andersonii exhibited greater diversity and free radical scavenging potentiality of skin antioxidant peptides to cope with UV radiation. This implied that O. andersonii evolved a much more complicated and powerful skin antioxidant peptide system to survive high-altitude UV levels. Our results provided valuable peptidomic clues for understanding the novel molecular basis for adaptation to high elevation habitats.

  12. Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau.

    Science.gov (United States)

    Qiao, Qin; Wang, Qia; Han, Xi; Guan, Yanlong; Sun, Hang; Zhong, Yang; Huang, Jinling; Zhang, Ticao

    2016-02-24

    The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.

  13. Sequential Dictionary Learning From Correlated Data: Application to fMRI Data Analysis.

    Science.gov (United States)

    Seghouane, Abd-Krim; Iqbal, Asif

    2017-03-22

    Sequential dictionary learning via the K-SVD algorithm has been revealed as a successful alternative to conventional data driven methods such as independent component analysis (ICA) for functional magnetic resonance imaging (fMRI) data analysis. fMRI datasets are however structured data matrices with notions of spatio-temporal correlation and temporal smoothness. This prior information has not been included in the K-SVD algorithm when applied to fMRI data analysis. In this paper we propose three variants of the K-SVD algorithm dedicated to fMRI data analysis by accounting for this prior information. The proposed algorithms differ from the K-SVD in their sparse coding and dictionary update stages. The first two algorithms account for the known correlation structure in the fMRI data by using the squared Q, R-norm instead of the Frobenius norm for matrix approximation. The third and last algorithm account for both the known correlation structure in the fMRI data and the temporal smoothness. The temporal smoothness is incorporated in the dictionary update stage via regularization of the dictionary atoms obtained with penalization. The performance of the proposed dictionary learning algorithms are illustrated through simulations and applications on real fMRI data.

  14. Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans

    Directory of Open Access Journals (Sweden)

    Lisa L. Liu

    2016-05-01

    Full Text Available Infection by human cytomegalovirus (HCMV leads to NKG2C-driven expansion of adaptive natural killer (NK cells, contributing to host defense. However, approximately 4% of all humans carry a homozygous deletion of the gene that encodes NKG2C (NKG2C−/−. Assessment of NK cell repertoires in 60 NKG2C−/− donors revealed a broad range of NK cell populations displaying characteristic footprints of adaptive NK cells, including a terminally differentiated phenotype, functional reprogramming, and epigenetic remodeling of the interferon (IFN-γ promoter. We found that both NKG2C− and NKG2C+ adaptive NK cells expressed high levels of CD2, which synergistically enhanced ERK and S6RP phosphorylation following CD16 ligation. Notably, CD2 co-stimulation was critical for the ability of adaptive NK cells to respond to antibody-coated target cells. These results reveal an unexpected redundancy in the human NK cell response to HCMV and suggest that CD2 provides “signal 2” in antibody-driven adaptive NK cell responses.

  15. Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

    DEFF Research Database (Denmark)

    Sandberg, Troy E.; Pedersen, Margit; LaCroix, Ryan A.

    2014-01-01

    Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation to a desired environment. Here, we performed ALE to 42 °C of ten parallel populations of Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental...... conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward a similar phenotype along distinct genetic paths. Adapted strains possessed as few as 6 and as many as 55 mutations, and of the 144 genes that mutated in total, 14 arose independently across...... reaffirmed the impact of the key mutations on the growth rate at 42 °C. Interestingly, most of the identified key gene targets differed significantly from those found in similar temperature adaptation studies, highlighting the sensitivity of genetic evolution to experimental conditions and ancestral genotype...

  16. Multiple Time Courses of Vestibular Set-Point Adaptation Revealed by Sustained Magnetic Field Stimulation of the Labyrinth.

    Science.gov (United States)

    Jareonsettasin, Prem; Otero-Millan, Jorge; Ward, Bryan K; Roberts, Dale C; Schubert, Michael C; Zee, David S

    2016-05-23

    A major focus in neurobiology is how the brain adapts its motor behavior to changes in its internal and external environments [1, 2]. Much is known about adaptively optimizing the amplitude and direction of eye and limb movements, for example, but little is known about another essential form of learning, "set-point" adaptation. Set-point adaptation balances tonic activity so that reciprocally acting, agonist and antagonist muscles have a stable platform from which to launch accurate movements. Here, we use the vestibulo-ocular reflex-a simple behavior that stabilizes the position of the eye while the head is moving-to investigate how tonic activity is adapted toward a new set point to prevent eye drift when the head is still [3, 4]. Set-point adaptation was elicited with magneto-hydrodynamic vestibular stimulation (MVS) by placing normal humans in a 7T MRI for 90 min. MVS is ideal for prolonged labyrinthine activation because it mimics constant head acceleration and induces a sustained nystagmus similar to natural vestibular lesions [5, 6]. The MVS-induced nystagmus diminished slowly but incompletely over multiple timescales. We propose a new adaptation hypothesis, using a cascade of imperfect mathematical integrators, that reproduces the response to MVS (and more natural chair rotations), including the gradual decrease in nystagmus as the set point changes over progressively longer time courses. MVS set-point adaptation is a biological model with applications to basic neurophysiological research into all types of movements [7], functional brain imaging [8], and treatment of vestibular and higher-level attentional disorders by introducing new biases to counteract pathological ones [9].

  17. Cross-adaptation combined with TMS reveals a functional overlap between vision and imagery in the early visual cortex.

    Science.gov (United States)

    Cattaneo, Zaira; Bona, Silvia; Silvanto, Juha

    2012-02-01

    The extent to which the generation of mental images draws on the neuronal representations involved in visual perception has been the subject of much debate. To investigate this overlap, we assessed whether adaptation to visual stimuli affects the ability to generate visual mental images; such cross-adaptation would indicate shared neural representations between visual perception and imagery. Mental imagery was tested using a modified version of the clock task, in which subjects are presented with a digital time (e.g. "2.15") and are asked to generate a mental image of the clock hands displaying this time on an empty clock face. Participants were adapted to oriented lines either on the upper or lower side of the clock face prior to the mental image generation. The results showed that mental imagery was impaired when the mental image had to be generated in the adapted region of visual space (Experiment 1). In Experiment 2, we used TMS to determine whether this adaptation effect occurs in the early visual cortex (EVC; V1/V2). Relative to control conditions (No TMS and Vertex TMS), EVC TMS facilitated mental imagery generation when the mental image spatially overlapped with the adapter. Our results thus show that neuronal representations in the EVC which encode (and are suppressed by) visual input play a causal role in visual mental imagery.

  18. Paradigm-free mapping with morphological component analysis: getting most out of fMRI data

    Science.gov (United States)

    Caballero Gaudes, César; Van De Ville, Dimitri; Petridou, Natalia; Lazeyras, François; Gowland, Penny

    2011-09-01

    Functional magnetic resonance imaging (fMRI) is a non-invasive imaging technique that maps the brain's response to neuronal activity based on the blood oxygenation level dependent (BOLD) effect. This work proposes a novel method for fMRI data analysis that enables the decomposition of the fMRI signal in its sources based on morphological descriptors. Beyond traditional fMRI hypothesis-based or blind data-driven exploratory approaches, this method allows the detection of BOLD responses without prior timing information. It is based on the deconvolution of the neuronal-related haemodynamic component of the fMRI signal with paradigm free mapping and also furnishes estimates of the movement-related effects, instrumental drifts and physiological fluctuations. Our algorithm is based on an overcomplete representation of the fMRI voxel time series with an additive linear model that is recovered by means of a L1-norm regularized least-squares estimators and an adapted block coordinate relaxation procedure. The performance of the technique is evaluated with simulated data and real experimental data acquired at 3T.

  19. Specialization and local adaptation of a fungal parasite on two host plant species as revealed by two fitness traits.

    Science.gov (United States)

    Sicard, Delphine; Pennings, Pleuni S; Grandclément, Catherine; Acosta, Jorge; Kaltz, Oliver; Shykoff, Jacqui A

    2007-01-01

    We investigate the geographic pattern of adaptation of a fungal parasite, Colletotrichum lindemuthianum, on two host species, Phaseolus vulgaris and P. coccineus for two parasite fitness traits: infectivity (ability to attack a host individual) and aggressivity (degree of sporulation and leaf surface damage). Using a cross-inoculation experiment, we show specialization of the fungus on its host species of origin for both traits even when fungi, which originated from hosts growing in sympatry, were tested on sympatric host populations. Within the two host species, we compared infectivity and aggressivity on local versus allopatric plant-fungus combinations. We found evidence for local adaptation for the two traits on P. vulgaris but not on P. coccineus. There was no significant correlation between the degrees of local adaptation for infectivity and aggressivity, indicating that the genetic basis and the effect of selection may differ between these two traits. For the two fitness traits, a positive correlation between the degree of specialization and the degree of local adaptation was found, suggesting that specialization can be reinforced by local adaptation.

  20. Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp.

    Science.gov (United States)

    Chen, Chao; Liu, Zhiguang; Pan, Qi; Chen, Xiao; Wang, Huihua; Guo, Haikun; Liu, Shidong; Lu, Hongfeng; Tian, Shilin; Li, Ruiqiang; Shi, Wei

    2016-05-01

    Studying the genetic signatures of climate-driven selection can produce insights into local adaptation and the potential impacts of climate change on populations. The honey bee (Apis mellifera) is an interesting species to study local adaptation because it originated in tropical/subtropical climatic regions and subsequently spread into temperate regions. However, little is known about the genetic basis of its adaptation to temperate climates. Here, we resequenced the whole genomes of ten individual bees from a newly discovered population in temperate China and downloaded resequenced data from 35 individuals from other populations. We found that the new population is an undescribed subspecies in the M-lineage of A. mellifera (Apis mellifera sinisxinyuan). Analyses of population history show that long-term global temperature has strongly influenced the demographic history of A. m. sinisxinyuan and its divergence from other subspecies. Further analyses comparing temperate and tropical populations identified several candidate genes related to fat body and the Hippo signaling pathway that are potentially involved in adaptation to temperate climates. Our results provide insights into the demographic history of the newly discovered A. m. sinisxinyuan, as well as the genetic basis of adaptation of A. mellifera to temperate climates at the genomic level. These findings will facilitate the selective breeding of A. mellifera to improve the survival of overwintering colonies.

  1. Common neural mechanisms for the evaluation of facial trustworthiness and emotional expressions as revealed by behavioral adaptation.

    Science.gov (United States)

    Engell, Andrew D; Todorov, Alexander; Haxby, James V

    2010-01-01

    People rapidly and automatically evaluate faces along many social dimensions. Here, we focus on judgments of trustworthiness, which approximate basic valence evaluation of faces, and test whether these judgments are an overgeneralization of the perception of emotional expressions. We used a behavioral adaptation paradigm to investigate whether the previously noted perceptual similarities between trustworthiness and emotional expressions of anger and happiness extend to their underlying neural representations. We found that adapting to angry or happy facial expressions causes trustworthiness evaluations of subsequently rated neutral faces to increase or decrease, respectively. Further, we found no such modulation of trustworthiness evaluations after participants were adapted to fearful expressions, suggesting that this effect is specific to angry and happy expressions. We conclude that, in line with the overgeneralization hypothesis, a common neural system is engaged during the evaluation of facial trustworthiness and expressions of anger and happiness.

  2. A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment

    Science.gov (United States)

    2013-01-01

    Background Propionibacterium freudenreichii is a food grade bacterium consumed both in cheeses and in probiotic preparations. Its promising probiotic potential, relying largely on the active release of beneficial metabolites within the gut as well as the expression of key surface proteins involved in immunomodulation, deserves to be explored more deeply. Adaptation to the colon environment is requisite for the active release of propionibacterial beneficial metabolites and constitutes a bottleneck for metabolic activity in vivo. Mechanisms allowing P. freudenreichii to adapt to digestive stresses have been only studied in vitro so far. Our aim was therefore to study P. freudenreichii metabolic adaptation to intra-colonic conditions in situ. Results We maintained a pure culture of the type strain P. freudenreichii CIRM BIA 1, contained in a dialysis bag, within the colon of vigilant piglets during 24 hours. A transcriptomic analysis compared gene expression to identify the metabolic pathways induced by this environment, versus control cultures maintained in spent culture medium. We observed drastic changes in the catabolism of sugars and amino-acids. Glycolysis, the Wood-Werkman cycle and the oxidative phosphorylation pathways were down-regulated but induction of specific carbohydrate catabolisms and alternative pathways were induced to produce NADH, NADPH, ATP and precursors (utilizing of propanediol, gluconate, lactate, purine and pyrimidine and amino-acids). Genes involved in stress response were down-regulated and genes specifically expressed during cell division were induced, suggesting that P. freudenreichii adapted its metabolism to the conditions encountered in the colon. Conclusions This study constitutes the first molecular demonstration of P. freudenreichii activity and physiological adaptation in vivo within the colon. Our data are likely specific to our pig microbiota composition but opens an avenue towards understanding probiotic action within the gut

  3. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

    Science.gov (United States)

    Emmanuelle Morin; Annegret Kohler; Adam R. Baker; Marie Foulongne-Oriol; Vincent Lombard; Laszlo G. Nagy; Robin A. Ohm; Aleksandrina Patyshakuliyeva; Annick Brun; Andrea L. Aerts; Andrew M. Bailey; Christophe Billette; Pedro M. Coutinho; Greg Deakin; Harshavardhan Doddapaneni; Dimitrios Floudas; Jane Grimwood; Kristiina Hild& #233; n; Ursula K& #252; es; Kurt M. LaButti; Alla Lapidus; Erika A. Lindquist; Susan M. Lucas; Claude Murat; Robert W. Riley; Asaf A. Salamov; Jeremy Schmutz; Venkataramanan Subrananian; Han A.B. W& #246; sten; Jianping Xu; Daniel C. Eastwood; Gary D. Foster; Anton S.M. Sonnenberg; Daniel Cullen; Ronald P. de Vries; Taina Lundell; David S. Hibbett; Bernard Henrissat; Kerry S. Burton; Richard W. Kerrigan; Michael P. Challen; Igor V. Grigoriev; Francis. Martin

    2012-01-01

    Agaricus bisporus is the model fungus for the adaptation, persistence,and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar...

  4. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

    NARCIS (Netherlands)

    Morin, E.; Kohler, A.; Baker, A.R.; Foulongne-Oriol, M.; Lombard, V.; Nagy, L.G.; Ohm, R.A.; Patyshakuliyeva, A.; Brun, A.; Aerts, A.L.; Bailey, A.M.; Billette, C.; Coutinho, P.M.; Deakin, G.; Doddapaneni, H.; Floudas, D.; Grimwood, J.; Hildén, K.; Kües, U.; LaButti, K.M.; Lapidus, A.; Lindquist, E.A.; Lucas, S.M.; Murat, C.; Riley, R.W.; Salamov, A.A.; Schmutz, J.; Subramanian, V.; Wösten, H.A.B.; Xu, J.; Eastwood, D.C.; Foster, G.D.; Sonnenberg, A.S.M.; Cullen, D.; Vries, de R.P.; Lundell, T.; Hibbett, D.S.; Henrissat, B.; Burton, K.S.; Kerrigan, R.W.; Challen, M.P.; Grigorievf, I.V.; Martin, M.

    2012-01-01

    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibi

  5. Abnormal baseline brain activity in patients with neuromyelitis optica: A resting-state fMRI study

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yaou [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Liang Peipeng [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); International WIC institute, Beijing University of Technology, Beijing 100024 (China); Duan Yunyun; Jia Xiuqin; Wang Fei; Yu Chunshui; Qin Wen [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Dong Huiqing; Ye Jing [Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Li Kuncheng, E-mail: likuncheng1955@yahoo.com.cn [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China)

    2011-11-15

    Purpose: Recent immunopathologic and MRI findings suggest that tissue damage in neuromyelitis optica (NMO) is not limited to spinal cord and optic nerve, but also in brain. Baseline brain activity can reveal the brain functional changes to the tissue damages and give clues to the pathophysiology of NMO, however, it has never been explored by resting-state functional MRI (fMRI). We used regional amplitude of low frequency fluctuation (ALFF) as an index in resting-state fMRI to investigate how baseline brain activity changes in patients with NMO. Methods: Resting-state fMRIs collected from seventeen NMO patients and seventeen age- and sex-matched normal controls were compared to investigate the ALFF difference between the two groups. The relationships between ALFF in regions with significant group differences and the EDSS (Expanded Disability Status Scale), disease duration were further explored. Results: Our results showed that NMO patients had significantly decreased ALFF in precuneus, posterior cingulate cortex (PCC) and lingual gyrus; and increased ALFF in middle frontal gyrus, caudate nucleus and thalamus, compared to normal controls. Moderate negative correlations were found between the EDSS and ALFF in the left middle frontal gyrus (r = -0.436, p = 0.040) and the left caudate (r = -0.542, p = 0.012). Conclusion: The abnormal baseline brain activity shown by resting-state fMRI in NMO is relevant to cognition, visual and motor systems. It implicates a complex baseline brain status of both functional impairments and adaptations caused by tissue damages in these systems, which gives clues to the pathophysiology of NMO.

  6. Salient features in locomotor evolutionary adaptations of proboscideans revealed via the differential scaling of limb long bones

    CERN Document Server

    Kokshenev, Valery B

    2009-01-01

    The standard differential scaling of proportions in limb long bones (length against circumference) is applied to a phylogenetically wide sample of the Proboscidea, Elephantidae and the Asian (Elephas maximus) and African elephant (Loxodonta africana). In order to investigate allometric patterns in proboscideans and terrestrial mammals with parasagittal limb kinematics, the computed slopes (slenderness exponents) are compared with published values for mammals and studied within a framework of theoretical models of long bone scaling under gravity and muscle forces. Limb bone allometry in E. maximus and the Elephantidae are congruent with adaptation to bending and/or torsion induced by muscular forces during fast locomotion, as in other mammals, whereas limb bones in L. africana appear adapted for coping with the compressive forces of gravity. Consequently, hindlimb bones are expected to be more compliant than forelimb bones in accordance with in vivo studies on elephant locomotory kinetics and kinematics, and t...

  7. Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles

    OpenAIRE

    Dashuai Mu; Xiuxia Yu; Zhenxing Xu; Zongjun Du; Guanjun Chen

    2016-01-01

    An increasing number of studies have investigated the effects of nanoparticles (NPs) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against NPs. Whether secondary metabolism biosynthesis is a response to NP stress and contributes to the adaption of bacteria to NPs is unclear. Here, a significant induction in the surfactin production and biofilm formation were detected by adding Al2O3 NPs to the B. subtilis fermentation broth. Physiologic...

  8. The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation

    Directory of Open Access Journals (Sweden)

    Morroll Shaun

    2009-08-01

    Full Text Available Abstract Background The high intracellular salt concentration required to maintain a halophilic lifestyle poses challenges to haloarchaeal proteins that must stay soluble, stable and functional in this extreme environment. Proliferating cell nuclear antigen (PCNA is a fundamental protein involved in maintaining genome integrity, with roles in both DNA replication and repair. To investigate the halophilic adaptation of such a key protein we have crystallised and solved the structure of Haloferax volcanii PCNA (HvPCNA to a resolution of 2.0 Å. Results The overall architecture of HvPCNA is very similar to other known PCNAs, which are highly structurally conserved. Three commonly observed adaptations in halophilic proteins are higher surface acidity, bound ions and increased numbers of intermolecular ion pairs (in oligomeric proteins. HvPCNA possesses the former two adaptations but not the latter, despite functioning as a homotrimer. Strikingly, the positive surface charge considered key to PCNA's role as a sliding clamp is dramatically reduced in the halophilic protein. Instead, bound cations within the solvation shell of HvPCNA may permit sliding along negatively charged DNA by reducing electrostatic repulsion effects. Conclusion The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the pore region, to facilitate functional interactions with DNA. In this way, HvPCNA may harness its environment as

  9. The regularity of sustained firing reveals two populations of slowly adapting touch receptors in mouse hairy skin.

    Science.gov (United States)

    Wellnitz, Scott A; Lesniak, Daine R; Gerling, Gregory J; Lumpkin, Ellen A

    2010-06-01

    Touch is initiated by diverse somatosensory afferents that innervate the skin. The ability to manipulate and classify receptor subtypes is prerequisite for elucidating sensory mechanisms. Merkel cell-neurite complexes, which distinguish shapes and textures, are experimentally tractable mammalian touch receptors that mediate slowly adapting type I (SAI) responses. The assessment of SAI function in mutant mice has been hindered because previous studies did not distinguish SAI responses from slowly adapting type II (SAII) responses, which are thought to arise from different end organs, such as Ruffini endings. Thus we sought methods to discriminate these afferent types. We developed an epidermis-up ex vivo skin-nerve chamber to record action potentials from afferents while imaging Merkel cells in intact receptive fields. Using model-based cluster analysis, we found that two types of slowly adapting receptors were readily distinguished based on the regularity of touch-evoked firing patterns. We identified these clusters as SAI (coefficient of variation = 0.78 +/- 0.09) and SAII responses (0.21 +/- 0.09). The identity of SAI afferents was confirmed by recording from transgenic mice with green fluorescent protein-expressing Merkel cells. SAI receptive fields always contained fluorescent Merkel cells (n = 10), whereas SAII receptive fields lacked these cells (n = 5). Consistent with reports from other vertebrates, mouse SAI and SAII responses arise from afferents exhibiting similar conduction velocities, receptive field sizes, mechanical thresholds, and firing rates. These results demonstrate that mice, like other vertebrates, have two classes of slowly adapting light-touch receptors, identify a simple method to distinguish these populations, and extend the utility of skin-nerve recordings for genetic dissection of touch receptor mechanisms.

  10. Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping.

    Science.gov (United States)

    Deagle, Bruce E; Jones, Felicity C; Absher, Devin M; Kingsley, David M; Reimchen, Thomas E

    2013-04-01

    Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine-freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent

  11. The role of disease perceptions and results sharing in psychological adaptation after genetic susceptibility testing: the REVEAL Study.

    Science.gov (United States)

    Ashida, Sato; Koehly, Laura M; Roberts, J Scott; Chen, Clara A; Hiraki, Susan; Green, Robert C

    2010-12-01

    This study evaluates the extent to which psychological adaptation (validated measures of depressive symptoms, anxiety, and test-specific distress) after genetic susceptibility testing is influenced by changes in beliefs about Alzheimer's disease (AD) and sharing of test results with others. Adult children of AD patients (N=269) from a randomized clinical trial involving genetic testing for apolipoprotein E (APOE) provided information before, as well as 6 weeks and 12 months after results disclosure. The levels of adaptation varied highly among participants at 12-month assessment. Participants who learned that they were ε4 negative (lower risk) had a reduction in perceived risk and concern about developing AD compared with those who learned that they were ε4 positive. Those who received results through an extended educational protocol (three in-person visits) had a larger decline in AD concern than those in a condensed protocol (educational brochure and two in-person visits). Increase in AD concern 6 weeks after disclosure was associated with increase in depression scores (b=0.20, Ptesting (b=0.18, P=0.02) 1 year after testing. Increase in perceived risk (b=0.16, P=0.04) was also associated with higher AD genetic testing distress. Sharing the test results with health professionals and friends (but not family) was associated with decrease in depression (b=-0.11, P=0.05) and anxiety levels (b=-0.16, Ptesting may help facilitate test recipients' long-term psychological adaptation.

  12. Next-generation transcriptome profiling reveals insights into genetic factors contributing to growth differences and temperature adaptation in Australian populations of barramundi (Lates calcarifer).

    Science.gov (United States)

    Newton, James R; Zenger, Kyall R; Jerry, Dean R

    2013-09-01

    Identification of genetically-regulated adaptation in fish is a precursor to understanding how populations will respond to future climate induced stressors like temperature. Australian populations of barramundi (Lates calcarifer) show strong evidence of local adaptation to temperature. However, the phenotypic consequences of this adaptation are unknown and the genetic mechanisms underlying this response are poorly understood. In the current study, two populations of barramundi from temperature extremes of the species Australian distribution were communally reared at cool (22°C), control (28°C) and hot (36°C) water temperatures for 3.5months. Southern populations of barramundi originating from a cooler environment grew significantly faster at 22°C than northern populations of warm adapted barramundi. However, no difference in population growth was present at either 28°C or 36°C. The underlying transcriptome profile of barramundi was examined via Illumina mRNA deep sequencing to determine the major contributing gene categories giving rise to phenotypic differences in barramundi population growth. Gene ontology (GO) analysis revealed enrichment in categories relating to the regulation of peptidase activity as well as microtubule, cytoplasmic and cellular metabolic based processes. Further analysis of the GO category "microtubule based process" with associated genes from the "response to stress" category revealed an apparent re-organization of cytoskeletal elements in response to an induced cold stress in northern barramundi reared at 22°C, when compared with northern barramundi reared at 36°C. Between southern barramundi and northern barramundi reared at 36°C, an analysis of the "endopeptidase inhibitor activity" GO category in conjunction with stress genes indicated a suppression of the complement system in southern barramundi along with an increase in the cellular stress response. The results of the present study show that southern populations of barramundi

  13. FMRI effective connectivity and TMS chronometry: complementary accounts of causality in the visuospatial judgment network.

    Directory of Open Access Journals (Sweden)

    Tom A de Graaf

    Full Text Available BACKGROUND: While traditionally quite distinct, functional neuroimaging (e.g. functional magnetic resonance imaging: fMRI and functional interference techniques (e.g. transcranial magnetic stimulation: TMS increasingly address similar questions of functional brain organization, including connectivity, interactions, and causality in the brain. Time-resolved TMS over multiple brain network nodes can elucidate the relative timings of functional relevance for behavior ("TMS chronometry", while fMRI functional or effective connectivity (fMRI EC can map task-specific interactions between brain regions based on the interrelation of measured signals. The current study empirically assessed the relation between these different methods. METHODOLOGY/PRINCIPAL FINDINGS: One group of 15 participants took part in two experiments: one fMRI EC study, and one TMS chronometry study, both of which used an established cognitive paradigm involving one visuospatial judgment task and one color judgment control task. Granger causality mapping (GCM, a data-driven variant of fMRI EC analysis, revealed a frontal-to-parietal flow of information, from inferior/middle frontal gyrus (MFG to posterior parietal cortex (PPC. FMRI EC-guided Neuronavigated TMS had behavioral effects when applied to both PPC and to MFG, but the temporal pattern of these effects was similar for both stimulation sites. At first glance, this would seem in contradiction to the fMRI EC results. However, we discuss how TMS chronometry and fMRI EC are conceptually different and show how they can be complementary and mutually constraining, rather than contradictory, on the basis of our data. CONCLUSIONS/SIGNIFICANCE: The findings that fMRI EC could successfully localize functionally relevant TMS target regions on the single subject level, and conversely, that TMS confirmed an fMRI EC identified functional network to be behaviorally relevant, have important methodological and theoretical implications. Our

  14. δ-Catenin, a Wnt/β-catenin modulator, reveals inducible mutagenesis promoting cancer cell survival adaptation and metabolic reprogramming.

    Science.gov (United States)

    Nopparat, J; Zhang, J; Lu, J-P; Chen, Y-H; Zheng, D; Neufer, P D; Fan, J M; Hong, H; Boykin, C; Lu, Q

    2015-03-19

    Mutations of Wnt/β-catenin signaling pathway has essential roles in development and cancer. Although β-catenin and adenomatous polyposis coli (APC) gene mutations are well established and are known to drive tumorigenesis, discoveries of mutations in other components of the pathway lagged, which hinders the understanding of cancer mechanisms. Here we report that δ-catenin (gene designation: CTNND2), a primarily neural member of the β-catenin superfamily that promotes canonical Wnt/β-catenin/LEF-1-mediated transcription, displays exonic mutations in human prostate cancer and promotes cancer cell survival adaptation and metabolic reprogramming. When overexpressed in cells derived from prostate tumor xenografts, δ-catenin gene invariably gives rise to mutations, leading to sequence disruptions predicting functional alterations. Ectopic δ-catenin gene integrating into host chromosomes is locus nonselective. δ-Catenin mutations promote tumor development in mouse prostate with probasin promoter (ARR2PB)-driven, prostate-specific expression of Myc oncogene, whereas mutant cells empower survival advantage upon overgrowth and glucose deprivation. Reprogramming energy utilization accompanies the downregulation of glucose transporter-1 and poly (ADP-ribose) polymerase cleavage while preserving tumor type 2 pyruvate kinase expression. δ-Catenin mutations increase β-catenin translocation to the nucleus and hypoxia-inducible factor 1α (HIF-1α) expression. Therefore, introducing δ-catenin mutations is an important milestone in prostate cancer metabolic adaptation by modulating β-catenin and HIF-1α signaling under glucose shortage to amplify its tumor-promoting potential.

  15. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

    Directory of Open Access Journals (Sweden)

    Adrien Zimmer

    Full Text Available Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.

  16. Investigation of fMRI activation in the internal capsule

    Directory of Open Access Journals (Sweden)

    Brewer Kimberley D

    2011-06-01

    Full Text Available Abstract Background Functional magnetic resonance imaging (fMRI in white matter has long been considered controversial. Recently, this viewpoint has been challenged by an emerging body of evidence demonstrating white matter activation in the corpus callosum. The current study aimed to determine whether white matter activation could be detected outside of the corpus callosum, in the internal capsule. Data were acquired from a 4 T MRI using a specialized asymmetric spin echo spiral sequence. A motor task was selected to elicit activation in the posterior limb of the internal capsule. Results White matter fMRI activation was examined at the individual and group levels. Analyses revealed that activation was present in the posterior limb of the internal capsule in 80% of participants. These results provide further support for white matter fMRI activation. Conclusions The ability to visualize functionally active tracts has strong implications for the basic scientific study of connectivity and the clinical assessment of white matter disease.

  17. Optic Neuritis and the Visual Pathway: Evaluation of Neuromyelitis Optica Spectrum by Resting-State fMRI and Diffusion Tensor MRI.

    Science.gov (United States)

    Lopes, Fernanda Cristina Rueda; Alves-Leon, Soniza Vieira; Godoy, Jose Mauricio; de Souza Batista Scherpenhuijzen, Simone; Fezer, Leticia; Gasparetto, Emerson Leandro

    2015-01-01

    Optic neuritis (ON) is an acute episode of inflammation in the visual pathway (VP). It may occur as part of a demyelinating disease, which can affect white matter (WM) throughout the VP. Compensatory cortical adaptations may occur following WM damage to maintain visual integrity. Our aim was to investigate whether resting-state functional MRI (rsfMRI) can detect cortical adaptations following ON attacks and to correlate rsfMRI with diffusion tensor imaging (DTI) of WM within the VP. Neuromyelitis optica spectrum patients were compared to healthy controls at least 6 months after ON onset. DTI and rsfMRI were performed and post-processed using FSL tools (TBSS for DTI and MELODIC for fMRI). Ptients had higher synchronization values than controls in the visual network (3.48 vs. 2.12, P < .05). A weak trend of correlation was revealed between fMRI and structural analysis by DTI using fractional anisotropy (right side: R = -.36, P < .08; left side: R = .075, P < .73). The rsfMRI detected cortical reorganization following ON attack, but WM was considerably preserved in the posterior VP. Copyright © 2015 by the American Society of Neuroimaging.

  18. Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose

    Science.gov (United States)

    Gao, Guangliang; Zhao, Xianzhi; Li, Qin; He, Chuan; Zhao, Wenjing; Liu, Shuyun; Ding, Jinmei; Ye, Weixing; Wang, Jun; Chen, Ye; Wang, Haiwei; Li, Jing; Luo, Yi; Su, Jian; Huang, Yong; Liu, Zuohua; Dai, Ronghua; Shi, Yixiang; Meng, He; Wang, Qigui

    2016-01-01

    The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes. PMID:27608918

  19. Micro-trace fossils reveal pervasive reworking of Pliocene sapropels by low-oxygen-adapted benthic meiofauna.

    Science.gov (United States)

    Löhr, S C; Kennedy, M J

    2015-03-12

    Animal burrowers leave an indelible signature on the sedimentary record in most marine environments, with the seeming exception of low-oxygen environments. In modern sedimentary settings, however, sub-millimetre-sized benthic animals (meiofauna) are adapted to low oxygen and even sulfidic conditions. Almost nothing is known about their impact on ancient marine sediments because they leave few recognizable traces. Here we show, in classic Pliocene-aged anoxic facies from the Mediterranean, the first reported trace fossil evidence of meiofaunal activity and its relation to changing oxygenation. A novel approach utilizing electron imaging of ion-polished samples shows that meiofauna pervasively reworked sediment under oxygen-depleted conditions that excluded macrofauna, fragmenting organic laminae and emplacing 15- to 70-μm-diameter faecal pellets without macroscopically influencing the fabric. The extent of reworking raises the question: how pervasively altered are other sediments presently assumed to lack animal influence and how far into the geological record does this influence extend?

  20. Multi-omic profiling of EPO-producing CHO cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    discovered indications of metabolic adaptation of the amino acid catabolism in favor of heterologous protein production. We established a panel of stably EPO expressing CHO-K1 clones spanning a 25-fold productivity range and characterized the clones in batch and chemostat cultures. For this, we employed......, EPO gene expression, intracellular protein levels and genomewide differential gene expression analysis of genes functionally related to secretory protein processing,respectively. Finally, we generated a network reconstruction of the amino acid catabolism in CHO cells. There construction was utilized...... clone during chemostat culture. The EPO productivity levels were not reflected in EPO gene load,EPO gene expression or intracellular protein retention, indicating that these processes were not limiting EPO productivity. The global gene expression analysis did not identify significant differentially...

  1. Jaws for a spiral-tooth whorl: CT images reveal novel adaptation and phylogeny in fossil Helicoprion.

    Science.gov (United States)

    Tapanila, Leif; Pruitt, Jesse; Pradel, Alan; Wilga, Cheryl D; Ramsay, Jason B; Schlader, Robert; Didier, Dominique A

    2013-04-23

    New CT scans of the spiral-tooth fossil, Helicoprion, resolve a longstanding mystery concerning the form and phylogeny of this ancient cartilaginous fish. We present the first three-dimensional images that show the tooth whorl occupying the entire mandibular arch, and which is supported along the midline of the lower jaw. Several characters of the upper jaw show that it articulated with the neurocranium in two places and that the hyomandibula was not part of the jaw suspension. These features identify Helicoprion as a member of the stem holocephalan group Euchondrocephali. Our reconstruction illustrates novel adaptations, such as lateral cartilage to buttress the tooth whorl, which accommodated the unusual trait of continuous addition and retention of teeth in a predatory chondrichthyan. Helicoprion exemplifies the climax of stem holocephalan diversification and body size in Late Palaeozoic seas, a role dominated today by sharks and rays.

  2. Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection.

    Science.gov (United States)

    Su, Yvonne C F; Bahl, Justin; Joseph, Udayan; Butt, Ka Man; Peck, Heidi A; Koay, Evelyn S C; Oon, Lynette L E; Barr, Ian G; Vijaykrishna, Dhanasekaran; Smith, Gavin J D

    2015-08-06

    Influenza A H1N1/2009 virus that emerged from swine rapidly replaced the previous seasonal H1N1 virus. Although the early emergence and diversification of H1N1/2009 is well characterized, the ongoing evolutionary and global transmission dynamics of the virus remain poorly investigated. To address this we analyse >3,000 H1N1/2009 genomes, including 214 full genomes generated from our surveillance in Singapore, in conjunction with antigenic data. Here we show that natural selection acting on H1N1/2009 directly after introduction into humans was driven by adaptation to the new host. Since then, selection has been driven by immunological escape, with these changes corresponding to restricted antigenic diversity in the virus population. We also show that H1N1/2009 viruses have been subject to regular seasonal bottlenecks and a global reduction in antigenic and genetic diversity in 2014.

  3. The Genome Sequence of Bacillus cereus ATCC 10987 Reveals Metabolic Adaptations and a Large Plasmid Related to Bacillus anthracis pXO1

    Science.gov (United States)

    2004-01-01

    R.L. and Waites,K.B. (2003) Bacillus cereus bacteremia in a preterm neonate. J. Clin. Microbiol., 41, 3441±3444. 9. Ginsburg,A.S., Salazar,L.G., True... bacteremia and pneumonia due to Bacillus cereus . J. Clin. Microbiol., 35, 504±507. 12. Okinaka,R., Cloud,K., Hampton,O., Hoffmaster,A., Hill,K., Keim,P...The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 David A. Rasko

  4. Mapping between fMRI responses to movies and their natural language annotations.

    Science.gov (United States)

    Vodrahalli, Kiran; Chen, Po-Hsuan; Liang, Yingyu; Baldassano, Christopher; Chen, Janice; Yong, Esther; Honey, Christopher; Hasson, Uri; Ramadge, Peter; Norman, Kenneth A; Arora, Sanjeev

    2017-06-23

    Several research groups have shown how to map fMRI responses to the meanings of presented stimuli. This paper presents new methods for doing so when only a natural language annotation is available as the description of the stimulus. We study fMRI data gathered from subjects watching an episode of BBCs Sherlock (Chen et al., 2017), and learn bidirectional mappings between fMRI responses and natural language representations. By leveraging data from multiple subjects watching the same movie, we were able to perform scene classification with 72% accuracy (random guessing would give 4%) and scene ranking with average rank in the top 4% (random guessing would give 50%). The key ingredients underlying this high level of performance are (a) the use of the Shared Response Model (SRM) and its variant SRM-ICA (Chen et al., 2015; Zhang et al., 2016) to aggregate fMRI data from multiple subjects, both of which are shown to be superior to standard PCA in producing low-dimensional representations for the tasks in this paper; (b) a sentence embedding technique adapted from the natural language processing (NLP) literature (Arora et al., 2017) that produces semantic vector representation of the annotations; (c) using previous timestep information in the featurization of the predictor data. These optimizations in how we featurize the fMRI data and text annotations provide a substantial improvement in classification performance, relative to standard approaches. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  5. A SVM-based quantitative fMRI method for resting-state functional network detection.

    Science.gov (United States)

    Song, Xiaomu; Chen, Nan-kuei

    2014-09-01

    Resting-state functional magnetic resonance imaging (fMRI) aims to measure baseline neuronal connectivity independent of specific functional tasks and to capture changes in the connectivity due to neurological diseases. Most existing network detection methods rely on a fixed threshold to identify functionally connected voxels under the resting state. Due to fMRI non-stationarity, the threshold cannot adapt to variation of data characteristics across sessions and subjects, and generates unreliable mapping results. In this study, a new method is presented for resting-state fMRI data analysis. Specifically, the resting-state network mapping is formulated as an outlier detection process that is implemented using one-class support vector machine (SVM). The results are refined by using a spatial-feature domain prototype selection method and two-class SVM reclassification. The final decision on each voxel is made by comparing its probabilities of functionally connected and unconnected instead of a threshold. Multiple features for resting-state analysis were extracted and examined using an SVM-based feature selection method, and the most representative features were identified. The proposed method was evaluated using synthetic and experimental fMRI data. A comparison study was also performed with independent component analysis (ICA) and correlation analysis. The experimental results show that the proposed method can provide comparable or better network detection performance than ICA and correlation analysis. The method is potentially applicable to various resting-state quantitative fMRI studies.

  6. FMRI evidence of 'mirror' responses to geometric shapes.

    Directory of Open Access Journals (Sweden)

    Clare Press

    Full Text Available Mirror neurons may be a genetic adaptation for social interaction. Alternatively, the associative hypothesis proposes that the development of mirror neurons is driven by sensorimotor learning, and that, given suitable experience, mirror neurons will respond to any stimulus. This hypothesis was tested using fMRI adaptation to index populations of cells with mirror properties. After sensorimotor training, where geometric shapes were paired with hand actions, BOLD response was measured while human participants experienced runs of events in which shape observation alternated with action execution or observation. Adaptation from shapes to action execution, and critically, observation, occurred in ventral premotor cortex (PMv and inferior parietal lobule (IPL. Adaptation from shapes to execution indicates that neuronal populations responding to the shapes had motor properties, while adaptation to observation demonstrates that these populations had mirror properties. These results indicate that sensorimotor training induced populations of cells with mirror properties in PMv and IPL to respond to the observation of arbitrary shapes. They suggest that the mirror system has not been shaped by evolution to respond in a mirror fashion to biological actions; instead, its development is mediated by stimulus-general processes of learning within a system adapted for visuomotor control.

  7. The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment

    Science.gov (United States)

    Flórez, Ana Belén; Mayo, Baltasar

    2015-01-01

    Lactococcus garvieae is a lactic acid bacterium found in raw-milk dairy products as well as a range of aquatic and terrestrial environments. The plasmids in L. garvieae have received little attention compared to those of dairy Lactococcus lactis, in which the genes carried by these extrachromosomal elements are considered of adaptive value. The present work reports the sequencing and analysis of the plasmid complement of L. garvieae IPLA 31405, a strain isolated from a traditional, Spanish, starter-free cheese made from raw-milk. It consists of pLG9 and pLG42, of 9,124 and 42,240 nucleotides, respectively. Based on sequence and structural homology in the putative origin of replication (ori) region, pLG9 and pLG42 are predicted to replicate via a theta mechanism. Real-time, quantitative PCR showed the number of copies per chromosome equivalent of pLG9 and pLG42 to be around two and five, respectively. Sequence analysis identified eight complete open reading frames (orfs) in pLG9 and 36 in pLG42; these were organized into functional modules or cassettes containing different numbers of genes. These modules were flanked by complete or interrupted insertion sequence (IS)-like elements. Among the modules of pLG42 was a gene cluster encoding specific components of a phosphoenolpyruvate-phosphotransferase (PEP-PTS) system, including a phospho-β-galacosidase. The cluster showed a complete nucleotide identity respect to that in plasmids of L. lactis. Loss of pLG42 showed this to be involved in lactose assimilation. In the same plasmid, an operon encoding a type I restriction/modification (R/M) system was also identified. The specificity of this R/M system might be broadened by different R/M specificity subunits detected in pLG9 and in the bacterial chromosome. However, challenges of L. garvieae IPLA 31405 against L. lactis phages proved that the R/M system was not involved in phage resistance. Together, these results support the hypothesis that, as in L. lactis, pLG42

  8. fMRI. Basics and clinical applications

    Energy Technology Data Exchange (ETDEWEB)

    Ulmer, Stephan; Jansen, Olav (eds.) [University Hospital of Schleswig-Holstein, Kiel (Germany). Inst. of Neuroradiology, Neurocenter

    2010-07-01

    Functional MRI (fMRI) and the basic method of BOLD imaging were introduced in 1993 by Seiji Ogawa. From very basic experiments, fMRI has evolved into a clinical application for daily routine brain imaging. There have been various improvements in both the imaging technique as such as well as in the statistical analysis. In this volume, experts in the field share their knowledge and point out possible technical barriers and problems explaining how to solve them. Starting from the very basics on the origin of the BOLD signal, the book covers technical issues, anatomical landmarks, presurgical applications, and special issues in various clinical fields. Other modalities for brain mapping such as PET, TMS, and MEG are also compared with fMRI. This book is intended to give a state-of-the-art overview and to serve as a reference and guide for clinical applications of fMRI. (orig.)

  9. On clustering fMRI time series

    DEFF Research Database (Denmark)

    Goutte, C; Toft, P; Rostrup, E

    1999-01-01

    Analysis of fMRI time series is often performed by extracting one or more parameters for the individual voxels. Methods based, e.g., on various statistical tests are then used to yield parameters corresponding to probability of activation or activation strength. However, these methods do not indi......Analysis of fMRI time series is often performed by extracting one or more parameters for the individual voxels. Methods based, e.g., on various statistical tests are then used to yield parameters corresponding to probability of activation or activation strength. However, these methods do...... between the activation stimulus and the fMRI signal. We present two different clustering algorithms and use them to identify regions of similar activations in an fMRI experiment involving a visual stimulus....

  10. Tissue-specific defense and thermo-adaptive mechanisms of soybean seedlings under heat stress revealed by proteomic approach.

    Science.gov (United States)

    Ahsan, Nagib; Donnart, Tifenn; Nouri, Mohammad-Zaman; Komatsu, Setsuko

    2010-08-06

    A comparative proteomic approach was employed to explore tissue-specific protein expression patterns in soybean seedlings under heat stress. The changes in the protein expression profiles of soybean seedling leaves, stems, and roots were analyzed after exposure to high temperatures. A total of 54, 35, and 61 differentially expressed proteins were identified from heat-treated leaves, stems, and roots, respectively. Differentially expressed heat shock proteins (HSPs) and proteins involved in antioxidant defense were mostly up-regulated, whereas proteins associated with photosynthesis, secondary metabolism, and amino acid and protein biosynthesis were down-regulated in response to heat stress. A group of proteins, specifically low molecular weight HSPs and HSP70, were up-regulated and expressed in a similar manner in all tissues. Proteomic analysis indicated that the responses of HSP70, CPN-60 beta, and ChsHSP were tissue specific, and this observation was validated by immunoblot analysis. The heat-responsive sHSPs were not induced by other stresses such as cold and hydrogen peroxide. Taken together, these results suggest that to cope with heat stress soybean seedlings operate tissue-specific defenses and adaptive mechanisms, whereas a common defense mechanism associated with the induction of several HSPs was employed in all three tissues. In addition, tissue-specific proteins may play a crucial role in defending each type of tissues against thermal stress.

  11. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

    Energy Technology Data Exchange (ETDEWEB)

    Mahajabeen, Padamsee; Kumas, T. K. Arun; Riley, Robert; Binder, Manfred; Boyd, Alex; Calvo, Ann M.; Furukawa, Kentaro; Hesse, Cedar; Hohmann, Stefan; James, Tim Y.; LaButti, Kurt; Lapidus, Alla; Lindquist, Erika; Lucas, Susan; Miller, Kari; Shantappa, Sourabha; Grigoriev, Igor V.; Hibbett, David S.; McLaughlin, David J.; Spatafora, Joseph W.; Aime, Mary C.

    2011-09-03

    Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identied 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebito colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is conrmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were idented although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic

  12. Changes in foliar carbon isotope composition and seasonal stomatal conductance reveal adaptive traits in Mediterranean coppices affected by drought

    Institute of Scientific and Technical Information of China (English)

    Giovanni Di Matteo; Luigi Perini; Paolo Atzori; Paolo De Angelis; Tiziano Mei; Giada Bertini; Gianfranco Fabbio; Giuseppe Scarascia Mugnozza

    2014-01-01

    We estimated water-use efficiency and potential photosyn-thetic assimilation of Holm oak (Quercus ilex L.) on slopes of NW and SW aspects in a replicated field test examining the effects of intensifying drought in two Mediterranean coppice forests. We used standard tech-niques for quantifying gas exchange and carbon isotopes in leaves and analyzed total chlorophyll, carotenoids and nitrogen in leaves collected from Mediterranean forests managed under the coppice system. We pos-tulated that responses to drought of coppiced trees would lead to differ-ential responses in physiological traits and that these traits could be used by foresters to adapt to predicted warming and drying in the Mediterra-nean area. We observed physiological responses of the coppiced trees that suggested acclimation in photosynthetic potential and water-use effi-ciency:(1) a significant reduction in stomatal conductance (p<0.01) was recorded as the drought increased at the SW site;(2) foliarδ13C increased as drought increased at the SW site (p<0.01);(3) variations in levels of carotenoids and foliar nitrogen, and differences in foliar morphology were recorded, and were tentatively attributed to variation in photosyn-thetic assimilation between sites. These findings increase knowledge of the capacity for acclimation of managed forests in the Mediterranean region of Europe.

  13. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses.

    Science.gov (United States)

    Pride, David T; Salzman, Julia; Relman, David A

    2012-09-01

    Explorations of human microbiota have provided substantial insight into microbial community composition; however, little is known about interactions between various microbial components in human ecosystems. In response to the powerful impact of viral predation, bacteria have acquired potent defences, including an adaptive immune response based on the clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas system. To improve our understanding of the interactions between bacteria and their viruses in humans, we analysed 13 977 streptococcal CRISPR sequences and compared them with 2 588 172 virome reads in the saliva of four human subjects over 17 months. We found a diverse array of viruses and CRISPR spacers, many of which were specific to each subject and time point. There were numerous viral sequences matching CRISPR spacers; these matches were highly specific for salivary viruses. We determined that spacers and viruses coexist at the same time, which suggests that streptococcal CRISPR/Cas systems are under constant pressure from salivary viruses. CRISPRs in some subjects were just as likely to match viral sequences from other subjects as they were to match viruses from the same subject. Because interactions between bacteria and viruses help to determine the structure of bacterial communities, CRISPR-virus analyses are likely to provide insight into the forces shaping the human microbiome.

  14. Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus

    Directory of Open Access Journals (Sweden)

    Shu-Feng Zhang

    2016-09-01

    Full Text Available Phosphorus (P is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20.8% of them altered significantly in abundance under different P conditions. Genes encoding key enzymes/proteins involved in P utilization, nucleotide metabolism, photosynthesis, glycolysis and cell cycle regulation were significantly up-regulated in P-deficient cells. Genes participating in circadian rhythm regulation, such as circadian clock associated 1, were also up-regulated in P-deficient cells. The response of S. costatum to ambient P deficiency shows several similarities to the well-described responses of other marine diatom species, but also has its unique features. S. costatum has evolved the ability to re-program its circadian clock and intracellular biological processes in response to ambient P deficiency. This study provides new insights into the adaptive mechanisms to ambient P deficiency in marine diatoms.

  15. Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

    Directory of Open Access Journals (Sweden)

    Rodriguez-Rivera Lorraine D

    2011-08-01

    Full Text Available Abstract Background Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization. Results Multi-locus sequence analysis (MLSA and single nucleotide polymorphisms (SNPs data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment. Conclusions S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.

  16. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.

    Science.gov (United States)

    Ceapa, Corina; Davids, Mark; Ritari, Jarmo; Lambert, Jolanda; Wels, Michiel; Douillard, François P; Smokvina, Tamara; de Vos, Willem M; Knol, Jan; Kleerebezem, Michiel

    2016-07-02

    Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. LasR Variant Cystic Fibrosis Isolates Reveal an Adaptable Quorum-Sensing Hierarchy in Pseudomonas aeruginosa

    Science.gov (United States)

    Feltner, John B.; Wolter, Daniel J.; Pope, Christopher E.; Groleau, Marie-Christine; Smalley, Nicole E.; Greenberg, E. Peter; Mayer-Hamblett, Nicole; Burns, Jane; Hoffman, Lucas R.

    2016-01-01

    ABSTRACT Chronic Pseudomonas aeruginosa infections cause significant morbidity in patients with cystic fibrosis (CF). Over years to decades, P. aeruginosa adapts genetically as it establishes chronic lung infections. Nonsynonymous mutations in lasR, the quorum-sensing (QS) master regulator, are common in CF. In laboratory strains of P. aeruginosa, LasR activates transcription of dozens of genes, including that for another QS regulator, RhlR. Despite the frequency with which lasR coding variants have been reported to occur in P. aeruginosa CF isolates, little is known about their consequences for QS. We sequenced lasR from 2,583 P. aeruginosa CF isolates. The lasR sequences of 580 isolates (22%) coded for polypeptides that differed from the conserved LasR polypeptides of well-studied laboratory strains. This collection included 173 unique lasR coding variants, 116 of which were either missense or nonsense mutations. We studied 31 of these variants. About one-sixth of the variant LasR proteins were functional, including 3 with nonsense mutations, and in some LasR-null isolates, genes that are LasR dependent in laboratory strains were nonetheless expressed. Furthermore, about half of the LasR-null isolates retained RhlR activity. Therefore, in some CF isolates the QS hierarchy is altered such that RhlR quorum sensing is independent of LasR regulation. Our analysis challenges the view that QS-silent P. aeruginosa is selected during the course of a chronic CF lung infection. Rather, some lasR sequence variants retain functionality, and many employ an alternate QS strategy involving RhlR. PMID:27703072

  18. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Gauthier

    Full Text Available Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit. More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that

  19. Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.

    Science.gov (United States)

    Surmann, Kristin; Michalik, Stephan; Hildebrandt, Petra; Gierok, Philipp; Depke, Maren; Brinkmann, Lars; Bernhardt, Jörg; Salazar, Manuela G; Sun, Zhi; Shteynberg, David; Kusebauch, Ulrike; Moritz, Robert L; Wollscheid, Bernd; Lalk, Michael; Völker, Uwe; Schmidt, Frank

    2014-01-01

    Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival and physiological adaptation of S. aureus HG001 after internalization by two human lung epithelial cell lines (S9 and A549), and human embryonic kidney cells (HEK 293). Combining enrichment of bacteria from host-pathogen assays by cell sorting and quantitation of the pathogen's proteome by mass spectrometry we characterized S. aureus adaptation during the initial phase between 2.5 h and 6.5 h post-infection. Starting with about 2 × 10(6) bacteria, roughly 1450 S. aureus proteins, including virulence factors and metabolic enzymes were identified by spectral comparison and classical database searches. Most of the bacterial adaptation reactions, such as decreased levels of ribosomal proteins and metabolic enzymes or increased amounts of proteins involved in arginine and lysine biosynthesis, enzymes coding for terminal oxidases and stress responsive proteins or activation of the sigma factor SigB were observed after internalization into any of the three cell lines studied. However, differences were noted in central carbon metabolism including regulation of fermentation and threonine degradation. Since these differences coincided with different intracellular growth behavior, complementary profiling of the metabolome of the different non-infected host cell types was performed. This revealed similar levels of intracellular glucose but host cell specific differences in the amounts of amino acids such as glycine, threonine or glutamate. With this comparative study we provide an impression of the common and specific features of the adaptation of S. aureus HG001 to specific host cell environments as a starting point for follow-up studies with different strain isolates and regulatory

  20. Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells

    Directory of Open Access Journals (Sweden)

    Kristin eSurmann

    2014-08-01

    Full Text Available Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival and physiological adaptation of S. aureus HG001 after internalization by two human lung epithelial cell lines (S9 and A549, and human embryonic kidney cells (HEK 293. Combining enrichment of bacteria from host-pathogen assays by cell sorting and quantitation of the pathogen´s proteome by mass spectrometry we characterized S. aureus adaptation during the initial phase between 2.5 h and 6.5 h post-infection. Starting with about 2x106 bacteria, roughly 1,450 S. aureus proteins, including virulence factors and metabolic enzymes were identified by spectral comparison and classical database searches. Most of the bacterial adaptation reactions, such as decreases in levels of ribosomal proteins and metabolic enzymes or increases in amounts of proteins involved in arginine and lysine biosynthesis, coding for terminal oxidases and stress responsive genes or activation of the sigma factor SigB were observed after internalization into any of the three cell lines studied. However, differences were noted in central carbon metabolism including regulation of fermentation and threonine degradation. Since these differences coincided with different intracellular growth behavior, complementary profiling of the metabolome of the different non-infected host cell types was performed. This revealed similar levels of intracellular glucose but host cell specific differences in the amounts of amino acids such as glycine, threonine or glutamate. With this comparative study we provide an impression of the common and specific features of the adaptation of S. aureus HG001 to specific host cell environments as a starting point for follow-up studies with different strain isolates and

  1. Optimizing preprocessing and analysis pipelines for single-subject fMRI. I. Standard temporal motion and physiological noise correction methods.

    Science.gov (United States)

    Churchill, Nathan W; Oder, Anita; Abdi, Hervé; Tam, Fred; Lee, Wayne; Thomas, Christopher; Ween, Jon E; Graham, Simon J; Strother, Stephen C

    2012-03-01

    Subject-specific artifacts caused by head motion and physiological noise are major confounds in BOLD fMRI analyses. However, there is little consensus on the optimal choice of data preprocessing steps to minimize these effects. To evaluate the effects of various preprocessing strategies, we present a framework which comprises a combination of (1) nonparametric testing including reproducibility and prediction metrics of the data-driven NPAIRS framework (Strother et al. [2002]: NeuroImage 15:747-771), and (2) intersubject comparison of SPM effects, using DISTATIS (a three-way version of metric multidimensional scaling (Abdi et al. [2009]: NeuroImage 45:89-95). It is shown that the quality of brain activation maps may be significantly limited by sub-optimal choices of data preprocessing steps (or "pipeline") in a clinical task-design, an fMRI adaptation of the widely used Trail-Making Test. The relative importance of motion correction, physiological noise correction, motion parameter regression, and temporal detrending were examined for fMRI data acquired in young, healthy adults. Analysis performance and the quality of activation maps were evaluated based on Penalized Discriminant Analysis (PDA). The relative importance of different preprocessing steps was assessed by (1) a nonparametric Friedman rank test for fixed sets of preprocessing steps, applied to all subjects; and (2) evaluating pipelines chosen specifically for each subject. Results demonstrate that preprocessing choices have significant, but subject-dependant effects, and that individually-optimized pipelines may significantly improve the reproducibility of fMRI results over fixed pipelines. This was demonstrated by the detection of a significant interaction with motion parameter regression and physiological noise correction, even though the range of subject head motion was small across the group (≪ 1 voxel). Optimizing pipelines on an individual-subject basis also revealed brain activation patterns

  2. Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment

    Science.gov (United States)

    Milani, Christian; Turroni, Francesca; Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Ferrario, Chiara; van Sinderen, Douwe

    2015-01-01

    Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome. PMID:26590291

  3. Analyses between Reproductive Behaviour, Genetic Diversity and Pythium Responsiveness in Zingiber spp. reveal an adaptive significance for hemiclonality

    Directory of Open Access Journals (Sweden)

    Geethu Elizabath Thomas

    2016-12-01

    continuous, sexual and genetically diverse, but were susceptible, whereas populations inhabiting the revenue land were fragmented and monoclonal, but were resistant. It may be possible that, when genetic recombination becomes at a premium due to the genetic constraints imparted by habitat fragmentation or pathogen pressure, Z. zerumbet trigger asexual methods in order to preserve genotypes with adaptive fitness. A co-evolutionary feedback seems to occur between defense and reproduction in Z. zerumbet. Presumably, species with hemiclonal potential may have a fair chance to survive ecological undulations.

  4. Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.

    Directory of Open Access Journals (Sweden)

    Bartholomeus Van den Bogert

    Full Text Available The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine.

  5. Metabolic analysis of two contrasting wild barley genotypes grown hydroponically reveals adaptive strategies in response to low nitrogen stress.

    Science.gov (United States)

    Quan, Xiaoyan; Qian, Qiufeng; Ye, Zhilan; Zeng, Jianbin; Han, Zhigang; Zhang, Guoping

    2016-11-01

    Nitrogen (N) is an essential macronutrient for plants. The increasingly severe environmental problems caused by N fertilizer application urge alleviation of N fertilizer dependence in crop production. In previous studies, we identified the Tibetan wild barley accessions with high tolerance to low nitrogen (LN). In this study, metabolic analysis was done on two wild genotypes (XZ149, tolerant and XZ56, sensitive) to understand the mechanism of LN tolerance, using a hydroponic experiment. Leaf and root samples were taken at seven time points within 18 d after LN treatment, respectively. XZ149 was much less affected by low N stress than XZ56 in plant biomass. A total of 51 differentially accumulated metabolites were identified between LN and normal N treated plants. LN stress induced tissue-specific changes in carbon and nitrogen partitioning, and XZ149 had a pattern of energy-saving amino acids accumulation and carbon distribution in favor of root growth that contribute to its higher LN tolerance. Moreover, XZ149 is highly capable of producing energy and maintaining the redox homeostasis under LN stress. The current results revealed the mechanisms underlying the wild barley in high LN tolerance and provided the valuable references for developing barley cultivars with LN tolerance. Copyright © 2016 Elsevier GmbH. All rights reserved.

  6. Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem

    Science.gov (United States)

    Van den Bogert, Bartholomeus; Boekhorst, Jos; Herrmann, Ruth; Smid, Eddy J.; Zoetendal, Erwin G.; Kleerebezem, Michiel

    2013-01-01

    The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine. PMID:24386196

  7. Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.

    Science.gov (United States)

    Van den Bogert, Bartholomeus; Boekhorst, Jos; Herrmann, Ruth; Smid, Eddy J; Zoetendal, Erwin G; Kleerebezem, Michiel

    2013-01-01

    The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine.

  8. Enhanced Thalamic Functional Connectivity with No fMRI Responses to Affected Forelimb Stimulation in Stroke-Recovered Rats

    Science.gov (United States)

    Shim, Woo H.; Suh, Ji-Yeon; Kim, Jeong K.; Jeong, Jaeseung; Kim, Young R.

    2017-01-01

    Neurological recovery after stroke has been extensively investigated to provide better understanding of neurobiological mechanism, therapy, and patient management. Recent advances in neuroimaging techniques, particularly functional MRI (fMRI), have widely contributed to unravel the relationship between the altered neural function and stroke-affected brain areas. As results of previous investigations, the plastic reorganization and/or gradual restoration of the hemodynamic fMRI responses to neural stimuli have been suggested as relevant mechanisms underlying the stroke recovery process. However, divergent study results and modality-dependent outcomes have clouded the proper interpretation of variable fMRI signals. Here, we performed both evoked and resting state fMRI (rs-fMRI) to clarify the link between the fMRI phenotypes and post-stroke functional recovery. The experiments were designed to examine the altered neural activity within the contra-lesional hemisphere and other undamaged brain regions using rat models with large unilateral stroke, which despite the severe injury, exhibited nearly full recovery at ∼6 months after stroke. Surprisingly, both blood oxygenation level-dependent and blood volume-weighted (CBVw) fMRI activities elicited by electrical stimulation of the stroke-affected forelimb were completely absent, failing to reveal the neural origin of the behavioral recovery. In contrast, the functional connectivity maps showed highly robust rs-fMRI activity concentrated in the contra-lesional ventromedial nucleus of thalamus (VM). The negative finding in the stimuli-induced fMRI study using the popular rat middle cerebral artery model denotes weak association between the fMRI hemodynamic responses and neurological improvement. The results strongly caution the indiscreet interpretation of stroke-affected fMRI signals and demonstrate rs-fMRI as a complementary tool for efficiently characterizing stroke recovery. PMID:28119575

  9. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

    Science.gov (United States)

    Mesquita, Rafael D.; Vionette-Amaral, Raquel J.; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A.; Minx, Patrick; Spieth, John; Carvalho, A. Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, André Q.; Ribeiro, Jose M. C.; Sorgine, Marcos H. F.; Waterhouse, Robert M.; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R.; Araujo, Helena M.; Aravind, L.; Atella, Georgia C.; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R.; Braz, Gloria R. C.; Calderón-Fernández, Gustavo; Carareto, Claudia M. A.; Christensen, Mikkel B.; Costa, Igor R.; Costa, Samara G.; Dansa, Marilvia; Daumas-Filho, Carlos R. O.; De-Paula, Iron F.; Dias, Felipe A.; Dimopoulos, George; Emrich, Scott J.; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D.; da Fonseca, Rodrigo N.; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A.; Gandara, Ana Caroline; Garcia, Eloi S.; Genta, Fernando A.; Giraldo-Calderón, Gloria I.; Gomes, Bruno; Gondim, Katia C.; Granzotto, Adriana; Guarneri, Alessandra A.; Guigó, Roderic; Harry, Myriam; Hughes, Daniel S. T.; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juárez, M. Patricia; Koerich, Leonardo B.; Lange, Angela B.; Latorre-Estivalis, José Manuel; Lavore, Andrés; Lawrence, Gena G.; Lazoski, Cristiano; Lazzari, Claudio R.; Lopes, Raphael R.; Lorenzo, Marcelo G.; Lugon, Magda D.; Marcet, Paula L.; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G.; Nouzova, Marcela; Nunes, Rodrigo D.; Oliveira, Raquel L. L.; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O.; Pascual, Agustina; Pavan, Marcio G.; Pedrini, Nicolás; Peixoto, Alexandre A.; Pereira, Marcos H.; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M.; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S.; Silva-Cardoso, Livia; Silva-Neto, Mario A. C.; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L.; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M. C.; Ursic-Bedoya, Raul; Venancio, Thiago M.; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C.; Wilson, Richard K.; Huebner, Erwin; Dotson, Ellen M.; Oliveira, Pedro L.

    2015-01-01

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. PMID:26627243

  10. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host.

    Science.gov (United States)

    Leontovyč, Roman; Young, Neil D; Korhonen, Pasi K; Hall, Ross S; Tan, Patrick; Mikeš, Libor; Kašný, Martin; Horák, Petr; Gasser, Robin B

    2016-02-01

    To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes) of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts' immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula) of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation), peptidases (cathepsins) and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes.

  11. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host.

    Directory of Open Access Journals (Sweden)

    Roman Leontovyč

    2016-02-01

    Full Text Available To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts' immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation, peptidases (cathepsins and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes.

  12. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

    Directory of Open Access Journals (Sweden)

    Ana Carolina Vieira Araujo

    2016-10-01

    Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

  13. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.

    Directory of Open Access Journals (Sweden)

    Giuseppina Rea

    Full Text Available Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues

  14. Decoding Complex Cognitive States Online by Manifold Regularization in Real-Time fMRI

    DEFF Research Database (Denmark)

    Hansen, Toke Jansen; Hansen, Lars Kai; Madsen, Kristoffer Hougaard

    2011-01-01

    Human decision making is complex and influenced by many factors on multiple time scales, reflected in the numerous brain networks and connectivity patterns involved as revealed by fMRI. We address mislabeling issues in paradigms involving complex cognition, by considering a manifold regularizing...... prior for modeling a sequence of neural events leading to a decision. The method is directly applicable for online learning in the context of real-time fMRI, and our experimental results show that the method can efficiently avoid model degeneracy caused by mislabeling....

  15. Characterization of VuMATE1 expression in response to iron nutrition and aluminum stress reveals adaptation of rice bean (Vigna umbellata to acid soils through cis regulation

    Directory of Open Access Journals (Sweden)

    Meiya eLiu

    2016-04-01

    Full Text Available Rice bean (Vigna umbellata VuMATE1 appears to be constitutively expressed at vascular system but root apex, and Al stress extends its expression to root apex. Whether VuMATE1 participates in both Al tolerance and Fe nutrition, and how VuMATE1 expression is regulated is of great interest. In this study, the role of VuMATE1 in Fe nutrition was characterized through in planta complementation assays. The transcriptional regulation of VuMATE1 was investigated through promoter analysis and promoter-GUS reporter assays. The results showed that the expression of VuMATE1 was regulated by Al stress but not Fe status. Complementation of frd3-1 with VuMATE1 under VuMATE1 promoter could not restore phenotype, but restored with 35SCaMV promoter. Immunostaining of VuMATE1 revealed abnormal localization of VuMATE1 in vasculature. In planta GUS reporter assay identified Al-responsive cis-acting elements resided between -1228 and -574 bp. Promoter analysis revealed several cis-acting elements, but transcription is not simply regulated by one of these elements. We demonstrated that cis regulation of VuMATE1 expression is involved in Al tolerance mechanism, while not involved in Fe nutrition. These results reveal the evolution of VuMATE1 expression for better adaptation of rice bean to acidic soils where Al stress imposed but Fe deficiency pressure released.

  16. Embedded sparse representation of fMRI data via group-wise dictionary optimization

    Science.gov (United States)

    Zhu, Dajiang; Lin, Binbin; Faskowitz, Joshua; Ye, Jieping; Thompson, Paul M.

    2016-03-01

    Sparse learning enables dimension reduction and efficient modeling of high dimensional signals and images, but it may need to be tailored to best suit specific applications and datasets. Here we used sparse learning to efficiently represent functional magnetic resonance imaging (fMRI) data from the human brain. We propose a novel embedded sparse representation (ESR), to identify the most consistent dictionary atoms across different brain datasets via an iterative group-wise dictionary optimization procedure. In this framework, we introduced additional criteria to make the learned dictionary atoms more consistent across different subjects. We successfully identified four common dictionary atoms that follow the external task stimuli with very high accuracy. After projecting the corresponding coefficient vectors back into the 3-D brain volume space, the spatial patterns are also consistent with traditional fMRI analysis results. Our framework reveals common features of brain activation in a population, as a new, efficient fMRI analysis method.

  17. Inner experience in the scanner: Can high fidelity apprehensions of inner experience be integrated with fMRI?

    Directory of Open Access Journals (Sweden)

    Simone eKühn

    2014-12-01

    Full Text Available To provide full accounts of human experience and behavior, research in cognitive neuroscience must be linked to inner experience, but introspective reports of inner experience have often been found to be unreliable. The present case study aimed at providing proof of principle that introspection using one method, Descriptive Experience Sampling (DES, can be reliably integrated with fMRI. A participant was trained in the DES method, followed by nine sessions of sampling within an MRI scanner. During moments where the DES interview revealed ongoing inner speaking, fMRI data reliably showed activation in classic speech processing areas including left inferior frontal gyrus. Further, the fMRI data validated the participant’s DES observations of the experiential distinction between inner speaking and innerly hearing her own voice. These results highlight the precision and validity of the DES method as a technique of exploring inner experience and the utility of combining such methods with fMRI.

  18. Genus-Wide Comparative Genome Analyses of Colletotrichum Species Reveal Specific Gene Family Losses and Gains during Adaptation to Specific Infection Lifestyles.

    Science.gov (United States)

    Gan, Pamela; Narusaka, Mari; Kumakura, Naoyoshi; Tsushima, Ayako; Takano, Yoshitaka; Narusaka, Yoshihiro; Shirasu, Ken

    2016-05-22

    Members from Colletotrichum genus adopt a diverse range of lifestyles during infection of plants and represent a group of agriculturally devastating pathogens. In this study, we present the draft genome of Colletotrichum incanum from the spaethianum clade of Colletotrichum and the comparative analyses with five other Colletotrichum species from distinct lineages. We show that the C. incanum strain, originally isolated from Japanese daikon radish, is able to infect both eudicot plants, such as certain ecotypes of the eudicot Arabidopsis, and monocot plants, such as lily. Being closely related to Colletotrichum species both in the graminicola clade, whose members are restricted strictly to monocot hosts, and to the destructivum clade, whose members are mostly associated with dicot infections, C. incanum provides an interesting model system for comparative genomics to study how fungal pathogens adapt to monocot and dicot hosts. Genus-wide comparative genome analyses reveal that Colletotrichum species have tailored profiles of their carbohydrate-degrading enzymes according to their infection lifestyles. In addition, we show evidence that positive selection acting on secreted and nuclear localized proteins that are highly conserved may be important in adaptation to specific hosts or ecological niches. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-Western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus; Perrea, Toula; Zhou, Yanfeng

    2011-01-01

    lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument...... values, attitudes and purchase behaviour, using frequency of consumption of pork products as an example. Three consumer segments were identified: concerned, uninvolved and traditional. This pattern replicates partly those identified in Western cultures. Moreover, all three segments showed consistent...... value-attitude-behaviour profiles. The results also suggest which dimensions may be missing in the instrument in a more comprehensive instrument adapted to Chinese conditions, most notably a broader treatment of eating out activities....

  20. Monkey cortex through fMRI glasses.

    Science.gov (United States)

    Vanduffel, Wim; Zhu, Qi; Orban, Guy A

    2014-08-06

    In 1998 several groups reported the feasibility of fMRI experiments in monkeys, with the goal to bridge the gap between invasive nonhuman primate studies and human functional imaging. These studies yielded critical insights in the neuronal underpinnings of the BOLD signal. Furthermore, the technology has been successful in guiding electrophysiological recordings and identifying focal perturbation targets. Finally, invaluable information was obtained concerning human brain evolution. We here provide a comprehensive overview of awake monkey fMRI studies mainly confined to the visual system. We review the latest insights about the topographic organization of monkey visual cortex and discuss the spatial relationships between retinotopy and category- and feature-selective clusters. We briefly discuss the functional layout of parietal and frontal cortex and continue with a summary of some fascinating functional and effective connectivity studies. Finally, we review recent comparative fMRI experiments and speculate about the future of nonhuman primate imaging.

  1. Abnormal auditory sensory gating-out in first-episode and never-medicated paranoid schizophrenia patients: an fMRI study.

    Science.gov (United States)

    Ji, Bin; Mei, Wei; Zhang, John X; Jing, Juzhen; Wu, Qiulin; Zhuo, Yongning; Xiao, Zhuangwei

    2013-08-01

    Numerous electrophysiological studies have showed auditory sensory gating-out abnormalities in chronic schizophrenia with antipsychotic medication. Previous research has used functional magnetic resonance imaging (fMRI) with excellent spatial resolution to identify the neural substrates of sensory gating-out deficits revealing increased hemodynamic response in the hippocampus, thalamus and prefrontal cortex. However, such results obtained from medicated patients may be confounded by antipsychotic medication. The present study scanned 15 first-episode schizophrenia patients not yet receiving any medical treatment and 15 healthy controls matched in gender, age and education when they performed a sensory gating-out task adapted for fMRI. The symptoms of the patients were assessed with the positive and negative syndrome scale. Different from previous findings, the schizophrenia patients showed decreased activation in hippocampus and thalamus during sensory gating-out, compared with the normal controls. The results support the theory attributing abnormal sensory gating-out in schizophrenia patients to the dysfunction of hippocampus and thalamus.

  2. Resting state FMRI research in child psychiatric disorders

    NARCIS (Netherlands)

    Oldehinkel, M.; Francx, W.; Beckmann, C.F.; Buitelaar, J.K.; Mennes, M.

    2013-01-01

    Concurring with the shift from linking functions to specific brain areas towards studying network integration, resting state FMRI (R-FMRI) has become an important tool for delineating the functional network architecture of the brain. Fueled by straightforward data collection, R-FMRI analysis methods

  3. Resting state FMRI research in child psychiatric disorders

    NARCIS (Netherlands)

    Oldehinkel, Marianne; Francx, Winke; Beckmann, Christian; Buitelaar, Jan K.; Mennes, Maarten

    2013-01-01

    Concurring with the shift from linking functions to specific brain areas towards studying network integration, resting state FMRI (R-FMRI) has become an important tool for delineating the functional network architecture of the brain. Fueled by straightforward data collection, R-FMRI analysis methods

  4. Learning and generalization under ambiguity: an fMRI study.

    Directory of Open Access Journals (Sweden)

    J R Chumbley

    2012-01-01

    Full Text Available Adaptive behavior often exploits generalizations from past experience by applying them judiciously in new situations. This requires a means of quantifying the relative importance of prior experience and current information, so they can be balanced optimally. In this study, we ask whether the brain generalizes in an optimal way. Specifically, we used Bayesian learning theory and fMRI to test whether neuronal responses reflect context-sensitive changes in ambiguity or uncertainty about experience-dependent beliefs. We found that the hippocampus expresses clear ambiguity-dependent responses that are associated with an augmented rate of learning. These findings suggest candidate neuronal systems that may be involved in aberrations of generalization, such as over-confidence.

  5. Finding multivariate outliers in fMRI time-series data.

    Science.gov (United States)

    Magnotti, John F; Billor, Nedret

    2014-10-01

    A fundamental challenge for researchers studying the brain is to explain how distributed patterns of brain activity relate to a specific representation or computation. Multivariate techniques are therefore becoming increasingly popular for pattern localization of functional magnetic resonance imaging (fMRI) data. The increased power of these techniques can be offset by their susceptibility to multivariate outliers, a problem not directly encountered when fMRI data are analyzed in more common univariate analysis techniques. We test how two algorithms, High Dimensional Blocked Adaptive Computationally Efficient Outlier Nominators (HD BACON) and Principal Component based Outlier detection (PCOut), can detect multivariate outliers in high-dimensional fMRI data, in which the number of variables is larger than the number of observations. We show how these methods can be applied to individual, voxel time-series to identify outlying voxels within a region of interest. Finally, we compare these methods with simulated data to identify which aspects of the data each method is most sensitive to. Voxels identified by both algorithms were primarily on the edges of univariate activation clusters and near the boundaries between different tissue types. Simulation results showed the PCOut outperformed HD BACON, maintaining both high sensitivity and specificity across a wide range of outlier contamination percentages. Our results suggest that multivariate analysis of fMRI can benefit from including multivariate outlier detection as a routine data quality check prior to model fitting. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

    Directory of Open Access Journals (Sweden)

    Sang Hu Kim

    2015-11-01

    Full Text Available The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1 with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from

  7. On clustering fMRI time series

    DEFF Research Database (Denmark)

    Goutte, Cyril; Toft, Peter Aundal; Rostrup, E.

    1999-01-01

    Analysis of fMRI time series is often performed by extracting one or more parameters for the individual voxels. Methods based, e.g., on various statistical tests are then used to yield parameters corresponding to probability of activation or activation strength. However, these methods do...

  8. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  9. Explorations of Object and Location Memory using fMRI

    Directory of Open Access Journals (Sweden)

    Antony D Passaro

    2013-08-01

    Full Text Available Content-specific sub-systems of visual working memory (VWM have been explored in many neuroimaging studies with inconsistent findings and procedures across experiments. The present study employed functional magnetic resonance imaging (fMRI and a change detection task using a high number of trials and matched stimulus displays across object and location change ("what" vs "where" conditions. Furthermore, individual task periods were studied independently across conditions to identify period-specific differences. Importantly, this combination of task controls has not previously been described in the fMRI literature. Composite results revealed differential frontoparietal activation during each task period. A separation of object and location conditions yielded a distributed system of dorsal and ventral streams during the encoding of information corresponding to bilateral inferior parietal lobule (IPL and lingual gyrus activation, respectively. Differential activity was also shown during the maintenance of information in middle frontal structures bilaterally for objects and the right IPL and left insula for locations. Together, these results reflect a domain-specific dissociation spanning several cortices and task periods. Furthermore, differential activations suggest a general caudal-rostral separation corresponding to object and location memory, respectively.

  10. Global analysis of the transcriptional response of whitefly to tomato yellow leaf curl China virus reveals the relationship of coevolved adaptations.

    Science.gov (United States)

    Luan, Jun-Bo; Li, Jun-Min; Varela, Nélia; Wang, Yong-Liang; Li, Fang-Fang; Bao, Yan-Yuan; Zhang, Chuan-Xi; Liu, Shu-Sheng; Wang, Xiao-Wei

    2011-04-01

    The begomoviruses are the largest and most economically important group of plant viruses transmitted exclusively by the whitefly Bemisia tabaci in a circulative, persistent manner. The circulation of the viruses within the insect vectors involves complex interactions between virus and vector components; however, the molecular mechanisms of these interactions remain largely unknown. Here we investigated the transcriptional response of the invasive B. tabaci Middle East-Asia Minor 1 species to Tomato yellow leaf curl China virus (TYLCCNV) using Illumina sequencing technology. Results showed that 1,606 genes involved in 157 biochemical pathways were differentially expressed in the viruliferous whiteflies. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that TYLCCNV can perturb the cell cycle and primary metabolism in the whitefly, which explains the negative effect of this virus on the longevity and fecundity of B. tabaci. Our data also demonstrated that TYLCCNV can activate whitefly immune responses, such as autophagy and antimicrobial peptide production, which might lead to a gradual decrease of viral particles within the body of the viruliferous whitefly. Furthermore, PCR results showed that TYLCCNV can invade the ovary and fat body tissues of the whitefly, and Lysotracker and Western blot analyses revealed that the invasion of TYLCCNV induced autophagy in both the ovary and fat body tissues. Surprisingly, TYLCCNV also suppressed the whitefly immune responses by downregulating the expression of genes involved in Toll-like signaling and mitogen-activated protein kinase (MAPK) pathways. Taken together, these results reveal the relationship of coevolved adaptations between begomoviruses and whiteflies and will provide a road map for future investigations into the complex interactions between plant viruses and their insect vectors.

  11. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-Western cultural environments? Its adaptation and application in urban China.

    Science.gov (United States)

    Grunert, Klaus G; Perrea, Toula; Zhou, Yanfeng; Huang, Guang; Sørensen, Bjarne T; Krystallis, Athanasios

    2011-04-01

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the food related lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument, in which a number of dimensions of the original instrument had to be omitted. This revised instrument was tested for statistical robustness and used as a basis for the derivation of consumer segments. Construct validity of the instrument was then investigated by profiling the segments in terms of consumer values, attitudes and purchase behaviour, using frequency of consumption of pork products as an example. Three consumer segments were identified: concerned, uninvolved and traditional. This pattern replicates partly those identified in Western cultures. Moreover, all three segments showed consistent value-attitude-behaviour profiles. The results also suggest which dimensions may be missing in the instrument in a more comprehensive instrument adapted to Chinese conditions, most notably a broader treatment of eating out activities.

  12. A least angle regression method for fMRI activation detection in phase-encoded experimental designs.

    Science.gov (United States)

    Li, Xingfeng; Coyle, Damien; Maguire, Liam; McGinnity, Thomas M; Watson, David R; Benali, Habib

    2010-10-01

    This paper presents a new regression method for functional magnetic resonance imaging (fMRI) activation detection. Unlike general linear models (GLM), this method is based on selecting models for activation detection adaptively which overcomes the limitation of requiring a predefined design matrix in GLM. This limitation is because GLM designs assume that the response of the neuron populations will be the same for the same stimuli, which is often not the case. In this work, the fMRI hemodynamic response model is selected from a series of models constructed online by the least angle regression (LARS) method. The slow drift terms in the design matrix for the activation detection are determined adaptively according to the fMRI response in order to achieve the best fit for each fMRI response. The LARS method is then applied along with the Moore-Penrose pseudoinverse (PINV) and fast orthogonal search (FOS) algorithm for implementation of the selected model to include the drift effects in the design matrix. Comparisons with GLM were made using 11 normal subjects to test method superiority. This paper found that GLM with fixed design matrix was inferior compared to the described LARS method for fMRI activation detection in a phased-encoded experimental design. In addition, the proposed method has the advantage of increasing the degrees of freedom in the regression analysis. We conclude that the method described provides a new and novel approach to the detection of fMRI activation which is better than GLM based analyses.

  13. The effect of ageing on fMRI: Correction for the confounding effects of vascular reactivity evaluated by joint fMRI and MEG in 335 adults

    Science.gov (United States)

    Henson, Richard N. A.; Tyler, Lorraine K.; Davis, Simon W.; Shafto, Meredith A.; Taylor, Jason R.; Williams, Nitin; Cam‐CAN; Rowe, James B.

    2015-01-01

    Abstract In functional magnetic resonance imaging (fMRI) research one is typically interested in neural activity. However, the blood‐oxygenation level‐dependent (BOLD) signal is a composite of both neural and vascular activity. As factors such as age or medication may alter vascular function, it is essential to account for changes in neurovascular coupling when investigating neurocognitive functioning with fMRI. The resting‐state fluctuation amplitude (RSFA) in the fMRI signal (rsfMRI) has been proposed as an index of vascular reactivity. The RSFA compares favourably with other techniques such as breath‐hold and hypercapnia, but the latter are more difficult to perform in some populations, such as older adults. The RSFA is therefore a candidate for use in adjusting for age‐related changes in vascular reactivity in fMRI studies. The use of RSFA is predicated on its sensitivity to vascular rather than neural factors; however, the extent to which each of these factors contributes to RSFA remains to be characterized. The present work addressed these issues by comparing RSFA (i.e., rsfMRI variability) to proxy measures of (i) cardiovascular function in terms of heart rate (HR) and heart rate variability (HRV) and (ii) neural activity in terms of resting state magnetoencephalography (rsMEG). We derived summary scores of RSFA, a sensorimotor task BOLD activation, cardiovascular function and rsMEG variability for 335 healthy older adults in the population‐based Cambridge Centre for Ageing and Neuroscience cohort (Cam‐CAN; www.cam-can.com). Mediation analysis revealed that the effects of ageing on RSFA were significantly mediated by vascular factors, but importantly not by the variability in neuronal activity. Furthermore, the converse effects of ageing on the rsMEG variability were not mediated by vascular factors. We then examined the effect of RSFA scaling of task‐based BOLD in the sensorimotor task. The scaling analysis revealed that much of the effects

  14. Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques.

    Science.gov (United States)

    Lamers, Susanna L; Nolan, David J; Rife, Brittany D; Fogel, Gary B; McGrath, Michael S; Burdo, Tricia H; Autissier, Patrick; Williams, Kenneth C; Goodenow, Maureen M; Salemi, Marco

    2015-08-01

    evolutionary patterns in the gp120 and nef genes leading to the emergence of host-specific viral populations and potentially linked to disease progression. Although each macaque exhibited unique immune profiles, macaque-specific nef sequences evolving under selection were consistently detected in plasma samples at 3 months postinfection, significantly earlier than in gp120 macaque-specific sequences. On the other hand, nef sequences in brain tissues, collected at necropsy of two animals with detectable infection in the central nervous system (CNS), revealed convergent evolution. The results not only indicate that early adaptation of nef in the new host may be essential for successful infection, but also suggest that specific nef variants may be required for SIV to efficiently invade CNS macrophages and/or enhance macrophage migration, resulting in HIV neuropathology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Genome-wide mRNA expression analysis of hepatic adaptation to high-fat diets reveals switch from an inflammatory to steatotic transcriptional program.

    Directory of Open Access Journals (Sweden)

    Marijana Radonjic

    Full Text Available BACKGROUND: Excessive exposure to dietary fats is an important factor in the initiation of obesity and metabolic syndrome associated pathologies. The cellular processes associated with the onset and progression of diet-induced metabolic syndrome are insufficiently understood. PRINCIPAL FINDINGS: To identify the mechanisms underlying the pathological changes associated with short and long-term exposure to excess dietary fat, hepatic gene expression of ApoE3Leiden mice fed chow and two types of high-fat (HF diets was monitored using microarrays during a 16-week period. A functional characterization of 1663 HF-responsive genes reveals perturbations in lipid, cholesterol and oxidative metabolism, immune and inflammatory responses and stress-related pathways. The major changes in gene expression take place during the early (day 3 and late (week 12 phases of HF feeding. This is also associated with characteristic opposite regulation of many HF-affected pathways between these two phases. The most prominent switch occurs in the expression of inflammatory/immune pathways (early activation, late repression and lipogenic/adipogenic pathways (early repression, late activation. Transcriptional network analysis identifies NF-kappaB, NEMO, Akt, PPARgamma and SREBP1 as the key controllers of these processes and suggests that direct regulatory interactions between these factors may govern the transition from early (stressed, inflammatory to late (pathological, steatotic hepatic adaptation to HF feeding. This transition observed by hepatic gene expression analysis is confirmed by expression of inflammatory proteins in plasma and the late increase in hepatic triglyceride content. In addition, the genes most predictive of fat accumulation in liver during 16-week high-fat feeding period are uncovered by regression analysis of hepatic gene expression and triglyceride levels. CONCLUSIONS: The transition from an inflammatory to a steatotic transcriptional program

  16. Genotypic Variation in Growth and Physiological Response to Drought Stress and Re-Watering Reveals the Critical Role of Recovery in Drought Adaptation in Maize Seedlings

    OpenAIRE

    Chen, Daoqian; Wang, Shiwen; Cao, Beibei; Cao, Dan; Leng, Guohui; Li, Hongbing; Yin, Lina; Shan, Lun; Deng, Xiping

    2016-01-01

    Non-irrigated crops in temperate climates and irrigated crops in arid climates are subjected to continuous cycles of water stress and re-watering. Thus, fast and efficient recovery from water stress may be among the key determinants of plant drought adaptation. The present study was designed to comparatively analyze the roles of drought resistance and drought recovery in drought adaptation and to investigate the physiological basis of genotypic variation in drought adaptation in maize (Zea ma...

  17. Genotypic variation in growth and physiological response to drought stress and re-watering reveals the critical role of recovery in drought adaptation in maize seedlings

    OpenAIRE

    Daoqian eChen; Shiwen eWang; Beibei eCao; Dan eCao; Guohui eLeng; Hongbing eLi; Lina eYin; Lun eShan; Xiping eDeng

    2016-01-01

    Non-irrigated crops in temperate climates and irrigated crops in arid climates are subjected to continuous cycles of water stress and re-watering. Thus, fast and efficient recovery from water stress may be among the key determinants of plant drought adaptation. The present study was designed to comparatively analyze the roles of drought resistance and drought recovery in drought adaptation and to investigate the physiological basis of genotypic variation in drought adaptation in maize (Zea ma...

  18. Hemispheric preference in visuospatial processing: a complementary approach with fMRI and lesion studies.

    Science.gov (United States)

    Ng, V W; Eslinger, P J; Williams, S C; Brammer, M J; Bullmore, E T; Andrew, C M; Suckling, J; Morris, R G; Benton, A L

    2000-06-01

    Historically, the left cerebral hemisphere has been considered specialized for language, whereas the right cerebral hemisphere is aligned with spatial processes. However, studies have called into question adherence to this model and suggested that both hemispheres participate in language and spatial cognition. Using functional Magnetic Resonance Imaging (fMRI) and human brain lesion studies, we determined whether these complementary techniques could clarify issues of hemispheric dominance. Using a modified Benton Judgement of Line Orientation (JLO) test, considered a relatively pure spatial processing task, we found robust and significant (p < 0.0005) bilateral superior parietal lobe activation on fMRI in ten right-handed male adult volunteers. This was corroborated by lesion data in a cohort of 17 patients who showed significant JLO impairments after either right or left parietal lobe damage, with right parietal damage associated with somewhat more severe deficit. Detailed wavelet analysis of the fMRI time-series did, however, reveal a more dominant role of the right parietal lobe in "kick-starting" the task. To our knowledge, this is a novel way of using fMRI to address functional hemispheric differences in a cognitive task that is known to have bilateral representation.

  19. Functional Imaging of Broca’s Area in Native Persian Speakers: An fMRI Study

    Directory of Open Access Journals (Sweden)

    A Mahdavi

    2008-12-01

    Full Text Available Background/Objective: The problem of localization of speech associated cortices using noninvasive methods has been of utmost importance in many neuroimaging studies, but the results are difficult to resolve for specific neurosurgical applications. In this study, we used fMRI to delineate language-related brain activation patterns with emphasis on the Broca's area during the execution of two Persian language tasks."nPatients and Methods: The subjects comprised of nine healthy right-handed men who participated voluntarily in this study. They performed two consequent fMRI paradigms namely; "Word Production" and "Reverse Word Reading". The fMRI data were collected and analyzed. Then, functional images were registered to anatomical images using FSL software. The laterality indices were also calculated in regions of interest with different threshold levels."nResults: The results indicate that Broca's area, as the classical language-production center, was robustly activated while performing these two tasks. In eight out of nine subjects, the left hemisphere dominancy and Broca's area activation were observed and in one case activation was prominent in the homologous area in the right hemisphere."nConclusion: Similar pattern of cortical activation during Persian word production and Anglophone languages such as English was revealed. fMRI is a valuable means for brain mapping in language studies.

  20. Crystal structure of the Bacillus anthracis nucleoside diphosphate kinase and its characterization reveals an enzyme adapted to perform under stress conditions.

    Science.gov (United States)

    Misra, Gauri; Aggarwal, Anita; Dube, Divya; Zaman, Mohd Saif; Singh, Yogendra; Ramachandran, Ravishankar

    2009-08-01

    Nucleoside diphosphate kinases (Ndks) play an important role in a plethora of regulatory and metabolic functions. Inhibition of the B. anthracis Ndk mRNA results in the formation of nonviable aberrant spores. We report the characterization and crystal structure of the enzyme from B. anthracis nucleoside diphosphate kinase (BaNdk), the first from sporulating bacteria. The enzyme, although from a mesophilic source, is active at extremes of pH (3.5-10.5), temperature (10-95 degrees C) and ionic strength (0.25-4.0M NaCl). It exists as a hexamer that is composed of two SDS-stable trimers interacting in a back-to-back association; mutational analysis confirms that the enzyme is a histidine kinase. The high-resolution crystal structure reported here reveals an unanticipated change in the conformation of residues between 43 and 63 that also regulates substrate entry in other Ndks. A comparative structural analysis involving Ndks from seven mesophiles and three thermophiles has resulted in the delineation of the structure into relatively rigid and flexible regions. The analysis suggests that the larger number of intramolecular hydrogen bonds and to a lesser extent ionic interactions in BaNdk contributes to its high thermostability. Mutational analysis and Molecular Dynamics simulations were used to probe the role of a highly conserved Gly19 (present at the oligomeric interface in most of the Ndks). The results suggest that the mutation leads to a rigidification of those residues that facilitate substrate entry and consequently leads to a large reduction in the kinase activity. Overall, the enzyme characterization helps to understand its apparent adaptation to perform under stress conditions.

  1. Pharmacological fMRI; a clinical exploration

    OpenAIRE

    Goekoop, R.

    2006-01-01

    Dit proefschrift beschrijft de resultaten van een verkennend onderzoek naar een nieuwe techniek die gebruikt kan worden om de effecten van geneesmiddelen op hersenaktiviteit af te beelden: pharmacologische functionele magnetic resonance imaging (farmacologische fMRI of phMRI). Met behulp van deze techniek werden de effecten onderzocht van drie verschillende medicijnen (de bètablokker propranolol, de selectieve oestrogeen-receptor modulator (SERM) raloxifene en de cholinesteraseremmer galantam...

  2. Behavior, neuropsychology and fMRI.

    Science.gov (United States)

    Bennett, Maxwell R; Hatton, Sean; Hermens, Daniel F; Lagopoulos, Jim

    Cognitive neuroscientists in the late 20th century began the task of identifying the part(s) of the brain concerned with normal behavior as manifest in the psychological capacities as affective powers, reasoning, behaving purposively and the pursuit of goals, following introduction of the 'functional magnetic resonance imaging' (fMRI) method for identifying brain activity. For this research program to be successful two questions require satisfactory answers. First, as the fMRI method can currently only be used on stationary subjects, to what extent can neuropsychological tests applicable to such stationary subjects be correlated with normal behavior. Second, to what extent can correlations between the various neuropsychological tests on the one hand, and sites of brain activity determined with fMRI on the other, be regarded as established. The extent to which these questions have yet received satisfactory answers is reviewed, and suggestions made both for improving correlations of neuropsychological tests with behavior as well as with the results of fMRI-based observations. Copyright © 2016. Published by Elsevier Ltd.

  3. Quantitative fMRI and oxidative neuroenergetics.

    Science.gov (United States)

    Hyder, Fahmeed; Rothman, Douglas L

    2012-08-15

    The discovery of functional magnetic resonance imaging (fMRI) has greatly impacted neuroscience. The blood oxygenation level-dependent (BOLD) signal, using deoxyhemoglobin as an endogenous paramagnetic contrast agent, exposes regions of interest in task-based and resting-state paradigms. However the BOLD contrast is at best a partial measure of neuronal activity, because the functional maps obtained by differencing or correlations ignore the total neuronal activity in the baseline state. Here we describe how studies of brain energy metabolism at Yale, especially with (13)C magnetic resonance spectroscopy and related techniques, contributed to development of quantitative functional brain imaging with fMRI by providing a reliable measurement of baseline energy. This narrative takes us on a journey, from molecules to mind, with illuminating insights about neuronal-glial activities in relation to energy demand of synaptic activity. These results, along with key contributions from laboratories worldwide, comprise the energetic basis for quantitative interpretation of fMRI data. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. A new method for FMRI activation detection

    Science.gov (United States)

    Wei, Jianing; Talavage, Thomas M.; Pollak, Ilya

    2009-02-01

    The objective of fMRI data analysis is to detect the region of the brain that gets activated in response to a specific stimulus presented to the subject. We develop a new algorithm for activation detection in event-related fMRI data. We utilize a forward model for fMRI data acquisition which explicitly incorporates physiological noise, scanner noise and the spatial blurring introduced by the scanner. After slice-by-slice image restoration procedure that independently restores each data slice corresponding to each time index, we estimate the parameters of the hemodynamic response function (HRF) model for each pixel of the restored data. In order to enforce spatial regularity in our estimates, we model the prior distribution of the HRF parameters as a generalized Gaussian Markov random field (GGMRF) model. We develop an algorithm to compute the maximum a posteriori (MAP) estimates of the parameters. We then threshold the amplitude parameters to obtain the final activation map. We illustrate our algorithm by comparing it with the widely used general linear model (GLM) method. In synthetic data experiments, under the same probability of false alarm, the probability of correct detection for our method is up to 15% higher than GLM. In real data experiments, through anatomical analysis and benchmark testing using block paradigm results, we demonstrate that our algorithm produces fewer false alarms than GLM.

  5. Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test

    Directory of Open Access Journals (Sweden)

    Berlin Sofia

    2005-11-01

    Full Text Available Abstract Background Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC, which has been previously shown by the use of likelihood ratio tests (LRTs to be under positive selection in mammals. Results We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8. The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. Conclusion We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.

  6. A Review of fMRI as a Tool for Enhancing Eeg-Based Brain-Machine Interfaces

    Directory of Open Access Journals (Sweden)

    Luis J. Barrios

    2012-01-01

    Full Text Available Human-robot interaction has been going stronger and stronger, up to find a notorious level on brain-machines interfaces. This assistive technology offers a great hope for patients suffering severe neuromuscular disorders. Starting from the current limitations hindering its extensive application outside the research laboratories, this paper reviews findings and prospects on functional magnetic resonance imaging showing how fMRI can help to overcome those limitations, while playing a key role on improving the development of brain-machine interfaces based on electroencephalography. The different types of derived benefits for this interfaces, as well as the different kinds of impact on their components, are presented under a field classification that reveals the distinctive roles that fMRI can play on the present context. The review concludes that fMRI provides complementary knowledge of immediate application, and that a greater profit could be obtained from the own EEG signal by integrating both neuroimaging modalities.

  7. Cerebral correlates of heart rate variations during a spontaneous panic attack in the fMRI scanner.

    Science.gov (United States)

    Spiegelhalder, Kai; Hornyak, Magdolna; Kyle, Simon David; Paul, Dominik; Blechert, Jens; Seifritz, Erich; Hennig, Jürgen; Tebartz van Elst, Ludger; Riemann, Dieter; Feige, Bernd

    2009-12-01

    We report the first published case study of a suddenly occurring panic attack in a patient with no prior history of panic disorder during combined functional magnetic resonance imaging (fMRI, 1.5 Tesla) and electrocardiogram (ECG) recording. The single case was a 46-year-old woman who developed a panic attack near the planned end of the fMRI acquisition session, which therefore had to be aborted. Correlational analysis of heart rate fluctuations and fMRI data revealed a significant negative association in the left middle temporal gyrus. Additionally, regions-of-interest (ROI) analyses indicated significant positive associations in the left amygdala, and trends towards significance in the right amygdala and left insula.

  8. QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici.

    Science.gov (United States)

    Lendenmann, M H; Croll, D; Palma-Guerrero, J; Stewart, E L; McDonald, B A

    2016-04-01

    Different thermal environments impose strong, differential selection on populations, leading to local adaptation, but the genetic basis of thermal adaptation is poorly understood. We used quantitative trait locus (QTL) mapping in the fungal wheat pathogen Zymoseptoria tritici to study the genetic architecture of thermal adaptation and identify candidate genes. Four wild-type strains originating from the same thermal environment were crossed to generate two mapping populations with 263 (cross 1) and 261 (cross 2) progeny. Restriction site-associated DNA sequencing was used to genotype 9745 (cross 1) and 7333 (cross 2) single-nucleotide polymorphism markers segregating within the mapping population. Temperature sensitivity was assessed using digital image analysis of colonies growing at two different temperatures. We identified four QTLs for temperature sensitivity, with unique QTLs found in each cross. One QTL had a logarithm of odds score >11 and contained only six candidate genes, including PBS2, encoding a mitogen-activated protein kinase kinase associated with low temperature tolerance in Saccharomyces cerevisiae. This and other QTLs showed evidence for pleiotropy among growth rate, melanization and growth morphology, suggesting that many traits can be correlated with thermal adaptation in fungi. Higher temperatures were highly correlated with a shift to filamentous growth among the progeny in both crosses. We show that thermal adaptation has a complex genetic architecture, with natural populations of Z. tritici harboring significant genetic variation for this trait. We conclude that Z. tritici populations have the potential to adapt rapidly to climate change and expand into new climatic zones.

  9. Graph-based inter-subject pattern analysis of FMRI data.

    Directory of Open Access Journals (Sweden)

    Sylvain Takerkart

    Full Text Available In brain imaging, solving learning problems in multi-subjects settings is difficult because of the differences that exist across individuals. Here we introduce a novel classification framework based on group-invariant graphical representations, allowing to overcome the inter-subject variability present in functional magnetic resonance imaging (fMRI data and to perform multivariate pattern analysis across subjects. Our contribution is twofold: first, we propose an unsupervised representation learning scheme that encodes all relevant characteristics of distributed fMRI patterns into attributed graphs; second, we introduce a custom-designed graph kernel that exploits all these characteristics and makes it possible to perform supervised learning (here, classification directly in graph space. The well-foundedness of our technique and the robustness of the performance to the parameter setting are demonstrated through inter-subject classification experiments conducted on both artificial data and a real fMRI experiment aimed at characterizing local cortical representations. Our results show that our framework produces accurate inter-subject predictions and that it outperforms a wide range of state-of-the-art vector- and parcel-based classification methods. Moreover, the genericity of our method makes it is easily adaptable to a wide range of potential applications. The dataset used in this study and an implementation of our framework are available at http://dx.doi.org/10.6084/m9.figshare.1086317.

  10. Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis.

    Science.gov (United States)

    Fallahi-Sichani, Mohammad; Moerke, Nathan J; Niepel, Mario; Zhang, Tinghu; Gray, Nathanael S; Sorger, Peter K

    2015-03-26

    Drugs that inhibit RAF/MEK signaling, such as vemurafenib, elicit profound but often temporary anti-tumor responses in patients with BRAF(V) (600E) melanoma. Adaptive responses to RAF/MEK inhibition occur on a timescale of hours to days, involve homeostatic responses that reactivate MAP kinase signaling and compensatory mitogenic pathways, and attenuate the anti-tumor effects of RAF/MEK inhibitors. We profile adaptive responses across a panel of melanoma cell lines using multiplex biochemical measurement, single-cell assays, and statistical modeling and show that adaptation involves at least six signaling cascades that act to reduce drug potency (IC50) and maximal effect (i.e., Emax ≪ 1). Among these cascades, we identify a role for JNK/c-Jun signaling in vemurafenib adaptation and show that RAF and JNK inhibitors synergize in cell killing. This arises because JNK inhibition prevents a subset of cells in a cycling population from becoming quiescent upon vemurafenib treatment, thereby reducing drug Emax. Our findings demonstrate the breadth and diversity of adaptive responses to RAF/MEK inhibition and a means to identify which steps in a signaling cascade are most predictive of phenotypic response.

  11. Decomposition of BOLD Activity into Tuned and Untuned Components Reveals Cohabitation of Stimulus and Choice Information in V1

    Directory of Open Access Journals (Sweden)

    Kyoung Whan Choe

    2012-10-01

    Full Text Available Recent studies on V1 report top-down modulation of input-driven responses of sensory neurons, implying that exogenous sensory drives and endogenous top-down drives jointly determine V1 responses. By measuring fMRI responses in conjunction with a classification task on ambiguous ring stimuli, we sought to understand how V1 carries out its encoding operation on afferent currents while being adaptively modulated by top-down currents associated with perceptual tasks. Population activity of V1, as in its raw eccentricity profiles, failed to resolve the threshold differences between the ring stimuli due to large moment-to-moment fluctuations. The analysis of variance indicated that stimulus-evoked responses explain only one-fifth of the total variance and fMRI responses were highly correlated among eccentricity-bins, implying that a substantial fraction of V1 responses fluctuate as a whole. This led us to decompose the raw fMRI responses into untuned and tuned components: average response across eccentricity-bins and residual responses from the average, respectively, the former varying only in time and the latter varying in both space and time. The tuned responses revealed the veridical encoding operation of V1 by readily distinguishing between the ring stimuli, which was impossible with the raw fMRI responses. In contrast, the untuned were correlated with two major aspects of choice behavior—inter-trial variability in response time and inter-subject variability in response bias. We propose that this cohabitation of stimulus and choice information in V1 indicates the presence of top-down exertion of gain modulation on the early processing stage by the high-tier stage that accumulates evidence for perceptual choices.

  12. fMRI and MEG in the study of typical and atypical cognitive development.

    Science.gov (United States)

    Taylor, M J; Donner, E J; Pang, E W

    2012-01-01

    The tremendous changes in brain structure over childhood are critical to the development of cognitive functions. Neuroimaging provides a means of linking these brain-behaviour relations, as task protocols can be adapted for use with young children to assess the development of cognitive functions in both typical and atypical populations. This paper reviews some of our research using magnetoencephalography (MEG) and functional MRI (fMRI) in the study of cognitive development, with a focus on frontal lobe functions. Working memory for complex abstract patterns showed clear development in terms of the recruitment of frontal regions, seen with fMRI, with indications of strategy differences across the age range, from 6 to 35 years of age. Right hippocampal involvement was also evident in these n-back tasks, demonstrating its involvement in recognition in simple working memory protocols. Children born very preterm (7 to 9 years of age) showed reduced fMRI activation particularly in the precuneus and right hippocampal regions relative to control children. In a large normative n-back study (n=90) with upright and inverted faces, MEG data also showed right hippocampal activation that was present across the age range; frontal sources were evident only from 10 years of age. Other studies have investigated the development of set shifting, an executive function that is often deficit in atypical populations. fMRI showed recruitment of frontal areas, including the insula, that have significantly different patterns in children (7 to 14 years of age) with autism spectrum disorder compared to typically developing children, indicating that successful performance implicated differing strategies in these two groups of children. These types of studies will help our understanding of both normal brain-behaviour development and cognitive dysfunction in atypically developing populations. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  13. Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRF

    Directory of Open Access Journals (Sweden)

    Thomas eVincent

    2014-04-01

    Full Text Available As part of fMRI data analysis, the pyhrf package provides a set of tools for addressing the two main issues involved in intra-subject fMRI data analysis: (i the localization of cerebral regions that elicit evoked activity and (ii the estimation of activation dynamics also known as Hemodynamic Response Function (HRF recovery. To tackle these two problems, pyhrf implements the Joint Detection-Estimation framework~(JDE which recovers parcel-level HRFs and embeds an adaptive spatio-temporal regularization scheme of activation maps. With respect to the sole detection issue~(i, the classical voxelwise GLM procedure is also available through nipy, whereas Finite Impulse Response~(FIR and temporally regularized FIR models are concerned with HRF estimation~(ii and are specifically implemented in pyhrf. Several parcellation tools are also integrated such as spatial and functional clustering. Parcellations may be used for spatial averaging prior to FIR/RFIR analysis or to specify the spatial support of the HRF estimates in the JDE approach. These analysis procedures can be applied either to volumic data sets or to data projected onto the cortical surface. For validation purpose, this package is shipped with artificial and real fMRI data sets, which are used in this paper to compare the outcome of the different available approaches. The artificial fMRI data generator is also described to illustrate how to simulate different activation configurations, HRF shapes or nuisance components. To cope with the high computational needs for inference, pyhrf handles distributing computing by exploiting cluster units as well as multi-core machines. Finally, a dedicated viewer is presented, which handles $n$-dimensional images and provides suitable features to explore whole brain hemodynamics~(time series, maps, ROI mask overlay.

  14. Adaptation to thermotolerance in Rhizopus coincides with virulence as revealed by avian and invertebrate infection models, phylogeny, physiological and metabolic flexibility.

    Science.gov (United States)

    Kaerger, Kerstin; Schwartze, Volker U; Dolatabadi, Somayeh; Nyilasi, Ildikó; Kovács, Stella A; Binder, Ulrike; Papp, Tamás; Hoog, Sybren de; Jacobsen, Ilse D; Voigt, Kerstin

    2015-01-01

    Mucormycoses are fungal infections caused by the ancient Mucorales. They are rare, but increasingly reported. Predisposing conditions supporting and favoring mucormycoses in humans and animals include diabetic ketoacidosis, immunosuppression and haematological malignancies. However, comprehensive surveys to elucidate fungal virulence in ancient fungi are limited and so far focused on Lichtheimia and Mucor. The presented study focused on one of the most important causative agent of mucormycoses, the genus Rhizopus (Rhizopodaceae). All known clinically-relevant species are thermotolerant and are monophyletic. They are more virulent compared to non-clinically, mesophilic species. Although adaptation to elevated temperatures correlated with the virulence of the species, mesophilic strains showed also lower virulence in Galleria mellonella incubated at permissive temperatures indicating the existence of additional factors involved in the pathogenesis of clinical Rhizopus species. However, neither specific adaptation to nutritional requirements nor stress resistance correlated with virulence, supporting the idea that Mucorales are predominantly saprotrophs without a specific adaptation to warm blooded hosts.

  15. Lying about Facial Recognition: An fMRI Study

    Science.gov (United States)

    Bhatt, S.; Mbwana, J.; Adeyemo, A.; Sawyer, A.; Hailu, A.; VanMeter, J.

    2009-01-01

    Novel deception detection techniques have been in creation for centuries. Functional magnetic resonance imaging (fMRI) is a neuroscience technology that non-invasively measures brain activity associated with behavior and cognition. A number of investigators have explored the utilization and efficiency of fMRI in deception detection. In this study,…

  16. Lying about Facial Recognition: An fMRI Study

    Science.gov (United States)

    Bhatt, S.; Mbwana, J.; Adeyemo, A.; Sawyer, A.; Hailu, A.; VanMeter, J.

    2009-01-01

    Novel deception detection techniques have been in creation for centuries. Functional magnetic resonance imaging (fMRI) is a neuroscience technology that non-invasively measures brain activity associated with behavior and cognition. A number of investigators have explored the utilization and efficiency of fMRI in deception detection. In this study,…

  17. Unified ICA-SPM analysis of fMRI experiments

    DEFF Research Database (Denmark)

    Bjerre, Troels; Henriksen, Jonas; Nielsen, Carsten Haagen

    2009-01-01

    We present a toolbox for exploratory analysis of functional magnetic resonance imaging (fMRI) data using independent component analysis (ICA) within the widely used SPM analysis pipeline. The toolbox enables dimensional reduction using principal component analysis, ICA using several different ICA...... effects in fMRI data from a visual experiment....

  18. fMRI activation patterns in an analytic reasoning task: consistency with EEG source localization

    Science.gov (United States)

    Li, Bian; Vasanta, Kalyana C.; O'Boyle, Michael; Baker, Mary C.; Nutter, Brian; Mitra, Sunanda

    2010-03-01

    Functional magnetic resonance imaging (fMRI) is used to model brain activation patterns associated with various perceptual and cognitive processes as reflected by the hemodynamic (BOLD) response. While many sensory and motor tasks are associated with relatively simple activation patterns in localized regions, higher-order cognitive tasks may produce activity in many different brain areas involving complex neural circuitry. We applied a recently proposed probabilistic independent component analysis technique (PICA) to determine the true dimensionality of the fMRI data and used EEG localization to identify the common activated patterns (mapped as Brodmann areas) associated with a complex cognitive task like analytic reasoning. Our preliminary study suggests that a hybrid GLM/PICA analysis may reveal additional regions of activation (beyond simple GLM) that are consistent with electroencephalography (EEG) source localization patterns.

  19. Neural activity during production of rorschach responses: An fMRI study.

    Science.gov (United States)

    Giromini, Luciano; Viglione, Donald J; Zennaro, Alessandro; Cauda, Franco

    2017-02-10

    Recently, a lot of effort has been made to ground Rorschach interpretations to their evidence base. To date, however, no studies have yet described, via fMRI, what brain areas get involved when one takes the Rorschach. To fill this gap in the literature, we administered the ten-inkblot stimuli to 26 healthy volunteers during fMRI. Analysis of BOLD signals revealed that, compared to fixating a cross, looking at the Rorschach inkblots while thinking of what they might be associated with higher temporo-occipital and fronto-parietal activations, and with greater activity in some small, sub-cortical regions included in the limbic system. These findings are in line with the traditional conceptualization of the test, as they suggest that taking the Rorschach involves (a) high-level visual processing, (b) top-down as well as bottom-up attentional processes, and (c) perception and processing of emotions and emotional memories.

  20. Residual fMRI sensitivity for identity changes in acquired prosopagnosia

    Directory of Open Access Journals (Sweden)

    Christopher J Fox

    2013-10-01

    Full Text Available While a network of cortical regions contribute to face processing, the lesions in acquired prosopagnosia are highly variable, and likely result in different combinations of spared and affected regions of this network. To assess the residual functional sensitivities of spared regions in prosopagnosia, we designed a rapid event-related functional magnetic resonance imaging (fMRI experiment that included pairs of faces with same or different identities and same or different expressions. By measuring the release from adaptation to these facial changes we determined the residual sensitivity of face-selective regions-of-interest. We tested three patients with acquired prosopagnosia, and all three of these patients demonstrated residual sensitivity for facial identity changes in surviving fusiform and occipital face areas of either the right or left hemisphere, but not in the right posterior superior temporal sulcus. The patients also showed some residual capabilities for facial discrimination with normal performance on the Benton Facial Recognition Test, but impaired performance on more complex tasks of facial discrimination. We conclude that fMRI can demonstrate residual processing of facial identity in acquired prosopagnosia, that this adaptation can occur in the same structures that show similar processing in healthy subjects, and further, that this adaptation may be related to behavioral indices of face perception.

  1. Residual fMRI sensitivity for identity changes in acquired prosopagnosia.

    Science.gov (United States)

    Fox, Christopher J; Iaria, Giuseppe; Duchaine, Bradley C; Barton, Jason J S

    2013-01-01

    While a network of cortical regions contribute to face processing, the lesions in acquired prosopagnosia are highly variable, and likely result in different combinations of spared and affected regions of this network. To assess the residual functional sensitivities of spared regions in prosopagnosia, we designed a rapid event-related functional magnetic resonance imaging (fMRI) experiment that included pairs of faces with same or different identities and same or different expressions. By measuring the release from adaptation to these facial changes we determined the residual sensitivity of face-selective regions-of-interest. We tested three patients with acquired prosopagnosia, and all three of these patients demonstrated residual sensitivity for facial identity changes in surviving fusiform and occipital face areas of either the right or left hemisphere, but not in the right posterior superior temporal sulcus. The patients also showed some residual capabilities for facial discrimination with normal performance on the Benton Facial Recognition Test, but impaired performance on more complex tasks of facial discrimination. We conclude that fMRI can demonstrate residual processing of facial identity in acquired prosopagnosia, that this adaptation can occur in the same structures that show similar processing in healthy subjects, and further, that this adaptation may be related to behavioral indices of face perception.

  2. fMR-adaptation indicates selectivity to audiovisual content congruency in distributed clusters in human superior temporal cortex

    Directory of Open Access Journals (Sweden)

    Blomert Leo

    2010-02-01

    Full Text Available Abstract Background Efficient multisensory integration is of vital importance for adequate interaction with the environment. In addition to basic binding cues like temporal and spatial coherence, meaningful multisensory information is also bound together by content-based associations. Many functional Magnetic Resonance Imaging (fMRI studies propose the (posterior superior temporal cortex (STC as the key structure for integrating meaningful multisensory information. However, a still unanswered question is how superior temporal cortex encodes content-based associations, especially in light of inconsistent results from studies comparing brain activation to semantically matching (congruent versus nonmatching (incongruent multisensory inputs. Here, we used fMR-adaptation (fMR-A in order to circumvent potential problems with standard fMRI approaches, including spatial averaging and amplitude saturation confounds. We presented repetitions of audiovisual stimuli (letter-speech sound pairs and manipulated the associative relation between the auditory and visual inputs (congruent/incongruent pairs. We predicted that if multisensory neuronal populations exist in STC and encode audiovisual content relatedness, adaptation should be affected by the manipulated audiovisual relation. Results The results revealed an occipital-temporal network that adapted independently of the audiovisual relation. Interestingly, several smaller clusters distributed over superior temporal cortex within that network, adapted stronger to congruent than to incongruent audiovisual repetitions, indicating sensitivity to content congruency. Conclusions These results suggest that the revealed clusters contain multisensory neuronal populations that encode content relatedness by selectively responding to congruent audiovisual inputs, since unisensory neuronal populations are assumed to be insensitive to the audiovisual relation. These findings extend our previously revealed mechanism for

  3. Evaluation of Multiband EPI Acquisitions for Resting State fMRI.

    Directory of Open Access Journals (Sweden)

    Christine Preibisch

    Full Text Available Functional magnetic resonance imaging (fMRI and particularly resting state fMRI (rs-fMRI is widely used to investigate resting state brain networks (RSNs on the systems level. Echo planar imaging (EPI is the state-of-the-art imaging technique for most fMRI studies. Therefore, improvements of EPI might lead to increased sensitivity for a large amount of studies performed every day. A number of developments to shorten acquisition time have been recently proposed and the multiband technique, allowing the simultaneous acquisition of multiple slices yielding an equivalent reduction of measurement time, is the most promising among them. While the prospect to significantly reduce acquisition time by means of high multiband acceleration factors (M appears tempting, signal quality parameters and the sensitivity to detect common RSNs with increasing M-factor have only been partially investigated up to now. In this study, we therefore acquired rs-fMRI data from 20 healthy volunteers to systematically investigate signal characteristics and sensitivity for brain network activity in datasets with increasing M-factor, M = 2 - 4. Combined with an inplane, sensitivity encoding (SENSE, acceleration factor, S = 2, we applied a maximal acceleration factor of 8 (S2×M4. Our results suggest that an M-factor of 2 (total acceleration of 4 only causes negligible SNR decrease but reveals common RSN with increased sensitivity and stability. Further M-factor increase produced random artifacts as revealed by signal quality measures that may affect interpretation of RSNs under common scanning conditions. Given appropriate hardware, a mb-EPI sequence with a total acceleration of 4 significantly reduces overall scanning time and clearly increases sensitivity to detect common RSNs. Together, our results suggest mb-EPI at moderate acceleration factors as a novel standard for fMRI that might increase our understanding of network dynamics in healthy and diseased brains.

  4. Repeated exposure of human fibroblasts to ionizing radiation reveals an adaptive response that is not mediated by interleukin-6 or TGF-{beta}

    Energy Technology Data Exchange (ETDEWEB)

    Dieriks, Birger, E-mail: birger.dieriks@ugent.be [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium); De Vos, Winnok [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium); Baatout, Sarah [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium); Radiobiology Unit, Laboratory Molecular and Cellular Biology, Radiobiology Unit, Belgian Nuclear Research Center, SCK.CEN, Boeretang 200, 2400 Mol (Belgium); Van Oostveldt, Patrick, E-mail: Patrick.VanOostveldt@UGent.be [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium)

    2011-10-01

    Exposing cells to a low dose can protect them against a subsequent higher exposure. This phenomenon is known as adaptive response and is frequently observed in a variety of cells. Even though similarities are suspected with other non-targeted effects, such as bystander effects, the exact mechanism behind adaptive response is not fully clarified. In this study human primary fibroblasts were tested for their response to ionizing radiation (IR) after administrating a low priming dose (0.1-0.5 Gy). Both the abundance of {gamma}H2AX as a marker for double-stranded breaks and the levels of cytokines, secreted in the medium, were monitored in time. Upon challenge, IR-primed cells showed modified {gamma}H2AX spot size distributions and altered repair kinetics, consistent with an adaptive response. In addition, 24 h after priming with IR, four cytokines were significantly upregulated in the medium - GM-CSF (1.33x); IL6 (4.24x); IL8 (1.33x); TGF-{beta} (1.46x). In order to mimick the protective effect of IR priming, we primed the cells with either IL6 or TGF-{beta}. This did not elicit an altered {gamma}H2AX response as observed in IR-primed cells, indicating that the adaptive response in these primary fibroblasts is regulated in an IL-6 and TGF-{beta} independent manner.

  5. Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs

    DEFF Research Database (Denmark)

    Hickman, Rachel A.; Munck, Christian; Sommer, Morten Otto Alexander

    2017-01-01

    at several time-points during adaptive evolution experiments involving five different antibiotic conditions. We monitor the mutational spectra in lineages evolved to be resistant to single antibiotics [amikacin (AMK), chloramphenicol (CHL), and ciprofloxacin (CIP)], as well as antibiotic combinations (AMK...

  6. Genetic characterization of an adapted pandemic 2009 H1N1 influenza virus that reveals improved replication rates in human lung epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Wörmann, Xenia [Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin (Germany); Lesch, Markus [Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin (Germany); Steinbeis Innovation gGmbH, Center for Systems Biomedicine, Falkensee (Germany); Welke, Robert-William [Department of Biology, Molecular Biophysics, IRI Life Sciences, Humboldt-Universität zu Berlin (Germany); Okonechnikov, Konstantin; Abdurishid, Mirshat [Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin (Germany); Sieben, Christian [Department of Biology, Molecular Biophysics, IRI Life Sciences, Humboldt-Universität zu Berlin (Germany); Geissner, Andreas [Department for Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Potsdam (Germany); Institute of Chemistry and Biochemistry, Free University, Berlin (Germany); Brinkmann, Volker [Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin (Germany); Kastner, Markus [Institute for Biophysics, Johannes Kepler University, Linz (Austria); Karner, Andreas [Center for Advanced Bioanalysis GmbH (CBL), Linz (Austria); Zhu, Rong; Hinterdorfer, Peter [Institute for Biophysics, Johannes Kepler University, Linz (Austria); Anish, Chakkumkal [Department for Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Potsdam (Germany); Seeberger, Peter H. [Department for Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Potsdam (Germany); Institute of Chemistry and Biochemistry, Free University, Berlin (Germany); Herrmann, Andreas [Department of Biology, Molecular Biophysics, IRI Life Sciences, Humboldt-Universität zu Berlin (Germany); and others

    2016-05-15

    The 2009 influenza pandemic originated from a swine-origin H1N1 virus, which, although less pathogenic than anticipated, may acquire additional virulence-associated mutations in the future. To estimate the potential risk, we sequentially passaged the isolate A/Hamburg/04/2009 in A549 human lung epithelial cells. After passage 6, we observed a 100-fold increased replication rate. High-throughput sequencing of viral gene segments identified five dominant mutations, whose contribution to the enhanced growth was analyzed by reverse genetics. The increased replication rate was pinpointed to two mutations within the hemagglutinin (HA) gene segment (HA{sub 1} D130E, HA{sub 2} I91L), near the receptor binding site and the stem domain. The adapted virus also replicated more efficiently in mice in vivo. Enhanced replication rate correlated with increased fusion pH of the HA protein and a decrease in receptor affinity. Our data might be relevant for surveillance of pre-pandemic strains and development of high titer cell culture strains for vaccine production. - Highlights: • We observed a spontaneous mutation of a 2009-pandemic H1N1 influenza virus in vitro. • The adaptation led to a 100-fold rise in replication rate in human A549 cells. • Adaptation was caused by two mutations in the HA gene segment. • Adaptation correlates with increased fusion pH and decreased receptor affinity.

  7. A 4-channel 3 Tesla phased array receive coil for awake rhesus monkey fMRI and diffusion MRI experiments.

    Science.gov (United States)

    Khachaturian, Mark Haig

    2010-01-01

    Awake monkey fMRI and diffusion MRI combined with conventional neuroscience techniques has the potential to study the structural and functional neural network. The majority of monkey fMRI and diffusion MRI experiments are performed with single coils which suffer from severe EPI distortions which limit resolution. By constructing phased array coils for monkey MRI studies, gains in SNR and anatomical accuracy (i.e., reduction of EPI distortions) can be achieved using parallel imaging. The major challenges associated with constructing phased array coils for monkeys are the variation in head size and space constraints. Here, we apply phased array technology to a 4-channel phased array coil capable of improving the resolution and image quality of full brain awake monkey fMRI and diffusion MRI experiments. The phased array coil is that can adapt to different rhesus monkey head sizes (ages 4-8) and fits in the limited space provided by monkey stereotactic equipment and provides SNR gains in primary visual cortex and anatomical accuracy in conjunction with parallel imaging and improves resolution in fMRI experiments by a factor of 2 (1.25 mm to 1.0 mm isotropic) and diffusion MRI experiments by a factor of 4 (1.5 mm to 0.9 mm isotropic).

  8. Partitioning of Multivariate Phenotypes using Regression Trees Reveals Complex Patterns of Adaptation to Climate across the Range of Black Cottonwood (Populus trichocarpa

    Directory of Open Access Journals (Sweden)

    Regis Wendpouire Oubida

    2015-03-01

    Full Text Available Local adaptation to climate in temperate forest trees involves the integration of multiple physiological, morphological, and phenological traits. Latitudinal clines are frequently observed for these traits, but environmental constraints also track longitude and altitude. We combined extensive phenotyping of 12 candidate adaptive traits, multivariate regression trees, quantitative genetics, and a genome-wide panel of SNP markers to better understand the interplay among geography, climate, and adaptation to abiotic factors in Populus trichocarpa. Heritabilities were low to moderate (0.13 to 0.32 and population differentiation for many traits exceeded the 99th percentile of the genome-wide distribution of FST, suggesting local adaptation. When climate variables were taken as predictors and the 12 traits as response variables in a multivariate regression tree analysis, evapotranspiration (Eref explained the most variation, with subsequent splits related to mean temperature of the warmest month, frost-free period (FFP, and mean annual precipitation (MAP. These grouping matched relatively well the splits using geographic variables as predictors: the northernmost groups (short FFP and low Eref had the lowest growth, and lowest cold injury index; the southern British Columbia group (low Eref and intermediate temperatures had average growth and cold injury index; the group from the coast of California and Oregon (high Eref and FFP had the highest growth performance and the highest cold injury index; and the southernmost, high-altitude group (with high Eref and low FFP performed poorly, had high cold injury index, and lower water use efficiency. Taken together, these results suggest variation in both temperature and water availability across the range shape multivariate adaptive traits in poplar.

  9. Cortical response variation with different sound pressure levels: a combined event-related potentials and FMRI study.

    Directory of Open Access Journals (Sweden)

    Irene Neuner

    Full Text Available Simultaneous recording of electroencephalography (EEG and functional magnetic resonance imaging (fMRI provides high spatial and temporal resolution. In this study we combined EEG and fMRI to investigate the structures involved in the processing of different sound pressure levels (SPLs.EEG data were recorded simultaneously with fMRI from 16 healthy volunteers using MR compatible devices at 3 T. Tones with different SPLs were delivered to the volunteers and the N1/P2 amplitudes were included as covariates in the fMRI data analysis in order to compare the structures activated with high and low SPLs. Analysis of variance (ANOVA and ROI analysis were also performed. Additionally, source localisation analysis was performed on the EEG data.The integration of averaged ERP parameters into the fMRI analysis showed an extended map of areas exhibiting covariation with the BOLD signal related to the auditory stimuli. The ANOVA and ROI analyses also revealed additional brain areas other than the primary auditory cortex (PAC which were active with the auditory stimulation at different SPLs. The source localisation analyses showed additional sources apart from the PAC which were active with the high SPLs.The PAC and the insula play an important role in the processing of different SPLs. In the fMRI analysis, additional activation was found in the anterior cingulate cortex, opercular and orbito-frontal cortices with high SPLs. A strong response of the visual cortex was also found with the high SPLs, suggesting the presence of cross-modal effects.

  10. Brain activity underlying auditory perceptual learning during short period training: simultaneous fMRI and EEG recording

    Directory of Open Access Journals (Sweden)

    de Souza Ana Cláudia Silva

    2013-01-01

    Full Text Available Abstract Background There is an accumulating body of evidence indicating that neuronal functional specificity to basic sensory stimulation is mutable and subject to experience. Although fMRI experiments have investigated changes in brain activity after relative to before perceptual learning, brain activity during perceptual learning has not been explored. This work investigated brain activity related to auditory frequency discrimination learning using a variational Bayesian approach for source localization, during simultaneous EEG and fMRI recording. We investigated whether the practice effects are determined solely by activity in stimulus-driven mechanisms or whether high-level attentional mechanisms, which are linked to the perceptual task, control the learning process. Results The results of fMRI analyses revealed significant attention and learning related activity in left and right superior temporal gyrus STG as well as the left inferior frontal gyrus IFG. Current source localization of simultaneously recorded EEG data was estimated using a variational Bayesian method. Analysis of current localized to the left inferior frontal gyrus and the right superior temporal gyrus revealed gamma band activity correlated with behavioral performance. Conclusions Rapid improvement in task performance is accompanied by plastic changes in the sensory cortex as well as superior areas gated by selective attention. Together the fMRI and EEG results suggest that gamma band activity in the right STG and left IFG plays an important role during perceptual learning.

  11. Multi-approaches analysis reveals local adaptation in the emmer wheat (Triticum dicoccoides) at macro- but not micro-geographical scale.

    Science.gov (United States)

    Volis, Sergei; Ormanbekova, Danara; Yermekbayev, Kanat; Song, Minshu; Shulgina, Irina

    2015-01-01

    Detecting local adaptation and its spatial scale is one of the most important questions of evolutionary biology. However, recognition of the effect of local selection can be challenging when there is considerable environmental variation across the distance at the whole species range. We analyzed patterns of local adaptation in emmer wheat, Triticum dicoccoides, at two spatial scales, small (inter-population distance less than one km) and large (inter-population distance more than 50 km) using several approaches. Plants originating from four distinct habitats at two geographic scales (cold edge, arid edge and two topographically dissimilar core locations) were reciprocally transplanted and their success over time was measured as 1) lifetime fitness in a year of planting, and 2) population growth four years after planting. In addition, we analyzed molecular (SSR) and quantitative trait variation and calculated the QST/FST ratio. No home advantage was detected at the small spatial scale. At the large spatial scale, home advantage was detected for the core population and the cold edge population in the year of introduction via measuring life-time plant performance. However, superior performance of the arid edge population in its own environment was evident only after several generations via measuring experimental population growth rate through genotyping with SSRs allowing counting the number of plants and seeds per introduced genotype per site. These results highlight the importance of multi-generation surveys of population growth rate in local adaptation testing. Despite predominant self-fertilization of T. dicoccoides and the associated high degree of structuring of genetic variation, the results of the QST - FST comparison were in general agreement with the pattern of local adaptation at the two spatial scales detected by reciprocal transplanting.

  12. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

    Science.gov (United States)

    Bonnet, Timothée; Wandeler, Peter; Camenisch, Glauco; Postma, Erik

    2017-01-01

    In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is

  13. Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels.

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    Ola T Westengen

    Full Text Available BACKGROUND: Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited. METHODOLOGY: A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs and a panel of 1127 landraces from the Americas (270 SNPs. Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset. CONCLUSIONS: The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress

  14. Time course analysis reveals gene-specific transcript and protein kinetics of adaptation to short-term aerobic exercise training in human skeletal muscle.

    Science.gov (United States)

    Egan, Brendan; O'Connor, Paul L; Zierath, Juleen R; O'Gorman, Donal J

    2013-01-01

    Repeated bouts of episodic myofibrillar contraction associated with exercise training are potent stimuli for physiological adaptation. However, the time course of adaptation and the continuity between alterations in mRNA expression and protein content are not well described in human skeletal muscle. Eight healthy, sedentary males cycled for 60 min at 80% of peak oxygen consumption (VO2peak) each day for fourteen consecutive days, resulting in an increase in VO2peak of 17.5±3.8%. Skeletal muscle biopsies were taken at baseline, and on the morning following (+16 h after exercise) the first, third, seventh, tenth and fourteenth training sessions. Markers of mitochondrial adaptation (Cyt c and COXIV expression, and citrate synthase activity) were increased within the first week of training, but the mtDNA/nDNA ratio was unchanged by two weeks of training. Accumulation of PGC-1α and ERRα protein during training suggests a regulatory role for these factors in adaptations of mitochondrial and metabolic gene expression. A subset of genes were transiently increased after one training session, but returned to baseline levels thereafter, which is supportive of the concept of transcriptional capacity being particularly sensitive to the onset of a new level of contractile activity. Thus, gene-specific temporal patterns of induction of mRNA expression and protein content are described. Our results illustrate the phenomenology of skeletal muscle plasticity and support the notion that transcript level adjustments, coupled to accumulation of encoded protein, underlie the modulation of skeletal muscle metabolism and phenotype by regular exercise.

  15. Time course analysis reveals gene-specific transcript and protein kinetics of adaptation to short-term aerobic exercise training in human skeletal muscle.

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    Brendan Egan

    Full Text Available Repeated bouts of episodic myofibrillar contraction associated with exercise training are potent stimuli for physiological adaptation. However, the time course of adaptation and the continuity between alterations in mRNA expression and protein content are not well described in human skeletal muscle. Eight healthy, sedentary males cycled for 60 min at 80% of peak oxygen consumption (VO2peak each day for fourteen consecutive days, resulting in an increase in VO2peak of 17.5±3.8%. Skeletal muscle biopsies were taken at baseline, and on the morning following (+16 h after exercise the first, third, seventh, tenth and fourteenth training sessions. Markers of mitochondrial adaptation (Cyt c and COXIV expression, and citrate synthase activity were increased within the first week of training, but the mtDNA/nDNA ratio was unchanged by two weeks of training. Accumulation of PGC-1α and ERRα protein during training suggests a regulatory role for these factors in adaptations of mitochondrial and metabolic gene expression. A subset of genes were transiently increased after one training session, but returned to baseline levels thereafter, which is supportive of the concept of transcriptional capacity being particularly sensitive to the onset of a new level of contractile activity. Thus, gene-specific temporal patterns of induction of mRNA expression and protein content are described. Our results illustrate the phenomenology of skeletal muscle plasticity and support the notion that transcript level adjustments, coupled to accumulation of encoded protein, underlie the modulation of skeletal muscle metabolism and phenotype by regular exercise.

  16. Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells

    OpenAIRE

    Surmann, Kristin; Michalik, Stephan; Hildebrandt, Petra; Gierok, Philipp; Depke, Maren; Brinkmann, Lars; Bernhardt, Jörg; Salazar, Manuela G.; Sun, Zhi; Shteynberg, David; Kusebauch, Ulrike; Moritz, Robert L; Wollscheid, Bernd; Lalk, Michael; Völker, Uwe

    2014-01-01

    Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival and physiological adaptation of S. aureus HG001 after internalization by two human lung epithelial cell lines (S9 and A549), and human embryonic kidney cells (HEK 293). Combining enrichment of bacter...

  17. Adaptive Immune Response to Model Antigens Is Impaired in Murine Leukocyte-Adhesion Deficiency-1 Revealing Elevated Activation Thresholds In Vivo

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    Thorsten Peters

    2012-01-01

    Full Text Available Absence of β2 integrins (CD11/CD18 leads to leukocyte-adhesion deficiency-1 (LAD1, a rare primary immunodeficiency syndrome. Although extensive in vitro work has established an essential function of β2 integrins in adhesive and signaling properties for cells of the innate and adaptive immune system, their respective participation in an altered adaptive immunity in LAD1 patients are complex and only partly understood in vivo. Therefore, we investigated adaptive immune responses towards different T-dependent antigens in a murine LAD1 model of β2 integrin-deficiency (CD18−/−. CD18−/− mice generated only weak IgG responses after immunization with tetanus toxoid (TT. In contrast, robust hapten- and protein-specific immune responses were observed after immunization with highly haptenated antigens such as (4-hydroxy-3-nitrophenyl21 acetyl chicken γ globulin (NP21-CG, even though regularly structured germinal centers with specificity for the defined antigens/haptens in CD18−/− mice remained absent. However, a decrease in the hapten/protein ratio lowered the efficacy of immune responses in CD18−/− mice, whereas a mere reduction of the antigen dose was less crucial. Importantly, haptenation of TT with NP (NP-TT efficiently restored a robust IgG response also to TT. Our findings may stimulate further studies on a modification of vaccination strategies using highly haptenated antigens in individuals suffering from LAD1.

  18. Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

    Science.gov (United States)

    Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2014-06-01

    To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

  19. Enhanced sympathetic arousal in response to FMRI scanning correlates with task induced activations and deactivations.

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    Markus Muehlhan

    Full Text Available It has been repeatedly shown that functional magnetic resonance imaging (fMRI triggers distress and neuroendocrine response systems. Prior studies have revealed that sympathetic arousal increases, particularly at the beginning of the examination. Against this background it appears likely that those stress reactions during the scanning procedure may influence task performance and neural correlates. However, the question how sympathetic arousal elicited by the scanning procedure itself may act as a potential confounder of fMRI data remains unresolved today. Thirty-seven scanner naive healthy subjects performed a simple cued target detection task. Levels of salivary alpha amylase (sAA, as a biomarker for sympathetic activity, were assessed in samples obtained at several time points during the lab visit. SAA increased two times, immediately prior to scanning and at the end of the scanning procedure. Neural activation related to motor preparation and timing as well as task performance was positively correlated with the first increase. Furthermore, the first sAA increase was associated with task induced deactivation (TID in frontal and parietal regions. However, these effects were restricted to the first part of the experiment. Consequently, this bias of scanner related sympathetic activation should be considered in future fMRI investigations. It is of particular importance for pharmacological investigations studying adrenergic agents and the comparison of groups with different stress vulnerabilities like patients and controls or adolescents and adults.

  20. Modality Specific Cerebro-Cerebellar Activations in Verbal Working Memory: An fMRI Study

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    Matthew P. Kirschen

    2010-01-01

    Full Text Available Verbal working memory (VWM engages frontal and temporal/parietal circuits subserving the phonological loop, as well as, superior and inferior cerebellar regions which have projections from these neocortical areas. Different cerebro-cerebellar circuits may be engaged for integrating aurally- and visually-presented information for VWM. The present fMRI study investigated load (2, 4, or 6 letters and modality (auditory and visual dependent cerebro-cerebellar VWM activation using a Sternberg task. FMRI revealed modality-independent activations in left frontal (BA 6/9/44, insular, cingulate (BA 32, and bilateral inferior parietal/supramarginal (BA 40 regions, as well as in bilateral superior (HVI and right inferior (HVIII cerebellar regions. Visual presentation evoked prominent activations in right superior (HVI/CrusI cerebellum, bilateral occipital (BA19 and left parietal (BA7/40 cortex while auditory presentation showed robust activations predominately in bilateral temporal regions (BA21/22. In the cerebellum, we noted a visual to auditory emphasis of function progressing from superior to inferior and from lateral to medial regions. These results extend our previous findings of fMRI activation in cerebro-cerebellar networks during VWM, and demonstrate both modality dependent commonalities and differences in activations with increasing memory load.

  1. Optimizing the imaging of the monkey auditory cortex: sparse vs. continuous fMRI.

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    Petkov, Christopher I; Kayser, Christoph; Augath, Mark; Logothetis, Nikos K

    2009-10-01

    The noninvasive imaging of the monkey auditory system with functional magnetic resonance imaging (fMRI) can bridge the gap between electrophysiological studies in monkeys and imaging studies in humans. Some of the recent imaging of monkey auditory cortical and subcortical structures relies on a technique of "sparse imaging," which was developed in human studies to sidestep the negative influence of scanner noise by adding periods of silence in between volume acquisition. Among the various aspects that have gone into the ongoing optimization of fMRI of the monkey auditory cortex, replacing the more common continuous-imaging paradigm with sparse imaging seemed to us to make the most obvious difference in the amount of activity that we could reliably obtain from awake or anesthetized animals. Here, we directly compare the sparse- and continuous-imaging paradigms in anesthetized animals. We document a strikingly greater auditory response with sparse imaging, both quantitatively and qualitatively, which includes a more expansive and robust tonotopic organization. There were instances where continuous imaging could better reveal organizational properties that sparse imaging missed, such as aspects of the hierarchical organization of auditory cortex. We consider the choice of imaging paradigm as a key component in optimizing the fMRI of the monkey auditory cortex.

  2. Motor function deficits in schizophrenia: an fMRI and VBM study

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Sadhana; Modi, Shilpi; Kumar, Pawan; Singh, Namita; Khushu, Subash [Institute of Nuclear Medicine and Allied Sciences (INMAS), NMR Research Center, Delhi (India); Goyal, Satnam; Bhatia, Triptish; Deshpande, Smita N. [RML Hospital, PGIMER, New Delhi (India)

    2014-05-15

    To investigate whether the motor functional alterations in schizophrenia (SZ) are also associated with structural changes in the related brain areas using functional magnetic resonance imaging (fMRI) and voxel-based morphometry (VBM). A sample of 14 right-handed SZ patients and 14 right-handed healthy control subjects matched for age, sex, and education were examined with structural high-resolution T1-weighted MRI; fMRI images were obtained during right index finger-tapping task in the same session. fMRI results showed reduced functional activation in the motor areas (contralateral precentral and postcentral gyrus) and ipsilateral cerebellum in SZ subjects as compared to healthy controls (n = 14). VBM analysis also revealed reduced grey matter in motor areas and white matter reduction in cerebellum of SZ subjects as compared to controls. The present study provides an evidence for a possible association between structural alterations in the motor cortex and disturbed functional activation in the motor areas in persons affected with SZ during a simple finger-tapping task. (orig.)

  3. Modality specific cerebro-cerebellar activations in verbal working memory: an fMRI study.

    Science.gov (United States)

    Kirschen, Matthew P; Chen, S H Annabel; Desmond, John E

    2010-01-01

    Verbal working memory (VWM) engages frontal and temporal/parietal circuits subserving the phonological loop, as well as, superior and inferior cerebellar regions which have projections from these neocortical areas. Different cerebro-cerebellar circuits may be engaged for integrating aurally- and visually-presented information for VWM. The present fMRI study investigated load (2, 4, or 6 letters) and modality (auditory and visual) dependent cerebro-cerebellar VWM activation using a Sternberg task. FMRI revealed modality-independent activations in left frontal (BA 6/9/44), insular, cingulate (BA 32), and bilateral inferior parietal/supramarginal (BA 40) regions, as well as in bilateral superior (HVI) and right inferior (HVIII) cerebellar regions. Visual presentation evoked prominent activations in right superior (HVI/CrusI) cerebellum, bilateral occipital (BA19) and left parietal (BA7/40) cortex while auditory presentation showed robust activations predominantly in bilateral temporal regions (BA21/22). In the cerebellum, we noted a visual to auditory emphasis of function progressing from superior to inferior and from lateral to medial regions. These results extend our previous findings of fMRI activation in cerebro-cerebellar networks during VWM, and demonstrate both modality dependent commonalities and differences in activations with increasing memory load.

  4. Preoperative therapeutic neuroscience education for lumbar radiculopathy: a single-case fMRI report.

    Science.gov (United States)

    Louw, Adriaan; Puentedura, Emilio J; Diener, Ina; Peoples, Randal R

    2015-01-01

    Therapeutic neuroscience education (TNE) has been shown to be effective in the treatment of mainly chronic musculoskeletal pain conditions. This case study aims to describe the changes in brain activation on functional magnetic resonance imaging (fMRI) scanning, before and after the application of a newly-designed preoperative TNE program. A 30-year-old female with a current acute episode of low back pain (LBP) and radiculopathy participated in a single preoperative TNE session. She completed pre- and post-education measures including visual analog scale (VAS) for LBP and leg pain; Oswestry Disability Index (ODI); Fear Avoidance Beliefs Questionnaire (FABQ); Pain Catastrophizing Scale (PCS) and a series of Likert-scale questions regarding beliefs and attitudes to lumbar surgery (LS). After a 30-minute TNE session, ODI decreased by 10%, PCS decreased by 10 points and her beliefs and attitudes shifted positively regarding LS. Immediately following TNE straight leg raise increased by 7° and forward flexion by 8 cm. fMRI testing following TNE revealed 3 marked differences compared to pre-education scanning: (1) deactivation of the periaqueductal gray area; (2) deactivation of the cerebellum; and (3) increased activation of the motor cortex. The immediate positive fMRI, psychometric and physical movement changes may indicate a cortical mechanism of TNE for patients scheduled for LS.

  5. Sensitivity and specificity considerations for fMRI encoding, decoding, and mapping of auditory cortex at ultra-high field.

    Science.gov (United States)

    Moerel, Michelle; De Martino, Federico; Kemper, Valentin G; Schmitter, Sebastian; Vu, An T; Uğurbil, Kâmil; Formisano, Elia; Yacoub, Essa

    2017-03-31

    Following rapid technological advances, ultra-high field functional MRI (fMRI) enables exploring correlates of neuronal population activity at an increasing spatial resolution. However, as the fMRI blood-oxygenation-level-dependent (BOLD) contrast is a vascular signal, the spatial specificity of fMRI data is ultimately determined by the characteristics of the underlying vasculature. At 7T, fMRI measurement parameters determine the relative contribution of the macro- and microvasculature to the acquired signal. Here we investigate how these parameters affect relevant high-end fMRI analyses such as encoding, decoding, and submillimeter mapping of voxel preferences in the human auditory cortex. Specifically, we compare a T2* weighted fMRI dataset, obtained with 2D gradient echo (GE) EPI, to a predominantly T2 weighted dataset obtained with 3D GRASE. We first investigated the decoding accuracy based on two encoding models that represented different hypotheses about auditory cortical processing. This encoding/decoding analysis profited from the large spatial coverage and sensitivity of the T2* weighted acquisitions, as evidenced by a significantly higher prediction accuracy in the GE-EPI dataset compared to the 3D GRASE dataset for both encoding models. The main disadvantage of the T2* weighted GE-EPI dataset for encoding/decoding analyses was that the prediction accuracy exhibited cortical depth dependent vascular biases. However, we propose that the comparison of prediction accuracy across the different encoding models may be used as a post processing technique to salvage the spatial interpretability of the GE-EPI cortical depth-dependent prediction accuracy. Second, we explored the mapping of voxel preferences. Large-scale maps of frequency preference (i.e., tonotopy) were similar across datasets, yet the GE-EPI dataset was preferable due to its larger spatial coverage and sensitivity. However, submillimeter tonotopy maps revealed biases in assigned frequency

  6. Flexible Connectivity in the Aging Brain Revealed by Task Modulations

    NARCIS (Netherlands)

    Geerligs, Linda; Saliasi, Emi; Renken, Remco J.; Maurits, Natasha M.; Lorist, Monicque M.

    Recent studies have shown that aging has a large impact on connectivity within and between functional networks. An open question is whether elderly still have the flexibility to adapt functional network connectivity (FNC) to the demands of the task at hand. To study this, we collected fMRI data in

  7. A new trigemino-nociceptive stimulation model for event-related fMRI.

    Science.gov (United States)

    Stankewitz, A; Voit, H L; Bingel, U; Peschke, C; May, A

    2010-04-01

    Functional imaging of human trigemino-nociceptive processing provides meaningful insights into altered pain processing in head and face pain diseases. Although functional magnetic resonance imaging (fMRI) offers high temporal and spatial resolution, most studies available were done with radioligand-positron emission tomography, as fMRI requires non-magnetic stimulus equipment and fast on-off conditions. We developed a new approach for painful stimulation of the trigeminal nerve that can be implemented within an event-related design using fMRI and aimed to detect increased blood-oxygen-level-dependent (BOLD) signals as surrogate markers of trigeminal pain processing. Using an olfactometer, 20 healthy volunteers received intranasally standardized trigeminal nociceptive stimuli (ammonia gas) as well as olfactory (rose odour) and odorless control stimuli (air puffs). Imaging revealed robust BOLD responses to the trigeminal nociceptive stimulation in cortical and subcortical brain areas known to be involved in pain processing. Focusing on the trigeminal pain pathway, significant activations were observed bilaterally in brainstem areas at the trigeminal nerve entry zone, which are agreeable with the principal trigeminal nuclei. Furthermore, increased signal changes could be detected ipsilaterally at anatomical localization of the trigeminal ganglion and bilaterally in the rostral medulla, which probably represents the spinal trigeminal nuclei. However, brainstem areas involved in the endogenous pain control system that are close to this anatomical localization, such as raphe nuclei, have to be discussed. Our findings suggest that mapping trigeminal pain processing using fMRI with this non-invasive experimental design is feasible and capable of evoking specific activations in the trigeminal nociceptive system. This method will provide an ideal opportunity to study the trigeminal pain system in both health and pathological conditions such as idiopathic headache disorders.

  8. Classification of autistic individuals and controls using cross-task characterization of fMRI activity

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    Guillaume Chanel

    2016-01-01

    Full Text Available Multivariate pattern analysis (MVPA has been applied successfully to task-based and resting-based fMRI recordings to investigate which neural markers distinguish individuals with autistic spectrum disorders (ASD from controls. While most studies have focused on brain connectivity during resting state episodes and regions of interest approaches (ROI, a wealth of task-based fMRI datasets have been acquired in these populations in the last decade. This calls for techniques that can leverage information not only from a single dataset, but from several existing datasets that might share some common features and biomarkers. We propose a fully data-driven (voxel-based approach that we apply to two different fMRI experiments with social stimuli (faces and bodies. The method, based on Support Vector Machines (SVMs and Recursive Feature Elimination (RFE, is first trained for each experiment independently and each output is then combined to obtain a final classification output. Second, this RFE output is used to determine which voxels are most often selected for classification to generate maps of significant discriminative activity. Finally, to further explore the clinical validity of the approach, we correlate phenotypic information with obtained classifier scores. The results reveal good classification accuracy (range between 69% and 92.3%. Moreover, we were able to identify discriminative activity patterns pertaining to the social brain without relying on a priori ROI definitions. Finally, social motivation was the only dimension which correlated with classifier scores, suggesting that it is the main dimension captured by the classifiers. Altogether, we believe that the present RFE method proves to be efficient and may help identifying relevant biomarkers by taking advantage of acquired task-based fMRI datasets in psychiatric populations.

  9. Classification of autistic individuals and controls using cross-task characterization of fMRI activity.

    Science.gov (United States)

    Chanel, Guillaume; Pichon, Swann; Conty, Laurence; Berthoz, Sylvie; Chevallier, Coralie; Grèzes, Julie

    2016-01-01

    Multivariate pattern analysis (MVPA) has been applied successfully to task-based and resting-based fMRI recordings to investigate which neural markers distinguish individuals with autistic spectrum disorders (ASD) from controls. While most studies have focused on brain connectivity during resting state episodes and regions of interest approaches (ROI), a wealth of task-based fMRI datasets have been acquired in these populations in the last decade. This calls for techniques that can leverage information not only from a single dataset, but from several existing datasets that might share some common features and biomarkers. We propose a fully data-driven (voxel-based) approach that we apply to two different fMRI experiments with social stimuli (faces and bodies). The method, based on Support Vector Machines (SVMs) and Recursive Feature Elimination (RFE), is first trained for each experiment independently and each output is then combined to obtain a final classification output. Second, this RFE output is used to determine which voxels are most often selected for classification to generate maps of significant discriminative activity. Finally, to further explore the clinical validity of the approach, we correlate phenotypic information with obtained classifier scores. The results reveal good classification accuracy (range between 69% and 92.3%). Moreover, we were able to identify discriminative activity patterns pertaining to the social brain without relying on a priori ROI definitions. Finally, social motivation was the only dimension which correlated with classifier scores, suggesting that it is the main dimension captured by the classifiers. Altogether, we believe that the present RFE method proves to be efficient and may help identifying relevant biomarkers by taking advantage of acquired task-based fMRI datasets in psychiatric populations.

  10. Prioritizing spatial accuracy in high-resolution fMRI data using multivariate feature weight mapping

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    Johannes eStelzer

    2014-04-01

    Full Text Available Although ultra-high-field fMRI at field strengths of 7T or above provides substantial gains in BOLD contrast-to-noise ratio, when very high-resolution fMRI is required such gains are inevitably reduced. The improvement in sensitivity provided by multivariate analysis techniques, as compared with univariate methods, then becomes especially welcome. Information mapping approaches are commonly used, such as the searchlight technique, which take into account the spatially distributed patterns of activation in order to predict stimulus conditions. However, the popular searchlight decoding technique, in particular, has been found to be prone to spatial inaccuracies. For instance, the spatial extent of informative areas is generally exaggerated, and their spatial configuration is distorted. We propose the combination of a nonparametric and permutation-based statistical framework with linear classifiers. We term this new combined method Feature Weight Mapping (FWM. The main goal of the proposed method is to map the specific contribution of each voxel to the classification decision while including a correction for the multiple comparisons problem. Next, we compare this new method to the searchlight approach using a simulation and ultra-high-field 7T experimental data. We found that the searchlight method led to spatial inaccuracies that are especially noticeable in high-resolution fMRI data. In contrast, FWM was more spatially precise, revealing both informative anatomical structures as well as the direction by which voxels contribute to the classification. By maximizing the spatial accuracy of ultra-high-field fMRI results, global multivariate methods provide a substantial improvement for characterizing structure-function relationships.

  11. New features on the environmental regulation of metabolism revealed by modeling the cellular proteomic adaptations induced by light, carbon and inorganic nitrogen in Chlamydomonas reinhardtii

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    Stéphanie Gérin

    2016-08-01

    Full Text Available Microalgae are currently emerging to be very promising organisms for the production of biofuels and high-added value compounds. Understanding the influence of environmental alterations on their metabolism is a crucial issue. Light, carbon and nitrogen availability have been reported to induce important metabolic adaptations. So far, the influence of these variables has essentially been studied while varying only one or two environmental factors at the same time. The goal of the present work was to model the cellular proteomic adaptations of the green microalga Chlamydomonas reinhardtii upon the simultaneous changes of light intensity, carbon concentrations (CO2 and acetate and inorganic nitrogen concentrations (nitrate and ammonium in the culture medium. Statistical design of experiments (DOE enabled to define 32 culture conditions to be tested experimentally. Relative protein abundance was quantified by two dimensional differential in-gel electrophoresis (2D-DIGE. Additional assays for respiration, photosynthesis, and lipid and pigment concentrations were also carried out. A hierarchical clustering survey enabled to partition biological variables (proteins + assays into eight co-regulated clusters. In most cases, the biological variables partitioned in the same cluster had already been reported to participate to common biological functions (acetate assimilation, bioenergetic processes, light harvesting, Calvin cycle and protein metabolism. The environmental regulation within each cluster was further characterized by a series of multivariate methods including principal component analysis and multiple linear regressions. This metadata analysis enabled to highlight the existence of a clear regulatory pattern for every cluster and to mathematically simulate the effects of light, carbon and nitrogen. The influence of these environmental variables on cellular metabolism is described in details and thoroughly discussed. This work provides an overview

  12. New Features on the Environmental Regulation of Metabolism Revealed by Modeling the Cellular Proteomic Adaptations Induced by Light, Carbon, and Inorganic Nitrogen in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Gérin, Stéphanie; Leprince, Pierre; Sluse, Francis E; Franck, Fabrice; Mathy, Grégory

    2016-01-01

    Microalgae are currently emerging to be very promising organisms for the production of biofuels and high-added value compounds. Understanding the influence of environmental alterations on their metabolism is a crucial issue. Light, carbon and nitrogen availability have been reported to induce important metabolic adaptations. So far, the influence of these variables has essentially been studied while varying only one or two environmental factors at the same time. The goal of the present work was to model the cellular proteomic adaptations of the green microalga Chlamydomonas reinhardtii upon the simultaneous changes of light intensity, carbon concentrations (CO2 and acetate), and inorganic nitrogen concentrations (nitrate and ammonium) in the culture medium. Statistical design of experiments (DOE) enabled to define 32 culture conditions to be tested experimentally. Relative protein abundance was quantified by two dimensional differential in-gel electrophoresis (2D-DIGE). Additional assays for respiration, photosynthesis, and lipid and pigment concentrations were also carried out. A hierarchical clustering survey enabled to partition biological variables (proteins + assays) into eight co-regulated clusters. In most cases, the biological variables partitioned in the same cluster had already been reported to participate to common biological functions (acetate assimilation, bioenergetic processes, light harvesting, Calvin cycle, and protein metabolism). The environmental regulation within each cluster was further characterized by a series of multivariate methods including principal component analysis and multiple linear regressions. This metadata analysis enabled to highlight the existence of a clear regulatory pattern for every cluster and to mathematically simulate the effects of light, carbon, and nitrogen. The influence of these environmental variables on cellular metabolism is described in details and thoroughly discussed. This work provides an overview of the

  13. A wavelet method for modeling and despiking motion artifacts from resting-state fMRI time series

    Science.gov (United States)

    Patel, Ameera X.; Kundu, Prantik; Rubinov, Mikail; Jones, P. Simon; Vértes, Petra E.; Ersche, Karen D.; Suckling, John; Bullmore, Edward T.

    2014-01-01

    The impact of in-scanner head movement on functional magnetic resonance imaging (fMRI) signals has long been established as undesirable. These effects have been traditionally corrected by methods such as linear regression of head movement parameters. However, a number of recent independent studies have demonstrated that these techniques are insufficient to remove motion confounds, and that even small movements can spuriously bias estimates of functional connectivity. Here we propose a new data-driven, spatially-adaptive, wavelet-based method for identifying, modeling, and removing non-stationary events in fMRI time series, caused by head movement, without the need for data scrubbing. This method involves the addition of just one extra step, the Wavelet Despike, in standard pre-processing pipelines. With this method, we demonstrate robust removal of a range of different motion artifacts and motion-related biases including distance-dependent connectivity artifacts, at a group and single-subject level, using a range of previously published and new diagnostic measures. The Wavelet Despike is able to accommodate the substantial spatial and temporal heterogeneity of motion artifacts and can consequently remove a range of high and low frequency artifacts from fMRI time series, that may be linearly or non-linearly related to physical movements. Our methods are demonstrated by the analysis of three cohorts of resting-state fMRI data, including two high-motion datasets: a previously published dataset on children (N = 22) and a new dataset on adults with stimulant drug dependence (N = 40). We conclude that there is a real risk of motion-related bias in connectivity analysis of fMRI data, but that this risk is generally manageable, by effective time series denoising strategies designed to attenuate synchronized signal transients induced by abrupt head movements. The Wavelet Despiking software described in this article is freely available for download at www

  14. Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles

    Directory of Open Access Journals (Sweden)

    Brodin David

    2010-03-01

    Full Text Available Abstract Background Gcn5 is a transcriptional coactivator with histone acetyltransferase activity that is conserved with regard to structure as well as its histone substrates throughout the eukaryotes. Gene regulatory networks within cells are thought to be evolutionarily diverged. The use of evolutionarily divergent yeast species, such as S. cerevisiae and S. pombe, which can be studied under similar environmental conditions, provides an opportunity to examine the interface between conserved regulatory components and their cellular applications in different organisms. Results We show that Gcn5 is important for a common set of stress responses in evolutionarily diverged yeast species and that the activity of the conserved histone acetyltransferase domain is required. We define a group of KCl stress response genes in S. cerevisiae that are specifically dependent on Gcn5. Gcn5 is localised to many Gcn5-dependent genes including Gcn5 repressed targets such as FLO8. Gcn5 regulates divergent sets of KCl responsive genes in S. cerevisiae and S. pombe. Genome-wide localization studies showed a tendency for redistribution of Gcn5 during KCl stress adaptation in S. cerevisiae from short genes to the transcribed regions of long genes. An analogous redistribution was not observed in S. pombe. Conclusions Gcn5 is required for the regulation of divergent sets of KCl stress-response genes in S. cerevisiae and S. pombe even though it is required a common group of stress responses, including the response to KCl. Genes that are physically associated with Gcn5 require its activity for their repression or activation during stress adaptation, providing support for a role of Gcn5 as a corepressor as well as a coactivator. The tendency of Gcn5 to re-localise to the transcribed regions of long genes during KCl stress adaptation suggests that Gcn5 plays a specific role in the expression of long genes under adaptive conditions, perhaps by regulating transcriptional

  15. Adaptive Laboratory Evolution Of Escherichia Coli Reveals Arduous Resistance Development To A Combination Of Three Novel Antimicrobial Compounds And To The Short Amp P9-4

    DEFF Research Database (Denmark)

    Citterio, Linda; Franzyk, Henrik; Gram, Lone

    2015-01-01

    Antimicrobial peptides (AMPs) were for long considered as promising new antimicrobials since resistance was not expected. However, adaptive evolution experiments have demonstrated that bacteria may indeed develop resistance also to AMPs. However, we and others hypothesize that the risk...... of resistance development decreases when two or more compounds are combined as compared to single-drug treatments. The purpose of this study was to determine if resistance could develop in Escherichia coli ATCC 25922 to the peptidomimetic HF-1002 2 and the AMPs novicidin and P9-4. The mentioned compounds were...

  16. fMRI Evidence of ‘Mirror’ Responses to Geometric Shapes

    Science.gov (United States)

    Press, Clare; Catmur, Caroline; Cook, Richard; Widmann, Hannah; Heyes, Cecilia; Bird, Geoffrey

    2012-01-01

    Mirror neurons may be a genetic adaptation for social interaction [1]. Alternatively, the associative hypothesis [2], [3] proposes that the development of mirror neurons is driven by sensorimotor learning, and that, given suitable experience, mirror neurons will respond to any stimulus. This hypothesis was tested using fMRI adaptation to index populations of cells with mirror properties. After sensorimotor training, where geometric shapes were paired with hand actions, BOLD response was measured while human participants experienced runs of events in which shape observation alternated with action execution or observation. Adaptation from shapes to action execution, and critically, observation, occurred in ventral premotor cortex (PMv) and inferior parietal lobule (IPL). Adaptation from shapes to execution indicates that neuronal populations responding to the shapes had motor properties, while adaptation to observation demonstrates that these populations had mirror properties. These results indicate that sensorimotor training induced populations of cells with mirror properties in PMv and IPL to respond to the observation of arbitrary shapes. They suggest that the mirror system has not been shaped by evolution to respond in a mirror fashion to biological actions; instead, its development is mediated by stimulus-general processes of learning within a system adapted for visuomotor control. PMID:23251653

  17. Compressive loading of the murine tibia reveals site-specific micro-scale differences in adaptation and maturation rates of bone.

    Science.gov (United States)

    Bergström, I; Kerns, J G; Törnqvist, A E; Perdikouri, C; Mathavan, N; Koskela, A; Henriksson, H B; Tuukkanen, J; Andersson, G; Isaksson, H; Goodship, A E; Windahl, S H

    2017-03-01

    Loading increases bone mass and strength in a site-specific manner; however, possible effects of loading on bone matrix composition have not been evaluated. Site-specific structural and material properties of mouse bone were analyzed on the macro- and micro/molecular scale in the presence and absence of axial loading. The response of bone to load is heterogeneous, adapting at molecular, micro-, and macro-levels. Osteoporosis is a degenerative disease resulting in reduced bone mineral density, structure, and strength. The overall aim was to explore the hypothesis that changes in loading environment result in site-specific adaptations at molecular/micro- and macro-scale in mouse bone. Right tibiae of adult mice were subjected to well-defined cyclic axial loading for 2 weeks; left tibiae were used as physiologically loaded controls. The bones were analyzed with μCT (structure), reference point indentation (material properties), Raman spectroscopy (chemical), and small-angle X-ray scattering (mineral crystallization and structure). The cranial and caudal sites of tibiae are structurally and biochemically different within control bones. In response to loading, cranial and caudal sites increase in cortical thickness with reduced mineralization (-14 and -3%, p micro-scale to maintain optimal function. Manipulation of this heterogeneity may affect bone strength, relative to specific applied loads.

  18. Structural Adaptation of Cold-Active RTX Lipase from Pseudomonas sp. Strain AMS8 Revealed via Homology and Molecular Dynamics Simulation Approaches

    Directory of Open Access Journals (Sweden)

    Mohd. Shukuri Mohamad Ali

    2013-01-01

    Full Text Available The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8 (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus maintained its stability more than the noncatalytic domain (C-terminus, but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

  19. Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches.

    Science.gov (United States)

    Mohamad Ali, Mohd Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

    2013-01-01

    The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

  20. The Genome Sequence of Psychrobacter arcticus 273-4, a Psychroactive Siberian Permafrost Bacterium, Reveals Mechanisms for Adaptation to Low-Temperature Growth

    Energy Technology Data Exchange (ETDEWEB)

    Ayala-del-Rio, Hector L. [Michigan State University, East Lansing; Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Grzymski, Joseph J. [Desert Research Institute, Reno, NV; Ponder, Monica [Michigan State University, East Lansing; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Bergholz, Peter [Michigan State University, East Lansing; Bartolo, Genevive [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Bakermans, Corien [Michigan State University, East Lansing; Rodrigues, Debora [Michigan State University, East Lansing; Klappenbach, Joel [Michigan State University, East Lansing; Zarka, Dan [Michigan State University, East Lansing; Larimer, Frank W [ORNL; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Murray, Alison [Desert Research Institute, Reno, NV; Thomashow, Michael [Michigan State University, East Lansing; Tiedje, James M. [Michigan State University, East Lansing

    2010-01-01

    Psychrobacter arcticus strain 273-4, which grows at temperatures as low as -10 degrees C, is the first cold-adapted bacterium from a terrestrial environment whose genome was sequenced. Analysis of the 2.65-Mb genome suggested that some of the strategies employed by P. arcticus 273-4 for survival under cold and stress conditions are changes in membrane composition, synthesis of cold shock proteins, and the use of acetate as an energy source. Comparative genome analysis indicated that in a significant portion of the P. arcticus proteome there is reduced use of the acidic amino acids and proline and arginine, which is consistent with increased protein flexibility at low temperatures. Differential amino acid usage occurred in all gene categories, but it was more common in gene categories essential for cell growth and reproduction, suggesting that P. arcticus evolved to grow at low temperatures. Amino acid adaptations and the gene content likely evolved in response to the long-term freezing temperatures (-10 degrees C to -12 degrees C) of the Kolyma (Siberia) permafrost soil from which this strain was isolated. Intracellular water likely does not freeze at these in situ temperatures, which allows P. arcticus to live at subzero temperatures.

  1. Examination of food chain-derived Listeria monocytogenes strains of different serotypes reveals considerable diversity in inlA genotypes, mutability, and adaptation to cold temperatures.

    Science.gov (United States)

    Kovacevic, Jovana; Arguedas-Villa, Carolina; Wozniak, Anna; Tasara, Taurai; Allen, Kevin J

    2013-03-01

    Listeria monocytogenes strains belonging to serotypes 1/2a and 4b are frequently linked to listeriosis. While inlA mutations leading to premature stop codons (PMSCs) and attenuated virulence are common in 1/2a, they are rare in serotype 4b. We observed PMSCs in 35% of L. monocytogenes isolates (n = 54) recovered from the British Columbia food supply, including serotypes 1/2a (30%), 1/2c (100%), and 3a (100%), and a 3-codon deletion (amino acid positions 738 to 740) seen in 57% of 4b isolates from fish-processing facilities. Caco-2 invasion assays showed that two isolates with the deletion were significantly more invasive than EGD-SmR (P cold temperature following a downshift from 37°C to 4°C. Overall, three distinct cold-adapting groups (CAG) were observed: 46% were fast (200 h) adaptors. Intermediate CAG strains (70%) more frequently possessed inlA PMSCs than did fast (20%) and slow (10%) CAGs; in contrast, 87% of fast adaptors lacked inlA PMSCs. In conclusion, we report food chain-derived 1/2a and 4b serotypes with a 3-codon deletion possessing invasive behavior and the novel association of inlA genotypes encoding a full-length InlA with fast cold-adaptation phenotypes.

  2. Brain network dynamics underlying visuospatial judgment: an FMRI connectivity study.

    Science.gov (United States)

    de Graaf, Tom A; Roebroeck, Alard; Goebel, Rainer; Sack, Alexander T

    2010-09-01

    Previous functional imaging research has consistently indicated involvement of bilateral fronto-parietal networks during the execution of visuospatial tasks. Studies with TMS have suggested that the right hemispheric network, but not the left, is functionally relevant for visuospatial judgments. However, very little is still known about the interactions within these fronto-parietal networks underlying visuospatial processing. In the current study, we investigated task modulation of functional connectivity (instantaneous correlations of regional time courses), and task-specific effective connectivity (direction of influences), within the right fronto-parietal network activated during visuospatial judgments. Ten healthy volunteers performed a behaviorally controlled visuospatial judgment task (ANGLE) or a control task (COLOR) in an fMRI experiment. Visuospatial task-specific activations were found in posterior parietal cortex (PPC) and middle/inferior frontal gyrus (MFG). Functional connectivity within this network was task-modulated, with significantly higher connectivity between PPC and MFG during ANGLE than during COLOR. Effective connectivity analysis for directed influence revealed that visuospatial task-specific projections within this network were predominantly in a frontal-to-parietal direction. Moreover, ANGLE-specific influences from thalamic nuclei to PPC were identified. Exploratory effective connectivity analysis revealed that closely neighboring clusters, within visuospatial regions, were differentially involved in the network. These neighboring clusters had opposite effective connectivity patterns to other nodes of the fronto-parietal network. Our data thus reveal that visuospatial judgments are supported by massive fronto-parietal backprojections, thalamo-parietal influence, and multiple stages, or loops, of information flow within the visuospatial network. We speculate on possible functional contributions of the various network nodes and

  3. Normalized cut group clustering of resting-state FMRI data.

    Directory of Open Access Journals (Sweden)

    Martijn van den Heuvel

    Full Text Available BACKGROUND: Functional brain imaging studies have indicated that distinct anatomical brain regions can show coherent spontaneous neuronal activity during rest. Regions that show such correlated behavior are said to form resting-state networks (RSNs. RSNs have been investigated using seed-dependent functional connectivity maps and by using a number of model-free methods. However, examining RSNs across a group of subjects is still a complex task and often involves human input in selecting meaningful networks. METHODOLOGY/PRINCIPAL FINDINGS: We report on a voxel based model-free normalized cut graph clustering approach with whole brain coverage for group analysis of resting-state data, in which the number of RSNs is computed as an optimal clustering fit of the data. Inter-voxel correlations of time-series are grouped at the individual level and the consistency of the resulting networks across subjects is clustered at the group level, defining the group RSNs. We scanned a group of 26 subjects at rest with a fast BOLD sensitive fMRI scanning protocol on a 3 Tesla MR scanner. CONCLUSIONS/SIGNIFICANCE: An optimal group clustering fit revealed 7 RSNs. The 7 RSNs included motor/visual, auditory and attention networks and the frequently reported default mode network. The found RSNs showed large overlap with recently reported resting-state results and support the idea of the formation of spatially distinct RSNs during rest in the human brain.

  4. Transient brain activity disentangles fMRI resting-state dynamics in terms of spatially and temporally overlapping networks.

    Science.gov (United States)

    Karahanoğlu, Fikret Işik; Van De Ville, Dimitri

    2015-07-16

    Dynamics of resting-state functional magnetic resonance imaging (fMRI) provide a new window onto the organizational principles of brain function. Using state-of-the-art signal processing techniques, we extract innovation-driven co-activation patterns (iCAPs) from resting-state fMRI. The iCAPs' maps are spatially overlapping and their sustained-activity signals temporally overlapping. Decomposing resting-state fMRI using iCAPs reveals the rich spatiotemporal structure of functional components that dynamically assemble known resting-state networks. The temporal overlap between iCAPs is substantial; typically, three to four iCAPs occur simultaneously in combinations that are consistent with their behaviour profiles. In contrast to conventional connectivity analysis, which suggests a negative correlation between fluctuations in the default-mode network (DMN) and task-positive networks, we instead find evidence for two DMN-related iCAPs consisting the posterior cingulate cortex that differentially interact with the attention network. These findings demonstrate how the fMRI resting state can be functionally decomposed into spatially and temporally overlapping building blocks using iCAPs.

  5. Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica.

    Science.gov (United States)

    Goordial, Jacqueline; Raymond-Bouchard, Isabelle; Zolotarov, Yevgen; de Bethencourt, Luis; Ronholm, Jennifer; Shapiro, Nicole; Woyke, Tanja; Stromvik, Martina; Greer, Charles W; Bakermans, Corien; Whyte, Lyle

    2016-02-01

    The permafrost soils of the high elevation McMurdo Dry Valleys are the most cold, desiccating and oligotrophic on Earth. Rhodococcus sp. JG3 is one of very few bacterial isolates from Antarctic Dry Valley permafrost, and displays subzero growth down to -5°C. To understand how Rhodococcus sp. JG3 is able to survive extreme permafrost conditions and be metabolically active at subzero temperatures, we sequenced its genome and compared it to the genomes of 14 mesophilic rhodococci. Rhodococcus sp. JG3 possessed a higher copy number of genes for general stress response, UV protection and protection from cold shock, osmotic stress and oxidative stress. We characterized genome wide molecular adaptations to cold, and identified genes that had amino acid compositions favourable for increased flexibility and functionality at low temperatures. Rhodococcus sp. JG3 possesses multiple complimentary strategies which may enable its survival in some of the harshest permafrost on Earth.

  6. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

    Energy Technology Data Exchange (ETDEWEB)

    de Wit, Pierre J. G. M.; van der Burgt, Ate; Okmen, Bilal; Stergiopoulos, Ioannis; Abd-Elsalam, Kamel A.; Aerts, Andrea L.; Bahkali, Ali H.; Beenen, Henriek G.; Chettri, Oranav; Cos, Murray P.; Datema, Erwin; de Vries, Ronald P.; DHillon, Braham; Ganley, Austen R.; Griffiths, Scott A.; Guo, Yanan; Gamelin, Richard C.; Henrissat, Bernard; Kabir, M. Shahjahan; Jashni, Mansoor Karimi; Kema, Gert; Klaubauf, Sylvia; Lapidus, Alla; Levasseur, Anthony; Lindquist, Erika; Mehrabi, Rahim; Ohm, Robin A.; Owen, Timothy J.; Salamov, Asaf; Schwelm, Arne; Schijlen, Elio; Sun, Hui; van den Burg, Harrold A.; van Burg, Roeland C. H. J.; Zhang, Shuguang; Goodwin, Stephen B.; Grigoriev, Igor V.; Collemare, Jerome; Bradshaw, Rosie E.

    2012-05-04

    We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70percent of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2percent in Cfu versus 3.2percent in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.

  7. The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry.

    Science.gov (United States)

    de Wit, Pierre J G M; van der Burgt, Ate; Ökmen, Bilal; Stergiopoulos, Ioannis; Abd-Elsalam, Kamel A; Aerts, Andrea L; Bahkali, Ali H; Beenen, Henriek G; Chettri, Pranav; Cox, Murray P; Datema, Erwin; de Vries, Ronald P; Dhillon, Braham; Ganley, Austen R; Griffiths, Scott A; Guo, Yanan; Hamelin, Richard C; Henrissat, Bernard; Kabir, M Shahjahan; Jashni, Mansoor Karimi; Kema, Gert; Klaubauf, Sylvia; Lapidus, Alla; Levasseur, Anthony; Lindquist, Erika; Mehrabi, Rahim; Ohm, Robin A; Owen, Timothy J; Salamov, Asaf; Schwelm, Arne; Schijlen, Elio; Sun, Hui; van den Burg, Harrold A; van Ham, Roeland C H J; Zhang, Shuguang; Goodwin, Stephen B; Grigoriev, Igor V; Collemare, Jérôme; Bradshaw, Rosie E

    2012-01-01

    We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.

  8. Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50° in latitude

    Directory of Open Access Journals (Sweden)

    A. Canion

    2013-09-01

    Full Text Available Despite decades of research on the physiology and biochemistry of nitrate/nitrite-respiring microorganisms, little is known regarding their metabolic response to temperature, especially under in situ conditions. The temperature regulation of microbial communities that mediate anammox and denitrification was investigated in near shore permeable sediments at polar, temperate, and subtropical sites with annual mean temperatures ranging from −5 to 23 °C. Total N2 production rates were determined using the isotope pairing technique in intact core incubations under diffusive and simulated advection conditions and ranged from 2 to 359 μmol N m−2 d−1. For the majority of sites studied, N2 removal was 2 to 7 times more rapid under advective flow conditions. Anammox comprised 6 to 14% of total N2 production at temperate and polar sites and was not detected at the subtropical site. Potential rates of denitrification and anammox were determined in anaerobic slurries in a temperature gradient block incubator across a temperature range of −1 to 42 °C. The highest optimum temperature (Topt for denitrification was 36 °C and was observed in subtropical sediments, while the lowest Topt of 21 °C was observed at the polar site. Seasonal variation in the Topt was observed at the temperate site with values of 26 and 34 °C in winter and summer, respectively. The Topt values for anammox were 9 and 26 °C at the polar and temperate sites, respectively. The results demonstrate adaptation of denitrifying communities to in situ temperatures in permeable marine sediments across a wide range of temperatures, whereas marine anammox bacteria may be predominately psychrophilic to psychrotolerant. To our knowledge, we provide the first rates of denitrification and anammox from permeable sediments of a polar permanently cold ecosystem. The adaptation of microbial communities to in situ temperatures suggests that the relationship between temperature and rates of N

  9. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species.

    Science.gov (United States)

    Papanicolaou, Alexie; Schetelig, Marc F; Arensburger, Peter; Atkinson, Peter W; Benoit, Joshua B; Bourtzis, Kostas; Castañera, Pedro; Cavanaugh, John P; Chao, Hsu; Childers, Christopher; Curril, Ingrid; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dolan, Amanda; Dugan, Shannon; Friedrich, Markus; Gasperi, Giuliano; Geib, Scott; Georgakilas, Georgios; Gibbs, Richard A; Giers, Sarah D; Gomulski, Ludvik M; González-Guzmán, Miguel; Guillem-Amat, Ana; Han, Yi; Hatzigeorgiou, Artemis G; Hernández-Crespo, Pedro; Hughes, Daniel S T; Jones, Jeffery W; Karagkouni, Dimitra; Koskinioti, Panagiota; Lee, Sandra L; Malacrida, Anna R; Manni, Mosè; Mathiopoulos, Kostas; Meccariello, Angela; Murali, Shwetha C; Murphy, Terence D; Muzny, Donna M; Oberhofer, Georg; Ortego, Félix; Paraskevopoulou, Maria D; Poelchau, Monica; Qu, Jiaxin; Reczko, Martin; Robertson, Hugh M; Rosendale, Andrew J; Rosselot, Andrew E; Saccone, Giuseppe; Salvemini, Marco; Savini, Grazia; Schreiner, Patrick; Scolari, Francesca; Siciliano, Paolo; Sim, Sheina B; Tsiamis, George; Ureña, Enric; Vlachos, Ioannis S; Werren, John H; Wimmer, Ernst A; Worley, Kim C; Zacharopoulou, Antigone; Richards, Stephen; Handler, Alfred M

    2016-09-22

    The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control. The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT. The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.

  10. Sparse representation of group-wise FMRI signals.

    Science.gov (United States)

    Lv, Jinglei; Li, Xiang; Zhu, Dajiang; Jiang, Xi; Zhang, Xin; Hu, Xintao; Zhang, Tuo; Guo, Lei; Liu, Tianming

    2013-01-01

    The human brain function involves complex processes with population codes of neuronal activities. Neuroscience research has demonstrated that when representing neuronal activities, sparsity is an important characterizing property. Inspired by this finding, significant amount of efforts from the scientific communities have been recently devoted to sparse representations of signals and patterns, and promising achievements have been made. However, sparse representation of fMRI signals, particularly at the population level of a group of different brains, has been rarely explored yet. In this paper, we present a novel group-wise sparse representation of task-based fMRI signals from multiple subjects via dictionary learning methods. Specifically, we extract and pool task-based fMRI signals for a set of cortical landmarks, each of which possesses intrinsic anatomical correspondence, from a group of subjects. Then an effective online dictionary learning algorithm is employed to learn an over-complete dictionary from the pooled population of fMRI signals based on optimally determined dictionary size. Our experiments have identified meaningful Atoms of Interests (AOI) in the learned dictionary, which correspond to consistent and meaningful functional responses of the brain to external stimulus. Our work demonstrated that sparse representation of group-wise fMRI signals is naturally suitable and effective in recovering population codes of neuronal signals conveyed in fMRI data.

  11. Optimizing stimulation and analysis protocols for neonatal fMRI.

    Science.gov (United States)

    Cusack, Rhodri; Wild, Conor; Linke, Annika C; Arichi, Tomoki; Lee, David S C; Han, Victor K

    2015-01-01

    The development of brain function in young infants is poorly understood. The core challenge is that infants have a limited behavioral repertoire through which brain function can be expressed. Neuroimaging with fMRI has great potential as a way of characterizing typical development, and detecting abnormal development early. But, a number of methodological challenges must first be tackled to improve the robustness and sensitivity of neonatal fMRI. A critical one of these, addressed here, is that the hemodynamic response function (HRF) in pre-term and term neonates differs from that in adults, which has a number of implications for fMRI. We created a realistic model of noise in fMRI data, using resting-state fMRI data from infants and adults, and then conducted simulations to assess the effect of HRF of the power of different stimulation protocols and analysis assumptions (HRF modeling). We found that neonatal fMRI is most powerful if block-durations are kept at the lower range of those typically used in adults (full on/off cycle duration 25-30s). Furthermore, we show that it is important to use the age-appropriate HRF during analysis, as mismatches can lead to reduced power or even inverted signal. Where the appropriate HRF is not known (for example due to potential developmental delay), a flexible basis set performs well, and allows accurate post-hoc estimation of the HRF.

  12. Processing of intentional and automatic number magnitudes in children born prematurely: evidence from fMRI.

    Science.gov (United States)

    Klein, Elise; Moeller, Korbinian; Kiechl-Kohlendorfer, Ursula; Kremser, Christian; Starke, Marc; Cohen Kadosh, Roi; Pupp-Peglow, Ulrike; Schocke, Michael; Kaufmann, Liane

    2014-01-01

    This study examined the neural correlates of intentional and automatic number processing (indexed by number comparison and physical Stroop task, respectively) in 6- and 7-year-old children born prematurely. Behavioral results revealed significant numerical distance and size congruity effects. Imaging results disclosed (1) largely overlapping fronto-parietal activation for intentional and automatic number processing, (2) a frontal to parietal shift of activation upon considering the risk factors gestational age and birth weight, and (3) a task-specific link between math proficiency and functional magnetic resonance imaging (fMRI) signal within distinct regions of the parietal lobes-indicating commonalities but also specificities of intentional and automatic number processing.

  13. Effect of "SOHAM" meditation on the human brain: an fMRI study.

    Science.gov (United States)

    Guleria, Anupam; Kumar, Uttam; Kishan, Sadguru Sri Kunal; Khetrapal, Chunni Lal

    2013-12-30

    The effect of "SOHAM" meditation has been investigated using functional magnetic resonance imaging (fMRI) in long-term meditators while they were meditating and not meditating. The results have revealed activation in left middle prefrontal cortex (MPFC) (Brodmann's area, BA 46), left inferior frontal gyrus (LIFG) (BA 44), left supplementary motor area (SMA) (BA 6) and left precuneus (BA 5) during the meditation period compared to the control period (no-meditation period). The results have been interpreted in terms of regulation of the emotional state, attention and working memory of the meditators.

  14. Semi-blind independent component analysis of fMRI based on real-time fMRI system.

    Science.gov (United States)

    Ma, Xinyue; Zhang, Hang; Zhao, Xiaojie; Yao, Li; Long, Zhiying

    2013-05-01

    Real-time functional magnetic resonance imaging (fMRI) is a type of neurofeedback tool that enables researchers to train individuals to actively gain control over their brain activation. Independent component analysis (ICA) based on data-driven model is seldom used in real-time fMRI studies due to large time cost, though it has been very popular to offline analysis of fMRI data. The feasibility of performing real-time ICA (rtICA) processing has been demonstrated by previous study. However, rtICA was only applied to analyze single-slice data rather than full-brain data. In order to improve the performance of rtICA, we proposed semi-blind real-time ICA (sb-rtICA) for our real-time fMRI system by adding regularization of certain estimated time courses using the experiment paradigm information to rtICA. Both simulated and real-time fMRI experiment were conducted to compare the two approaches. Results from simulated and real full-brain fMRI data demonstrate that sb-rtICA outperforms rtICA in robustness, computational time and spatial detection power. Moreover, in contrast to rtICA, the first component estimated by sb-rtICA tends to be the target component in more sliding windows.

  15. Secretome profile analysis of hypervirulent Mycobacterium tuberculosis CPT31 reveals increased production of EsxB and proteins involved in adaptation to intracellular lifestyle.

    Science.gov (United States)

    Vargas-Romero, Fernado; Guitierrez-Najera, Nora; Mendoza-Hernández, Guillermo; Ortega-Bernal, Daniel; Hernández-Pando, Rogelio; Castañón-Arreola, Mauricio

    2016-03-01

    Epidemiological information and animal models have shown various Mycobacterium tuberculosis phenotypes ranging from hyper- to hypovirulent forms. Recent genomic and proteomic studies suggest that the outcome of infection depends on the M. tuberculosis fitness, which is a direct consequence of its phenotype. However, little is known about the molecular and cellular mechanisms used by mycobacteria to survive, replicate and persist during infection. The aim of this study was to perform a comprehensive proteomic analysis of culture filtrate from hypo- (CPT23) and hypervirulent (CPT31) M. tuberculosis isolates. Using two-dimensional electrophoresis we observed that 70 proteins were unique, or more abundant in culture filtrate of CPT31, and 15 of these were identified by mass spectrometry. Our analysis of protein expression showed that most of the proteins identified are involved in lipid metabolism (FadA3, FbpB and EchA3), detoxification and adaptation (GroEL2, SodB and HspX) and cell wall processes (LprA, Tig and EsxB). These results suggest that overrepresented proteins in M. tuberculosis CPT31 secretome could facilitate mycobacterial infection and persistence.

  16. Host transcriptomic responses to pneumonic plague reveal that Yersinia pestis inhibits both the initial adaptive and innate immune responses in mice.

    Science.gov (United States)

    Yang, Huiying; Wang, Tong; Tian, Guang; Zhang, Qingwen; Wu, Xiaohong; Xin, Youqian; Yan, Yanfeng; Tan, Yafang; Cao, Shiyang; Liu, Wanbing; Cui, Yujun; Yang, Ruifu; Du, Zongmin

    2017-01-01

    Pneumonic plague is the most deadly form of infection caused by Yersinia pestis and can progress extremely fast. However, our understanding on the host transcriptomic response to pneumonic plague is insufficient. Here, we used RNA-sequencing technology to analyze transcriptomic responses in mice infected with fully virulent strain 201 or EV76, a live attenuated vaccine strain lacking the pigmentation locus. Approximately 600 differentially expressed genes (DEGs) were detected in lungs from both 201- and EV76-infected mice at 12h post-infection (hpi). DEGs in lungs of 201-infected mice exceeded 2000 at 48hpi, accompanied by sustained large numbers of DEGs in the liver and spleen; however, limited numbers of DEGs were detected in those organs of EV-infected mice. Remarkably, DEGs in lungs were significantly enriched in critical immune responses pathways in EV76-infected but not 201-infected mice, including antigen processing and presentation, T cell receptor signaling among others. Pathological and bacterial load analyses confirmed the rapid systemic dissemination of 201-infection and the confined EV76-infection in lungs. Our results suggest that fully virulent Y. pestis inhibits both the innate and adaptive immune responses that are substantially stimulated in a self-limited infection, which update our holistic views on the transcriptomic response to pneumonic plague. Copyright © 2016 Elsevier GmbH. All rights reserved.

  17. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Perrea, Toula; Zhou, Yanfeng

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the Food Related...... Lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument...

  18. FMRI and brain activation after sport concussion: a tale of two cases.

    Science.gov (United States)

    Hutchison, Michael G; Schweizer, Tom A; Tam, Fred; Graham, Simon J; Comper, Paul

    2014-01-01

    Sport-related concussions are now recognized as a major public health concern: the number of participants in sport and recreation is growing, possibly playing their games faster, and there is heightened public awareness of injuries to some high-profile athletes. However, many clinicians still rely on subjective symptom reports for the clinical determination of recovery. Relying on subjective symptom reports can be problematic, as it has been shown that some concussed athletes may downplay their symptoms. The use of neuropsychological (NP) testing has enabled clinicians to measure the effects and extent of impairment following concussion more precisely, providing more objective metrics for determining recovery. Nevertheless, there is a remaining concern that brain abnormalities may exist beyond the point at which individuals achieve recovery in self-reported symptoms and cognition measured by NP testing. Our understanding of brain recovery after concussion is important, not only from a neuroscience perspective, but also from the perspective of clinical decision-making for safe return-to-play. A number of advanced neuroimaging tools, including blood oxygen level dependent functional magnetic resonance imaging (fMRI), have independently yielded early information on abnormal brain functioning. In the two cases presented in this article, we report contrasting brain activation patterns and recovery profiles using fMRI. Importantly, fMRI was conducted using adapted versions of the most sensitive computerized NP tests administered in our current clinical practice to determine impairments and recovery after sport-related concussion. One of the cases is consistent with the concept of lagging brain recovery.

  19. fMRI and brain activation after sport concussion: a tale of two cases

    Directory of Open Access Journals (Sweden)

    Michael G Hutchison

    2014-04-01

    Full Text Available Sport-related concussions are now recognized as a major public health concern: The number of participants in sport and recreation is growing, possibly playing their games faster, and there is heightened public awareness of injuries to some high-profile athletes. However, many clinicians still rely on subjective symptom reports for the clinical determination of recovery. Relying on subjective symptom reports can be dangerous, as it has been shown that some concussed athletes may downplay their symptoms. The use of neuropsychological (NP testing tools has enabled clinicians to measure the effects and extent of impairment following concussion more precisely, providing more objective metrics for determining recovery after concussion. Nevertheless, there is a remaining concern that brain abnormalities may exist beyond the point at which individuals achieve recovery in self-reported symptoms and cognition measured by NP testing. Our understanding of brain recovery after concussion is important not only from a neuroscience perspective, but also from the perspective of clinical decision making for safe return-to-play (RTP. A number of advanced neuroimaging tools, including blood oxygen level dependent (BOLD functional magnetic resonance imaging (fMRI, have independently yielded early information on these abnormal brain functions. In the two cases presented in this article, we report contrasting brain activation patterns and recovery profiles using fMRI. Importantly, fMRI was conducted using adapted versions of the most sensitive computerized NP tests administered in current clinical practice to determine impairments and recovery after sport-related concussion. One of the cases is consistent with the concept of lagging brain recovery.

  20. Multi-echo fMRI: A review of applications in fMRI denoising and analysis of BOLD signals.

    Science.gov (United States)

    Kundu, Prantik; Voon, Valerie; Balchandani, Priti; Lombardo, Michael V; Poser, Benedikt A; Bandettini, Peter A

    2017-07-01

    In recent years the field of fMRI research has enjoyed expanded technical abilities related to resolution, as well as use across many fields of brain research. At the same time, the field has also dealt with uncertainty related to many known and unknown effects of artifact in fMRI data. In this review we discuss an emerging fMRI technology, called multi-echo (ME)-fMRI, which focuses on improving the fidelity and interpretability of fMRI. Where the essential problem of standard single-echo fMRI is the indeterminacy of sources of signals, whether BOLD or artifact, this is not the case for ME-fMRI. By acquiring multiple echo images per slice, the ME approach allows T2* decay to be modeled at every voxel at every time point. Since BOLD signals arise by changes in T2* over time, an fMRI experiment sampling the T2* signal decay can be analyzed to distinguish BOLD from artifact signal constituents. While the ME approach has a long history of use in theoretical and validation studies, modern MRI systems enable whole-brain multi-echo fMRI at high resolution. This review covers recent multi-echo fMRI acquisition methods, and the analysis steps for this data to make fMRI at once more principled, straightforward, and powerful. After a brief overview of history and theory, T2* modeling and applications will be discussed. These applications include T2* mapping and combining echoes from ME data to increase BOLD contrast and mitigate dropout artifacts. Next, the modeling of fMRI signal changes to detect signal origins in BOLD-related T2* versus artifact-related S0 changes will be reviewed. A focus is on the use of ME-fMRI data to extract and classify components from spatial ICA, called multi-echo ICA (ME-ICA). After describing how ME-fMRI and ME-ICA lead to a general model for analysis of fMRI signals, applications in animal and human imaging will be discussed. Applications include removing motion artifacts in resting state data at subject and group level. New imaging methods such

  1. Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis.

    Science.gov (United States)

    Halter, David; Casiot, Corinne; Heipieper, Hermann J; Plewniak, Frédéric; Marchal, Marie; Simon, Stéphane; Arsène-Ploetze, Florence; Bertin, Philippe N

    2012-02-01

    Euglena mutabilis is a protist ubiquitously found in extreme environments such as acid mine drainages which are often rich in arsenic. The response of E. mutabilis to this metalloid was compared to that of Euglena gracilis, a protist not found in such environments. Membrane fatty acid composition, cell surface properties, arsenic accumulation kinetics, and intracellular arsenic speciation were determined. The results revealed a modification in fatty acid composition leading to an increased membrane fluidity in both Euglena species under sublethal arsenic concentrations exposure. This increased membrane fluidity correlated to an induced gliding motility observed in E. mutabilis in the presence of this metalloid but did not affect the flagellar dependent motility of E. gracilis. Moreover, when compared to E. gracilis, E. mutabilis showed highly hydrophobic cell surface properties and a higher tolerance to water-soluble arsenical compounds but not to hydrophobic ones. Finally, E. mutabilis showed a lower accumulation of total arsenic in the intracellular compartment and an absence of arsenic methylated species in contrast to E. gracilis. Taken together, our results revealed the existence of a specific arsenical response of E. mutabilis that may play a role in its hypertolerance to this toxic metalloid.

  2. The diminishing dominance of the dominant hemisphere: Language fMRI in focal epilepsy.

    Science.gov (United States)

    Tailby, Chris; Abbott, David F; Jackson, Graeme D

    2017-01-01

    "Which is the dominant hemisphere?" is a question that arises frequently in patients considered for neurosurgery. The concept of the dominant hemisphere implies uniformity of language lateralisation throughout the brain. It is increasingly recognised that this is not the case in the healthy control brain, and it is especially not so in neurological diseases such as epilepsy. In the present work we adapt our published objective lateralisation method (based on the construction of laterality curves) for use with sub-lobar cortical, subcortical and cerebellar regions of interest (ROIs). We apply this method to investigate regional lateralisation of language activation in 12 healthy controls and 18 focal epilepsy patients, using three different block design language fMRI paradigms, each tapping different aspects of language processing. We compared lateralisation within each ROI across tasks, and investigated how the quantity of data collected affected the ability to robustly estimate laterality across ROIs. In controls, lateralisation was stronger, and the variance across individuals smaller, in cortical ROIs, particularly in the Inferior Frontal (Broca) region. Lateralisation within temporal ROIs was dependent on the nature of the language task employed. One of the healthy controls was left lateralised anteriorly and right lateralised posteriorly. Consistent with previous work, departures from normality occurred in ~ 15-50% of focal epilepsy patients across the different ROIs, with atypicality most common in the Lateral Temporal (Wernicke) region. Across tasks and ROIs the absolute magnitude of the laterality estimate increased and its across participant variance decreased as more cycles of task and rest were included, stabilising at ~ 4 cycles (~ 4 min of data collection). Our data highlight the importance of considering language as a complex task where lateralisation varies at the subhemispheric scale. This is especially important for presurgical planning for

  3. The Cyst-Dividing Bacterium Ramlibacter tataouinensis TTB310 Genome Reveals a Well-Stocked Toolbox for Adaptation to a Desert Environment

    Science.gov (United States)

    Ortet, Philippe; Fochesato, Sylvain; Jourlin-Castelli, Cécile; Ansaldi, Mireille; Py, Béatrice; Fichant, Gwennaele; Coutinho, Pedro M.; Voulhoux, Romé; Bastien, Olivier; Maréchal, Eric; Henrissat, Bernard; Quentin, Yves; Noirot, Philippe; Filloux, Alain; Méjean, Vincent; DuBow, Michael S.; Barras, Frédéric; Barbe, Valérie; Weissenbach, Jean; Mihalcescu, Irina; Verméglio, André; Achouak, Wafa; Heulin, Thierry

    2011-01-01

    Ramlibacter tataouinensis TTB310T (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical “cyst-like” cells (“cyst-cyst” division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed. PMID:21912644

  4. Physiological responses of emerald ash borer larvae to feeding on different ash species reveal putative resistance mechanisms and insect counter-adaptations.

    Science.gov (United States)

    Rigsby, C M; Showalter, D N; Herms, D A; Koch, J L; Bonello, P; Cipollini, D

    2015-07-01

    Emerald ash borer, Agrilus planipennis Fairmaire, an Asian wood-boring beetle, has devastated ash (Fraxinus spp.) trees in North American forests and landscapes since its discovery there in 2002. In this study, we collected living larvae from EAB-resistant Manchurian ash (Fraxinus mandschurica), and susceptible white (Fraxinus americana) and green (Fraxinus pennsylvanica) ash hosts, and quantified the activity and production of selected detoxification, digestive, and antioxidant enzymes. We hypothesized that differences in larval physiology could be used to infer resistance mechanisms of ash. We found no differences in cytochrome P450, glutathione-S-transferase, carboxylesterase, sulfotransferase, and tryptic BApNAase activities between larvae feeding on different hosts. Despite this, Manchurian ash-fed larvae produced a single isozyme of low electrophoretic mobility that was not produced in white or green ash-fed larvae. Additionally, larvae feeding on white and green ash produced two serine protease isozymes of high electrophoretic mobility that were not observed in Manchurian ash-fed larvae. We also found lower activity of β-glucosidase and higher activities of monoamine oxidase, ortho-quinone reductase, catalase, superoxide dismutase, and glutathione reductase in Manchurian ash-fed larvae compared to larvae that had fed on susceptible ash. A single isozyme was detected for both catalase and superoxide dismutase in all larval groups. The activities of the quinone-protective and antioxidant enzymes are consistent with the resistance phenotype of the host species, with the highest activities measured in larvae feeding on resistant Manchurian ash. We conclude that larvae feeding on Manchurian ash could be under quinone and oxidative stress, suggesting these may be potential mechanisms of resistance of Manchurian ash to EAB larvae, and that quinone-protective and antioxidant enzymes are important counter-adaptations of larvae for dealing with these resistance

  5. Mycobiome of the bat white nose syndrome affected caves and mines reveals diversity of fungi and local adaptation by the fungal pathogen Pseudogymnoascus (Geomyces destructans.

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    Full Text Available Current investigations of bat White Nose Syndrome (WNS and the causative fungus Pseudogymnoascus (Geomyces destructans (Pd are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010-2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD and culture-independent (CI methods to catalogue all fungi ('mycobiome'. CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS. The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS.

  6. Optimized design and analysis of sparse-sampling FMRI experiments.

    Science.gov (United States)

    Perrachione, Tyler K; Ghosh, Satrajit S

    2013-01-01

    Sparse-sampling is an important methodological advance in functional magnetic resonance imaging (fMRI), in which silent delays are introduced between MR volume acquisitions, allowing for the presentation of auditory stimuli without contamination by acoustic scanner noise and for overt vocal responses without motion-induced artifacts in the functional time series. As such, the sparse-sampling technique has become a mainstay of principled fMRI research into the cognitive and systems neuroscience of speech, language, hearing, and music. Despite being in use for over a decade, there has been little systematic investigation of the acquisition parameters, experimental design considerations, and statistical analysis approaches that bear on the results and interpretation of sparse-sampling fMRI experiments. In this report, we examined how design and analysis choices related to the duration of repetition time (TR) delay (an acquisition parameter), stimulation rate (an experimental design parameter), and model basis function (an analysis parameter) act independently and interactively to affect the neural activation profiles observed in fMRI. First, we conducted a series of computational simulations to explore the parameter space of sparse design and analysis with respect to these variables; second, we validated the results of these simulations in a series of sparse-sampling fMRI experiments. Overall, these experiments suggest the employment of three methodological approaches that can, in many situations, substantially improve the detection of neurophysiological response in sparse fMRI: (1) Sparse analyses should utilize a physiologically informed model that incorporates hemodynamic response convolution to reduce model error. (2) The design of sparse fMRI experiments should maintain a high rate of stimulus presentation to maximize effect size. (3) TR delays of short to intermediate length can be used between acquisitions of sparse-sampled functional image volumes to increase

  7. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Perrea, Toula; Zhou, Yanfeng

    Lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument......, which was tested for statistical robustness and used as a basis for the derivation of consumer segments. Construct validity of the instrument was then investigated by profiling the segments in terms of consumer values, attitudes and purchase behaviour, using frequency of consumption of pork products...... as an example. Three consumer segments were identified: concerned, uninvolved and traditional. This pattern is not unlike those identified in Western cultures. Moreover, all three segments showed remarkably consistent value-attitude-behaviour profiles. The present study offers empirical evidence...

  8. Brain imaging studies in children with attention-deficit hyperactivity disorder revealed by resting-state fMRI fALFF analysis%注意缺陷多动障碍儿童静息态功能磁共振比率低频振幅的研究

    Institute of Scientific and Technical Information of China (English)

    杨志龙; 王苏弘; 曹健; 任艳玲; 蔡婧; 张毅力; 马岭; 董选

    2010-01-01

    目的 使用静息态功能磁共振(fMRI)比率低频振幅(fALFF)测量技术,从能量的角度对注意缺陷多动障碍(ADHD)儿童与正常儿童进行比较分析,探讨ADHD儿童执行控制脑功能失调病理机制.方法 分别对30例学龄期ADHD儿童与30名性别、年龄、受教育程度均相匹配的正常儿童进行静息态fMRI扫描,采用比率低频振幅算法作为指标进行比较分析.结果 同正常组比较,fALFF值降低区:双侧额上回(BA10,t=5.40,4.11,Z=4.81,3.82),双侧额中回(BA9,BA46,t=5.72,5.37,Z=5.04,3.08),右侧额内侧回(BA10,t=5.53,Z=4.90),左楔叶(t=3.81,Z=3.57);fALFF值升高区:双侧边缘叶(BA36,t=4.37,5.20,Z=4.02,4.66),右侧脑干(t=4.77,Z=4.34),双侧小脑(t=4.65,4.83,Z=4.24,4.38).结论 研究提示在静息状态下前额叶的激活降低,其调控的执行控制功能缺陷是ADHD的核心缺陷.在一些脑区表现的高激活区,可能与ADHD执行控制脑功能失调代偿作用有关.%Objective To investigate pathological mechanism of dysfunction of executive control in children with attention-deficit hyperactivity disorder (ADHD) ,using a new resting-state functional magnetic resonance imaging(fMRI) index, fractional amplitude of low frequency fluctuation (fALFF). Methods Thirty children of school age with ADHD and thirty gender, age and education-matched healthy controls were experienced restingstate fMRI scans. fALFF approach was used to analyze blood oxygen level-dependent fMRI(BOLD-fMRI) data in resting state. Results Compared with the normal controls,the ADHD showed decreased fALFF in the bilateral superior frontal gyrus( BA10, t=5. 40,4.11 ,Z =4.81,3.82),bilateral middle frontal gyrus( BA9,BA46, t=5.72,5.37, Z = 5.04,3.08 ), right medial frontal gyrus ( BA 10, t = 5.53, Z = 4.90 ) and left precuneus ( t = 3.81, Z =3.57). And the ADHD showed increased fALFF in the bilateral limbic lobe (BA36, t = 4.37,5.20, Z = 4.02,4.66 ), right brainstem ( t = 4.77, Z = 4.34) and bilateral

  9. High resolution fMRI of subcortical regions during visual erotic stimulation at 7 T.

    Science.gov (United States)

    Walter, Martin; Stadler, Joerg; Tempelmann, Claus; Speck, Oliver; Northoff, Georg

    2008-03-01

    Involvement of distinct subcortical structures during sexual arousal was shown in animals and functional imaging studies gave coarse evidence for a similar organisation in humans. In contrast to previous imaging studies at lower field strengths, we tried to investigate activation in distinguishable subcortical structures at high spatial resolution during a short stimulating paradigm to further account for potential effects of attenuation or adaptation. Seven healthy subjects were investigated using functional magnetic resonance imaging (fMRI) on a 7 T scanner. High resolution EPI images of 1.4 x 1.4 mm2 inplane resolution were acquired in a single functional session of 13.6 minutes. During the session erotic and non-erotic pictures were presented in an event-related design. In the unsmoothed data with preserved high spatial resolution significant effects were detected in relevant structures, including anterior caudate and mediodorsal thalamus. These effects were restricted to subcortical target structures and their anatomical boundaries. This study demonstrates that fMRI at high fields provides an ideal tool to investigate functional anatomy of subcortical structures. Due to an increased signal-to-noise ratio, functional scans of short duration can be acquired at high resolution without the need for further spatial smoothing.

  10. fMRI neurofeedback facilitates anxiety regulation in females with spider phobia

    Directory of Open Access Journals (Sweden)

    Anna eZilverstand

    2015-06-01

    Full Text Available Background: Spider phobics show an exaggerated fear response when encountering spiders. This fear response is aggravated by negative and irrational beliefs about the feared object. Cognitive reappraisal can target these beliefs, and therefore has a fear regulating effect. The presented study investigated if neurofeedback derived from functional magnetic resonance imaging (fMRI would facilitate anxiety regulation by cognitive reappraisal, using spider phobia as a model of anxiety disorders. Feedback was provided based on activation in left dorsolateral prefrontal cortex and right insula, as indicators of engagement and regulation success, respectively.Methods: Eighteen female spider phobics participated in a randomized, controlled, single-blinded study. All participants completed a training session in the MRI scanner. Participants assigned to the neurofeedback condition were instructed to shape their regulatory strategy based on the provided feedback. Participants assigned to the control condition were asked to adapt their strategy intuitively.Results: Neurofeedback participants exhibited lower anxiety levels than the control group at the end of the training. In addition, only neurofeedback participants achieved down-regulation of insula activation levels by cognitive reappraisal. Group differences became more pronounced over time, supporting learning as a mechanism behind this effect. Importantly, within the neurofeedback group, achieved changes in insula activation levels during training predicted long-term anxiety reduction.Conclusions: The conducted study provides first evidence that fMRI neurofeedback has a facilitating effect on anxiety regulation in spider phobia.

  11. fMRI. Basics and clinical applications. 2. ed.

    Energy Technology Data Exchange (ETDEWEB)

    Ulmer, Stephan [Medizinisch Radiologisces Institut (MRI), Zuerich (Switzerland); Universitaetsklinikum Schleswig-Holstein, Kiel (Germany). Inst. fuer Neuroradiologie; Jansen, Olav (eds.) [Universitaetsklinikum Schleswig-Holstein, Kiel (Germany). Inst. fuer Neuroradiologie

    2013-11-01

    State of the art overview of fMRI. Covers technical issues, methods of statistical analysis, and the full range of clinical applications. Revised and expanded edition including discussion of novel aspects of analysis and further important applications. Includes comparisons with other brain mapping techniques and discussion of potential combined uses. Since functional MRI (fMRI) and the basic method of BOLD imaging were introduced in 1993 by Seiji Ogawa, fMRI has evolved into an invaluable clinical tool for routine brain imaging, and there have been substantial improvements in both the imaging technique itself and the associated statistical analysis. This book provides a state of the art overview of fMRI and its use in clinical practice. Experts in the field share their knowledge and explain how to overcome diverse potential technical barriers and problems. Starting from the very basics on the origin of the BOLD signal, the book covers technical issues, anatomical landmarks, the full range of clinical applications, methods of statistical analysis, and special issues in various clinical fields. Comparisons are made with other brain mapping techniques, such as DTI, PET, TMS, EEG, and MEG, and their combined use with fMRI is also discussed. Since the first edition, original chapters have been updated and new chapters added, covering both novel aspects of analysis and further important clinical applications.

  12. Changes in Brain Activation Associated with Spontaneous Improvization and Figural Creativity After Design-Thinking-Based Training: A Longitudinal fMRI Study.

    Science.gov (United States)

    Saggar, Manish; Quintin, Eve-Marie; Bott, Nicholas T; Kienitz, Eliza; Chien, Yin-Hsuan; Hong, Daniel W-C; Liu, Ning; Royalty, Adam; Hawthorne, Grace; Reiss, Allan L

    2016-06-15

    Creativity is widely recognized as an essential skill for entrepreneurial success and adaptation to daily-life demands. However, we know little about the neural changes associated with creative capacity enhancement. For the first time, using a prospective, randomized control design, we examined longitudinal changes in brain activity associated with participating in a five-week design-thinking-based Creative Capacity Building Program (CCBP), when compared with Language Capacity Building Program (LCBP). Creativity, an elusive and multifaceted construct, is loosely defined as an ability to produce useful/appropriate and novel outcomes. Here, we focus on one of the facets of creative thinking-spontaneous improvization. Participants were assessed pre- and post-intervention for spontaneous improvization skills using a game-like figural Pictionary-based fMRI task. Whole-brain group-by-time interaction revealed reduced task-related activity in CCBP participants (compared with LCBP participants) after training in the right dorsolateral prefrontal cortex, anterior/paracingulate gyrus, supplementary motor area, and parietal regions. Further, greater cerebellar-cerebral connectivity was observed in CCBP participants at post-intervention when compared with LCBP participants. In sum, our results suggest that improvization-based creative capacity enhancement is associated with reduced engagement of executive functioning regions and increased involvement of spontaneous implicit processing.

  13. Targeted capture sequencing in whitebark pine reveals range-wide demographic and adaptive patterns despite challenges of a large, repetitive genome

    Directory of Open Access Journals (Sweden)

    John eSyring

    2016-04-01

    Full Text Available Whitebark pine (Pinus albicaulis inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and it is suffering significant mortality range-wide, prompting the tree to be listed as ‘globally endangered’ by the International Union for Conservation of Nature (IUCN and ‘endangered’ by the Canadian government. Conservation collections (in situ and ex situ are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 30+ GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp, and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits, targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect

  14. Brain correlates of hypnotic paralysis-a resting-state fMRI study.

    Science.gov (United States)

    Pyka, M; Burgmer, M; Lenzen, T; Pioch, R; Dannlowski, U; Pfleiderer, B; Ewert, A W; Heuft, G; Arolt, V; Konrad, C

    2011-06-15

    Hypnotic paralysis has been used since the times of Charcot to study altered states of consciousness; however, the underlying neurobiological correlates are poorly understood. We investigated human brain function during hypnotic paralysis using resting-state functional magnetic resonance imaging (fMRI), focussing on two core regions of the default mode network and the representation of the paralysed hand in the primary motor cortex. Hypnotic suggestion induced an observable left-hand paralysis in 19 participants. Resting-state fMRI at 3T was performed in pseudo-randomised order awake and in the hypnotic condition. Functional connectivity analyses revealed increased connectivity of the precuneus with the right dorsolateral prefrontal cortex, angular gyrus, and a dorsal part of the precuneus. Functional connectivity of the medial frontal cortex and the primary motor cortex remained unchanged. Our results reveal that the precuneus plays a pivotal role during maintenance of an altered state of consciousness. The increased coupling of selective cortical areas with the precuneus supports the concept that hypnotic paralysis may be mediated by a modified representation of the self which impacts motor abilities. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. fMRI characterization of visual working memory recognition.

    Science.gov (United States)

    Rahm, Benjamin; Kaiser, Jochen; Unterrainer, Josef M; Simon, Juliane; Bledowski, Christoph

    2014-04-15

    Encoding and maintenance of information in visual working memory have been extensively studied, highlighting the crucial and capacity-limiting role of fronto-parietal regions. In contrast, the neural basis of recognition in visual working memory has remained largely unspecified. Cognitive models suggest that recognition relies on a matching process that compares sensory information with the mental representations held in memory. To characterize the neural basis of recognition we varied both the need for recognition and the degree of similarity between the probe item and the memory contents, while independently manipulating memory load to produce load-related fronto-parietal activations. fMRI revealed a fractionation of working memory functions across four distributed networks. First, fronto-parietal regions were activated independent of the need for recognition. Second, anterior parts of load-related parietal regions contributed to recognition but their activations were independent of the difficulty of matching in terms of sample-probe similarity. These results argue against a key role of the fronto-parietal attention network in recognition. Rather the third group of regions including bilateral temporo-parietal junction, posterior cingulate cortex and superior frontal sulcus reflected demands on matching both in terms of sample-probe-similarity and the number of items to be compared. Also, fourth, bilateral motor regions and right superior parietal cortex showed higher activation when matching provided clear evidence for a decision. Together, the segregation between the well-known fronto-parietal activations attributed to attentional operations in working memory from those regions involved in matching supports the theoretical view of separable attentional and mnemonic contributions to working memory. Yet, the close theoretical and empirical correspondence to perceptual decision making may call for an explicit consideration of decision making mechanisms in

  16. Brain imaging studies in children with attention-deficit hyperactivity disorder revealed by resting-state fMRI degree centrality analysis%注意缺陷多动障碍儿童静息态功能磁共振度中心度的研究

    Institute of Scientific and Technical Information of China (English)

    江凯华; 沈惠娟; 李红新; 高敏; 易阳; 吴婷; 屠文娟; 张琴芬; 董选

    2014-01-01

    Objective To investigate the pathologic mechanisms of functional brain regions in attentiondeficit hyperactivity disorder (ADHD) patients through making comparisons of normal and ADHD children from the perspective of the network nodes with degree centrality(DC) analysis approach of resting-state functional magnetic resonance imaging(fMRI).Methods To carry out data analysis through DC approach on 30 school-age children and 30 ADHD children,both of whom had been examined by resting-state fMRI scans.Results It showed that ADHD children's scores were lower in the right posterior cingulate gyms,left medial superior frontal gyms,right inferior parietal gyrus,right middle frontal gyrus,left superior frontal gyrus and right superior frontal gyrus(t=-5.21,-3.53,-4.87,-4.21,-3.56,-4.06).There was statistically significant difference between the two groups (P<0.05).However,the ADHD group got higher DC scores in the cerebellar anterior lobe,right middle occipital,left middle cingulte gyrus and right middle cingulte gyrus than those of normal children (t =4.27,4.25,4.80,5.33).There was statistically significant difference between the two groups(P<0.05).Conclusion It is deemed that the decrease of DC in the default mode of network (DMN) and frontal gyrus results in the damage of central brain structure,which further leads to ADHD children' s difficulties in cognitive memory and executive control.Together with the influence of ADHD cerebral functional compensation,the increase of DC is believed to be connected with executive control disorders and aprosexia.DC is regarded as a new research method to study cognitive disorders of ADHD children.%目的 运用静息态功能磁共振(functional magnetic resonance imaging,fMRI)度中心度(degree centrality,DC)的分析技术,从网络节点的角度对注意缺陷多动障碍(attention-deficit hyperactivity disorder,ADHD)儿童与正常儿童进行比较研究,探讨ADHD功能脑区的病理机制.方法 学

  17. Archetypal Analysis for Modeling Multisubject fMRI Data

    DEFF Research Database (Denmark)

    Hinrich, Jesper Løve; Bardenfleth, Sophia Elizabeth; Røge, Rasmus

    2016-01-01

    Functional magnetic resonance imaging (fMRI) is widely used to measure brain function during various cognitive states. However, it remains a challenge to obtain low-rank models of functional networks in fMRI that have interpretable latent features and generalize across groups of subjects, due...... are assumed to be generated by a set of 'prototype' time series. Archetypal analysis (AA) provides a promising alternative, combining the advantages of component-model flexibility with highly interpretable latent 'archetypes' (similar to cluster-model prototypes). To date, AA has not been applied to group......-level fMRI; a major limitation is that it does not generalize to multi-subject datasets, which may have significant variations in blood oxygenation-level-dependent signal and heteroscedastic noise. We develop multi-subject AA (MS-AA), which accounts for group-level data by assuming that archetypal...

  18. fMRI as a molecular imaging procedure for the functional reorganization of motor systems in chronic stroke

    Science.gov (United States)

    LAZARIDOU, ASIMINA; ASTRAKAS, LOUKAS; MINTZOPOULOS, DIONYSSIOS; KHANCHICEH, AZADEH; SINGHAL, ANEESH; MOSKOWITZ, MICHAEL; ROSEN, BRUCE; TZIKA, ARIA

    2013-01-01

    Previous brain imaging studies suggest that stroke alters functional connectivity in motor execution networks. Moreover, current understanding of brain plasticity has led to new approaches in stroke rehabilitation. Recent studies showed a significant role of effective coupling of neuronal activity in the SMA (supplementary motor area) and M1 (primary motor cortex) network for motor outcome in patients after stroke. After a subcortical stroke, functional magnetic resonance imaging (fMRI) during movement reveals cortical reorganization that is associated with the recovery of function. The aim of the present study was to explore connectivity alterations within the motor-related areas combining motor fMRI with a novel MR-compatible hand-induced robotic device (MR_CHIROD) training. Patients completed training at home and underwent serial MR evaluation at baseline and after 8 weeks of training. Training at home consisted of squeezing a gel exercise ball with the paretic hand at ~75% of maximum strength for 1 h/day, 3 days/week. The fMRI analysis revealed alterations in M1, SMA, PMC (premotor cortex) and Cer (cerebellum) in both stroke patients and healthy controls after the training. Findings of the present study suggest that enhancement of SMA activity could benefit M1 dysfunction in stroke survivors. These results also indicate that connectivity alterations between motor areas might assist the counterbalance of a functionally abnormal M1 in chronic stroke survivors and possibly other patients with motor dysfunction. PMID:23900349

  19. Compensatory cortical activation observed by fMRI during a cognitive task at the earliest stage of MS.

    Science.gov (United States)

    Audoin, Bertrand; Ibarrola, Danielle; Ranjeva, Jean-Philippe; Confort-Gouny, Sylviane; Malikova, Irina; Ali-Chérif, André; Pelletier, Jean; Cozzone, Patrick

    2003-10-01

    Recent functional magnetic resonance imaging (fMRI) studies have suggested that functional cortical changes seen in patients with early relapsing-remitting multiple sclerosis (MS) can have an adaptive role to limit the clinical impact of tissue injury. To determine whether cortical reorganization occurs during high cognitive processes at the earliest stage of multiple sclerosis (MS), we performed an fMRI experiment using the conventional Paced Auditory Serial Addition Test (PASAT) as paradigm in a population of ten patients with clinically isolated syndrome suggestive of multiple sclerosis (CISSMS). At the time of the fMRI exploration, mean disease duration was 6.8 +/- 3.3 months. We compared these results to those obtained in a group of ten education-, age-, and sex-matched healthy controls. Subjects were explored on a 1.5 T MRI system using single-shot gradient-echo EPI sequence. Performances of the two groups during PASAT recorded inside the MR scanner were not different. Statistical assessment of brain activation was based on the random effect analysis (between-group analysis two-sample t-test P < 0.005 confirmed by individual analyses performed in the surviving regions P < 0.05 Mann Whitney U-test). Compared to controls, patients showed significantly greater activation in the right frontopolar cortex, the bilateral lateral prefrontal cortices, and the right cerebellum. Healthy controls did not show greater activation compared to CISSMS patients. The present study argues in favor of the existence of compensatory cortical activations at the earliest stage of MS mainly located in regions involved in executive processing in patients performing PASAT. It also suggests that fMRI can evidence the active processes of neuroplasticity contributing to mask the clinical cognitive expression of brain pathology at the earliest stage of MS.

  20. Multimodal integration of EEG, MEG and fMRI data for the solution of the neuroimage puzzle.

    Science.gov (United States)

    Babiloni, Fabio; Mattia, Donetella; Babiloni, Claudio; Astolfi, Laura; Salinari, Serenella; Basilisco, Alessandra; Rossini, Paolo Maria; Marciani, Maria Grazia; Cincotti, Febo

    2004-12-01

    In this paper, advanced methods for the modeling of human cortical activity from combined high-resolution electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) data are presented. These methods include a subject's multicompartment head model (scalp, skull, dura mater, cortex) constructed from magnetic resonance images, multidipole source model and regularized linear inverse source estimates of cortical current density. Determination of the priors in the resolution of the linear inverse problem was performed with the use of information from the hemodynamic responses of the cortical areas as revealed by block-designed (strength of activated voxels) fMRI. Examples of the application of these methods to the estimation of the time varying cortical current density activity in selected region of interest (ROI) are presented for movement-related high-resolution EEG data.

  1. The role of the DLPFC in inductive reasoning of MCI patients and normal agings: an fMRI study.

    Science.gov (United States)

    Yang, YanHui; Liang, PeiPeng; Lu, ShengFu; Li, KunCheng; Zhong, Ning

    2009-08-01

    Previous studies of young people have revealed that the left dorsolateral prefrontal cortex (DLPFC) plays an important role in inductive reasoning. An fMRI experiment was performed in this study to examine whether the left DLPFC was involved in inductive reasoning of MCI patients and normal aging, and whether the activation pattern of this region was different between MCI patients and normal aging. The fMRI results indicated that MCI patients had no difference from normal aging in behavior performance (reaction time and accuracy) and the activation pattern of DLPFC. However, the BOLD response of the DLPFC region for MCI patients was weaker than that for normal aging, and the functional connectivity between the bilateral DLPFC regions for MCI patients was significantly higher than for normal aging. Taken together, these results indicated that DLPFC plays an important role in inductive reasoning of aging, and the functional abnormity of DLPFC may be an earlier marker of MCI before structural alterations.

  2. Olfactory fMRI in patients with Parkinson’s disease

    Directory of Open Access Journals (Sweden)

    Thomas Hummel

    2010-10-01

    Full Text Available Hyposmia is one of the early signs in Idiopathic Parkinson´s Disease (PD. Olfactory stimuli were applied during fMRI scanning to show disease-related modulation of central nervous system structures and to advance our understanding of olfactory dysfunction in PD patients. All participants received either unpleasant stimuli smelling like rotten eggs or pleasant ones smelling like roses. Using a block design at a 1.5 T scanner we investigated a total of 8 PD patients (mean age 60 ± 10.9 years and 13 age matched controls (mean age 58 ± 9.6 years. PD duration ranged from 1 to 9 years (mean 6.63 years; patients had an average “Unified Parkinson’s Disease Rating Scale III” score of 23.25 (range, 6-46. Olfactory function was established using the “Sniffin’ Sticks” test battery. Patients tended to rate the stimuli presented during fMRI scans as less intense, but also as more pleasant than controls. FMRI results revealed differences between PD patients and controls which depended on the type of stimulation. While both pleasant and unpleasant stimulation was associated with lower activation in the amygdalo-hippocampal complex in patients compared to controls, increased activity in response to pleasant stimuli was observed in the striatum and the left inferior frontal gyrus. In contrast, unpleasant stimulation led to hypoactivation of the ventral striatum in patients (but not in controls and did not enhance left inferior frontal activity. These results may partly reflect differences between PD patients and healthy controls in the processing of primary dimensions of odors, intensity and valence.

  3. Perception of biological motion in schizophrenia and healthy individuals: a behavioral and FMRI study.

    Directory of Open Access Journals (Sweden)

    Jejoong Kim

    Full Text Available BACKGROUND: Anomalous visual perception is a common feature of schizophrenia plausibly associated with impaired social cognition that, in turn, could affect social behavior. Past research suggests impairment in biological motion perception in schizophrenia. Behavioral and functional magnetic resonance imaging (fMRI experiments were conducted to verify the existence of this impairment, to clarify its perceptual basis, and to identify accompanying neural concomitants of those deficits. METHODOLOGY/FINDINGS: In Experiment 1, we measured ability to detect biological motion portrayed by point-light animations embedded within masking noise. Experiment 2 measured discrimination accuracy for pairs of point-light biological motion sequences differing in the degree of perturbation of the kinematics portrayed in those sequences. Experiment 3 measured BOLD signals using event-related fMRI during a biological motion categorization task. Compared to healthy individuals, schizophrenia patients performed significantly worse on both the detection (Experiment 1 and discrimination (Experiment 2 tasks. Consistent with the behavioral results, the fMRI study revealed that healthy individuals exhibited strong activation to biological motion, but not to scrambled motion in the posterior portion of the superior temporal sulcus (STSp. Interestingly, strong STSp activation was also observed for scrambled or partially scrambled motion when the healthy participants perceived it as normal biological motion. On the other hand, STSp activation in schizophrenia patients was not selective to biological or scrambled motion. CONCLUSION: Schizophrenia is accompanied by difficulties discriminating biological from non-biological motion, and associated with those difficulties are altered patterns of neural responses within brain area STSp. The perceptual deficits exhibited by schizophrenia patients may be an exaggerated manifestation of neural events within STSp associated with

  4. fMRI in patients with lumbar disc disease: a paradigm to study patients over time

    Directory of Open Access Journals (Sweden)

    Sharma HA

    2011-12-01

    Full Text Available Harish A Sharma1, Rajarsi Gupta2, William Olivero31Robarts Imaging, University of Western Ontario, London, ON, Canada; 2University of Illinois, Urbana, IL, USA; 3Neurological Surgery, University of Illinois UC/Carle Foundation Hospital, Urbana, IL, USAAbstract: Low back pain is a common human ailment. It is estimated that over 70% of the population will experience low back pain that will require medication and/or medical attention. There are many causes for low back pain, one being herniation of the discs of the lumbar spine. Treatment options are very limited. Why patients develop chronic pain especially when there is no known organic cause or when the offending painful stimulus has been removed remains poorly understood. Functional magnetic resonance imaging (fMRI is a technique that allows researchers to image which regions of the brain that are activated during motor, cognitive, and sensory experiences. Using fMRI to study pain has revealed new information about how the brain responds to painful stimuli and what regions of the brain are activated during pain. However, many of the paradigms used do not replicate the subject's pain or use painful stimuli in volunteers without pain. Also, following patients from their acute phase of pain to the chronic phase with serial fMRI has not been performed. In this study we developed a paradigm that would allow studying patients with low back pain and leg pain including lumbar radiculopathy to better mimic a clinical pain syndrome and to have a method of following patients with this type of pain over time.Keywords: functional magnetic resonance imaging, low back pain, pain syndrome, chronic pain

  5. Investigating Inhibitory Control in Children with Epilepsy: An fMRI Study

    Science.gov (United States)

    Triplett, Regina L.; Velanova, Katerina; Luna, Beatriz; Padmanabhan, Aarthi; Gaillard, William D.; Asato, Miya R.

    2014-01-01

    SUMMARY Objective Deficits in executive function are increasingly noted in children with epilepsy and have been associated with poor academic and psychosocial outcomes. Impaired inhibitory control contributes to executive dysfunction in children with epilepsy; however, its neuroanatomic basis has not yet been investigated. We used functional Magnetic Resonance Imaging (fMRI) to probe the integrity of activation in brain regions underlying inhibitory control in children with epilepsy. Methods This cross-sectional study consisted of 34 children aged 8 to 17 years: 17 with well-controlled epilepsy and 17 age-and sex-matched controls. Participants performed the antisaccade (AS) task, representative of inhibitory control, during fMRI scanning. We compared AS performance during neutral and reward task conditions and evaluated task-related blood-oxygen level dependent (BOLD) activation. Results Children with epilepsy demonstrated impaired AS performance compared to controls during both neutral (non-reward) and reward trials, but exhibited significant task improvement during reward trials. Post-hoc analysis revealed that younger patients made more errors than older patients and all controls. fMRI results showed preserved activation in task-relevant regions in patients and controls, with the exception of increased activation in the left posterior cingulate gyrus in patients specifically with generalized epilepsy across neutral and reward trials. Significance Despite impaired inhibitory control, children with epilepsy accessed typical neural pathways as did their peers without epilepsy. Children with epilepsy showed improved behavioral performance in response to the reward condition, suggesting potential benefits of the use of incentives in cognitive remediation. PMID:25223606

  6. Neural underpinnings of nocebo hyperalgesia in visceral pain: A fMRI study in healthy volunteers.

    Science.gov (United States)

    Schmid, Julia; Bingel, Ulrike; Ritter, Christoph; Benson, Sven; Schedlowski, Manfred; Gramsch, Carolin; Forsting, Michael; Elsenbruch, Sigrid

    2015-10-15

    Despite the clinical relevance of nocebo effects, few studies have addressed their underlying neural mechanisms in clinically-relevant pain models. We aimed to address the contribution of nocebo effects and their underlying neural circuitry to central pain amplification in visceral pain, as it may develop over repeated painful experiences due to negative pain-related expectations. Healthy volunteers received verbal suggestions of pain sensitization (nocebo group, N=28) or neutral instructions (control group, N=16). fMRI was used to investigate changes in neural responses during cued pain anticipation and painful rectal distensions delivered in successive fMRI sessions. Pain intensity was rated trial-by-trial, and expected pain intensity, state anxiety and tension were assessed prior to each session. Behavioral analyses demonstrated significantly greater increases in both expected and perceived pain in the nocebo group. The fMRI analysis performed on nocebo-responders only (N=14) revealed that these behavioral changes were associated with increased activation within the secondary somatosensory cortex and amygdala during pain anticipation and within the thalamus, insula and amygdala during painful stimulation when compared to controls. A subsequent psycho-physiological interaction analysis of the pain phase showed increased functional connectivity between the anterior insula, which was set-up as seed region based on group results, and midcingulate cortex as a function of negative expectations. These findings support that negative pain-related expectations can play a crucial role in pain amplification of visceral pain, which is mediated, at least in part, by a neural up-regulation of pain-associated areas and their connectivity. These findings may have implications for the pathophysiology and treatment of chronic abdominal pain. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Altered Dynamics of the fMRI Response to Faces in Individuals with Autism

    Science.gov (United States)

    Kleinhans, Natalia M.; Richards, Todd; Greenson, Jessica; Dawson, Geraldine; Aylward, Elizabeth

    2016-01-01

    Abnormal fMRI habituation in autism spectrum disorders (ASDs) has been proposed as a critical component in social impairment. This study investigated habituation to fearful faces and houses in ASD and whether fMRI measures of brain activity discriminate between ASD and typically developing (TD) controls. Two identical fMRI runs presenting masked…

  8. Neuroethics and fMRI: Mapping a fledgling relationship

    DEFF Research Database (Denmark)

    Garnett, Alex; Whiteley, Louise Emma; Piwowar, Heather;

    2011-01-01

    of moral judgments. It is at the centre of debate surrounding the importance of neuroscience findings for concepts such as personhood and free will, and the extent of their practical consequences. Here, we map the landscape of fMRI and neuroethics, using citation analysis to uncover salient topics. We find...... that this landscape is sparsely populated: despite previous calls for debate, there are few articles that discuss both fMRI and ethical, legal, or social implications (ELSI), and even fewer direct citations between the two literatures. Recognizing that practical barriers exist to integrating ELSI discussion...

  9. Mixed-effects and fMRI studies

    DEFF Research Database (Denmark)

    Friston, K.J; Stephan, K.E; Ellegaard Lund, Torben

    2005-01-01

    This note concerns mixed-effect (MFX) analyses in multisession functional magnetic resonance imaging (fMRI) studies. It clarifies the relationship between mixed-effect analyses and the two-stage 'summary statistics' procedure (Holmes, A.P., Friston, K.J., 1998. Generalisability, random effects...... and population inference. NeuroImage 7, S754) that has been adopted widely for analyses of fMRI data at the group level. We describe a simple procedure, based on restricted maximum likelihood (ReML) estimates of covariance components, that enables full mixed-effects analyses in the context of statistical...

  10. Temporal and Spatial Independent Component Analysis for fMRI Data Sets Embedded in the AnalyzeFMRI R Package

    Directory of Open Access Journals (Sweden)

    Pierre Lafaye de Micheaux

    2011-10-01

    Full Text Available For statistical analysis of functional magnetic resonance imaging (fMRI data sets, we propose a data-driven approach based on independent component analysis (ICA implemented in a new version of the AnalyzeFMRI R package. For fMRI data sets, spatial dimension being much greater than temporal dimension, spatial ICA is the computationally tractable approach generally proposed. However, for some neuroscientific applications, temporal independence of source signals can be assumed and temporal ICA becomes then an attractive exploratory technique. In this work, we use a classical linear algebra result ensuring the tractability of temporal ICA. We report several experiments on synthetic data and real MRI data sets that demonstrate the potential interest of our R package.

  11. Spinal fMRI during proprioceptive and tactile tasks in healthy subjects: activity detected using cross-correlation, general linear model and independent component analysis

    Energy Technology Data Exchange (ETDEWEB)

    Valsasina, P.; Agosta, F.; Filippi, M. [Scientific Institute Ospedale San Raffaele, Neuroimaging Research Unit, Milan (Italy); Caputo, D. [Scientific Institute Fondazione Don Gnocchi, Department of Neurology, Milan (Italy); Stroman, P.W. [Queen' s University, Department of Diagnostic Radiology, Centre for Neuroscience Studies, Kingston, ON (Canada)

    2008-10-15

    Functional MRI (fMRI) of the spinal cord is able to provide maps of neuronal activity. Spinal fMRI data have been analyzed in previous studies by calculating the cross-correlation (CC) between the stimulus and the time course of every voxel and, more recently, by using the general linear model (GLM). The aim of this study was to compare three different approaches (CC analysis, GLM and independent component analysis (ICA)) for analyzing fMRI scans of the cervical spinal cord. We analyzed spinal fMRI data from healthy subjects during a proprioceptive and a tactile stimulation by using two model-based approaches, i.e., CC analysis between the stimulus shape and the time course of every voxel, and the GLM. Moreover, we applied independent component analysis, a model-free approach which decomposes the data in a set of source signals. All methods were able to detect cervical cord areas of activity corresponding to the expected regions of neuronal activations. Model-based approaches (CC and GLM) revealed similar patterns of activity. ICA could identify a component correlated to fMRI stimulation, although with a lower statistical threshold than model-based approaches, and many components, consistent across subjects, which are likely to be secondary to noise present in the data. Model-based approaches seem to be more robust for estimating task-related activity, whereas ICA seems to be useful for eliminating noise components from the data. Combined use of ICA and GLM might improve the reliability of spinal fMRI results. (orig.)

  12. Pre-surgical integration of FMRI and DTI of the sensorimotor system in transcortical resection of a high-grade insular astrocytoma

    Directory of Open Access Journals (Sweden)

    Chelsea eEkstrand

    2016-03-01

    Full Text Available Herein we report on a patient with a WHO Grade III astrocytoma in the right insular region in close proximity to the internal capsule who underwent a right frontotemporal craniotomy. Total gross resection of insular gliomas remains surgically challenging based on the possibility of damage to the corticospinal tracts. However, maximizing the extent of resection has been shown to decrease future adverse outcomes. Thus, the goal of such surgeries should focus on maximizing extent of resection while minimizing possible adverse outcomes. In this case, pre-surgical planning included integration of functional magnetic resonance imaging (fMRI and diffusion tensor imaging (DTI, to localize motor and sensory pathways. Novel fMRI tasks were individually developed for the patient to maximize both somatosensory and motor activation simultaneously in areas in close proximity to the tumor. Information obtained was used to optimize resection trajectory and extent, facilitating gross total resection of the astrocytoma. Across all three motor-sensory tasks administered, fMRI revealed an area of interest just superior and lateral to the astrocytoma. Further, DTI analyses showed displacement of the corona radiata around the superior dorsal surface of the astrocytoma, extending in the direction of the activation found using fMRI. Taking into account these results, a transcortical superior temporal gyrus surgical approach was chosen in order to avoid the area of interest identified by fMRI and DTI. Total gross resection was achieved and minor post-surgical motor and sensory deficits were temporary. This case highlights the utility of comprehensive pre-surgical planning, including fMRI and DTI, to maximize surgical outcomes on a case-by-case basis.

  13. Impact of Global Normalization in fMRI Acupuncture Studies

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    Jinbo Sun

    2012-01-01

    Full Text Available Global normalization is often used as a preprocessing step for dispelling the “nuisance effects.” However, it has been shown in cognitive and emotion tasks that this preprocessing step might greatly distort statistical results when the orthogonality assumption of global normalization is violated. The present study examines this issue in fMRI acupuncture studies. Thirty healthy subjects were recruited to evaluate the impacts of the global normalization on the BOLD responses evoked by acupuncture stimulation during De-qi sensation and tactile stimulation during nonpainful sensations. To this end, we compared results by conducting global normalization (PSGS and not conducting global normalization (NO PSGS based on a proportional scaling model. The orthogonality assumption of global normalization was violated, and significant changes between BOLD responses for NO PSGS and PSGS were shown in most subjects. Extensive deactivations of acupuncture in fMRI were the non-specifically pernicious consequences of global normalization. The central responses of acupuncture during De-qi are non-specifically activation-dominant at the somatosensory-related brain network, whose statistical power is specifically enhanced by PSGS. In conclusion, PSGS should be unjustified for acupuncture studies in fMRI. The differences including the global normalization or not may partly contribute to conflicting results and interpretations in previous fMRI acupuncture studies.

  14. Bayesian Modelling of fMRI Time Series

    DEFF Research Database (Denmark)

    Højen-Sørensen, Pedro; Hansen, Lars Kai; Rasmussen, Carl Edward

    2000-01-01

    We present a Hidden Markov Model (HMM) for inferring the hidden psychological state (or neural activity) during single trial fMRI activation experiments with blocked task paradigms. Inference is based on Bayesian methodology, using a combination of analytical and a variety of Markov Chain Monte...

  15. The Effect of Strategy on Problem Solving: An FMRI Study

    Science.gov (United States)

    Newman, Sharlene D.; Pruce, Benjamin; Rusia, Akash; Burns, Thomas, Jr.

    2010-01-01

    fMRI was used to examine the differential effect of two problem-solving strategies. Participants were trained to use both a pictorial/spatial and a symbolic/algebraic strategy to solve word problems. While these two strategies activated similar cortical regions, a number of differences were noted in the level of activation. These differences…

  16. fMRI in Parkinson’s Disease