Biology subjects

Duncan, J.

Publications and source records attributed to Duncan, J..

49 records · Page 3Linked to original sources

bioRxiv2020

Comparison of CRISPR and marker based methods for the engineering of phage T7

With the recent rise in interest in using lytic bacteriophages as therapeutic agents, there is an urgent requirement to understand their fundamental biology to enable the engineering of their genomes. Current methods of phage engineering rely on homologous recombination, followed by a system of selection to identify recombinant phages. For bacteriophage T7, the host genes cmk or trx have been used as a selection mechanism along with both type I and II CRISPR systems to select against wild-type phage and enrich for the desired mutant. Here we systematically compare all three systems; we show that the use of marker-based selection is the most efficient method and we use this to generate multiple T7 tail fiber mutants. Furthermore, we found the type II CRISPR-Cas system is easier to use and generally more efficient than a type I system in the engineering of phage T7. These results provide a foundation for the future, more efficient engineering of bacteriophage T7.

molecular biology↗

bioRxiv2019

The functional convergence and heterogeneity of social, episodic, and self-referential thought in the default mode network

The default mode network (DMN) is engaged in a variety of cognitive settings, including social, semantic, temporal, spatial, and self-related tasks. Andrews-Hanna et al. (2010, 2012) proposed that the DMN consists of three distinct functional-anatomical subsystems - a dorsal medial prefrontal cortex (dMPFC) subsystem that supports social processing and introspection about mental states; a medial temporal lobe (MTL) subsystem that contributes to memory retrieval and construction of mental scenes; and a set of midline core hubs that are involved in processing self-referential information. We examined activity in the DMN subsystems during six different tasks: (1) theory of mind and (2) moral dilemmas (for social cognition), (3) autobiographical memory and (4) spatial navigation (for memory-based construction/simulation), (5) self/other adjective judgement (for self-related cognition), and finally, (6) a rest condition compared to a working memory task. At a broad level, we observed similar whole-brain activity maps for the six contrasts, and some response to every contrast in each of the three subsystems. In more detail, both univariate analysis and multivariate activity patterns showed partial functional separation, much of it in close accord with the proposals of separate dMPFC and MTL subsystems, though with less support for common activity across anterior and posterior regions of a midline core. Integrating social, spatial, self-related, and other aspects of a cognitive situation or episode, multiple components of the DMN may work closely together to provide the broad context for current mental activity.\n\nSignificance StatementActivity in the default mode network (DMN) can been found across a wide range of high-level tasks that involve social, semantic, episodic, or self-referential cognition. Given this diversity, an important proposal is that the DMN can be parcellated into subsystems with different cognitive functions. The current experiment employed a wide range of experimental tasks to directly test for functional convergence and heterogeneity between DMN regions. The results support both partial differentiation and integration; working together, distributed DMN regions may assemble the multiple contextual components of a cognitive situation or episode.

neuroscience↗

bioRxiv2019

Representation of task episodes in human cortical networks

Task episodes consist of sequences of steps that are performed to achieve a goal. We used fMRI to examine neural representation of task identity, component items, and sequential position, focusing on two major cortical systems - the multiple-demand (MD) and default mode networks (DMN). Human participants (20 male, 22 female) learned six tasks each consisting of four steps. Inside the scanner, participants were cued which task to perform and then sequentially identified the target item of each step in the correct order. Univariate time-course analyses indicated that intra-episode progress was tracked by a tonically increasing global response, plus an increasing phasic step response specific to MD regions. Inter-episode boundaries evoked a widespread response at episode onset, plus a marked offset response specific to DMN regions. Representational similarity analysis was used to examine encoding of task identity and component steps. Both networks represented the content and position of individual steps, but the DMN preferentially represented task identity while the MD network preferentially represented step-level information. Thus, although both DMN and MD networks are sensitive to step-level and episode-level information in the context of hierarchical task performance, they exhibit dissociable profiles in terms of both temporal dynamics and representational content. The results suggest collaboration of multiple brain regions in control of multi-step behavior, with MD regions particularly involved in processing the detail of individual steps, and DMN adding representation of broad task context. Significance StatementAchieving ones goals requires knowing what to do and when. Tasks are typically hierarchical, with smaller steps nested within overarching goals. For effective, flexible behavior, the brain must represent both levels. We contrast response time-courses and information content of two major cortical systems - the multiple-demand (MD) and default mode networks (DMN) - during multi-step task episodes. Both networks are sensitive to step-level and episode-level information, but with dissociable profiles. Intra-episode progress is tracked by tonically increasing global responses, plus MD-specific increasing phasic step responses. Inter-episode boundaries evoke widespread responses at episode onset, plus DMN-specific offset responses. Both networks encode content and position of individual steps, but the DMN and MD networks favor task identity and step-level information respectively.

neuroscience↗

bioRxiv2019

Discoidan Domain Receptor 1 (DDR1) Tyrosine Kinase is Upregulated in PKD Kidneys But Does Not Play a Role in the Pathogenesis of Polycystic Kidney Disease

Tolvaptan is the only drug approved to slow cyst growth and preserve kidney function in patients with autosomal dominant polycystic kidney disease (ADPKD). However, its limited efficacy combined with significant side effects underscores the need to identify new and safe therapeutic drug targets to slow progression to end stage kidney disease. We identified DDR1 as receptor tyrosine kinase upregulated in vivo in 3 mouse models of ADPKD using a novel mass spectrometry approach to identify kinases upregulated in ADPKD. Previous studies demonstrating critical roles for DDR1 to cancer progression, its potential role in the pathogenesis of a variety of other kidney disease, along with the possibility that DDR1 could provide new insight into how extracellular matrix impacts cyst growth led us to study the role of DDR1 in ADPKD pathogenesis. However, genetic deletion of DDR1 using CRISPR/Cas9 failed to slow cyst growth or preserve kidney function in both a rapid and slow mouse model of ADPKD demonstrating that DDR1 does not play a role in PKD pathogenesis and is thus a not viable drug target. In spite of the negative results, our studies will be of interest to the nephrology community as it will prevent others from potentially conducting similar experiments on DDR1 and reinforces the potential of performing unbiased screens coupled with in vivo gene editing using CRISPR/Cas9 to rapidly identify and confirm new potential drug targets for ADPKD.

cell biology↗

bioRxiv2019

The time-course of component processes of selective attention

Attentional selection shapes human perception, enhancing relevant information, according to behavioral goals. While many studies have investigated individual neural signatures of attention, here we used multivariate decoding of electrophysiological brain responses (MEG/EEG) to track and compare multiple component processes of selective attention. Auditory cues instructed participants to select a particular visual target, embedded within a subsequent stream of displays. Combining single and multi-item displays with different types of distractors allowed multiple aspects of information content to be decoded, distinguishing distinct components of attention, as the selection process evolved. Although the task required comparison of items to an attentional \"template\" held in memory, signals consistent with such a template were largely undetectable throughout the preparatory period but re-emerged after presentation of a non-target choice display. Choice displays evoked strong neural representation of multiple target features, evolving over different timescales. We quantified five distinct processing operations with different time-courses. First, visual properties of the stimulus were strongly represented. Second, the candidate target was rapidly identified and localized in multi-item displays, providing the earliest evidence of modulation by behavioral relevance. Third, the identity of the target continued to be enhanced, relative to distractors. Fourth, only later was the behavioral significance of the target explicitly represented in single-item displays. Finally, if the target was not identified and search was to be resumed, then an attentional template was weakly reactivated. The observation that an items behavioral relevance directs attention in multi-item displays prior to explicit representation of target/non-target status in single-item displays is consistent with two-stage models of attention.

neuroscience↗

bioRxiv2019

A Domain-general Cognitive Core defined in Multimodally Parcellated Human Cortex

Numerous brain imaging studies identified a domain-general or "multiple-demand" (MD) activation pattern accompanying many tasks and may play a core role in cognitive control. Though this finding is well established, the limited spatial localization provided by traditional imaging methods precluded a consensus regarding the precise anatomy, functional differentiation and connectivity of the MD system. To address these limitations, we used data from 449 subjects from the Human Connectome Project, with cortex of each individual parcellated using neurobiologically grounded multi-modal MRI features. The conjunction of three cognitive contrasts reveals a core of 10 widely distributed MD parcels per hemisphere that are most strongly activated and functionally interconnected, surrounded by a penumbra of 17 additional areas. Outside cerebral cortex, MD activation is most prominent in the caudate and cerebellum. Comparison with canonical resting state networks shows MD regions concentrated in the fronto-parietal network but also engaging three other networks. MD activations show modest relative task preferences accompanying strong co-recruitment. With distributed anatomical organization, mosaic functional preferences, and strong interconnectivity, we suggest MD regions are well positioned to integrate and assemble the diverse components of cognitive operations. Our precise delineation of MD regions provides a basis for refined analyses of their functions.

neuroscience↗

bioRxiv2018

Drug prescription pattern in European neonatal units

BackgroundHospitalized neonates receive the highest number of drugs compared to all other age groups, but consumption rates vary between studies depending on patient characteristics and local practices. There are no large scale international studies on drug use in neonatal units. We aimed to describe drug use in European neonatal units and characterize its associations with geographic region and gestational age (GA).\n\nMethodsA one-day point prevalence study (PPS) was performed as part of the European Study of Neonatal Exposure to Excipients (ESNEE) from January to June 2012. All neonatal prescriptions and demographic data were registered in a web-based database. The impact of GA and region on prescription rate were analyzed with logistic regression.\n\nResultsIn total, 21 European countries with 89 neonatal units participated. Altogether 2173 prescriptions given to 726 neonates were registered. The 10 drugs with the highest prescription rate were multivitamins, vitamin D, caffeine, gentamicin, amino acids for parenteral nutrition, phytomenadione, ampicillin, benzylpenicillin, fat emulsion for parenteral nutrition and probiotics. The six most commonly prescribed ATC groups (alimentary tract and metabolism, blood and blood-forming organs, systemic anti-infectives, nervous, respiratory and cardiovascular system) covered 98% of prescriptions. GA significantly affected the use of all commonly used drug groups. Geographic region influenced the use of alimentary tract and metabolism, blood and blood-forming organs, systemic anti-infectives, nervous and respiratory system drugs.\n\nConclusionsWhile GA-dependent differences in neonatal drug use were expected, regional variations (except for systemic anti-infectives) indicate a need for cooperation in developing harmonized evidence-based guidelines and suggest priorities for collaborative work.

pharmacology and toxicology↗

bioRxiv2018

Distinguishing between parallel and serial processing in visual attention from neurobiological data

Serial and parallel processing in visual search have been long debated in psychology but the processing mechanism remains an open issue. Serial processing allows only one object at a time to be processed, whereas parallel processing assumes that various objects are processed simultaneously. Here we present novel neural models for the two types of processing mechanisms based on analysis of simultaneously recorded spike trains using electrophysiological data from prefrontal cortex of rhesus monkeys while processing task-relevant visual displays. We combine mathematical models describing neuronal attention and point process models for spike trains. The same model can explain both serial and parallel processing by adopting different parameter regimes. We present statistical methods to distinguish between serial and parallel processing based on both maximum likelihood estimates and decoding the momentary focus of attention when two stimuli are presented simultaneously. Results show that both processing mechanisms are in play for the simultaneously recorded neurons, but neurons tend to follow parallel processing in the beginning after the onset of the stimulus pair, whereas they tend to serial processing later on. This could be explained by parallel processing being related to sensory bottom-up signals or feedforward processing, which typically occur in the beginning after stimulus onset, whereas top-down signals related to cognitive modulatory influences guiding attentional effects in recurrent feedback connections occur after a small delay, and is related to serial processing, where all processing capacities are being directed towards the attended object.\n\nAuthor summaryA fundamental question concerning processing of visual objects in our brain is how a population of cortical cells respond when presented with more than a single object in their receptive fields. Is one object processed at a time (serial processing), or are all objects processed simultaneously (parallel processing)? Inferring the dynamics of attentional states in simultaneously recorded spike trains from sensory neurons while being exposed to a pair of visual stimuli is key to advance our understanding of visual cognition. We propose novel statistical models and measures to quantify and follow the time evolution of the visual cognition processes right after stimulus onset. We find that in the beginning processing appears to be predominantly parallel, which develops into serial processing 150 - 200 ms after stimulus onset in prefrontal cortex of rhesus monkeys.

neuroscience↗

bioRxiv2018

A randomised exploratory investigation of the effects of Attention vs Working Memory Training on cognitive performance and everyday functioning following stroke.

Difficulties with attention are common following stroke and are associated with poor outcome. Home-based online cognitive training may have to the potential to provide an efficient and effective way to improve attentional functions in such patients. Little work has been carried out to assess the efficacy of this approach in stroke patients, and the lack of studies with active control conditions and rigorous evaluations of cognitive functioning pre and post training means understanding is limited as to whether and how such interventions may be effective. Here we compare the effects of 20 days of active cognitive training using either novel Selective Attention Training (SAT) or commercial Working Memory Training (WMT) programme, versus a waitlist control group, on a wide range of attentional and working memory tasks, as well as on self-reported everyday functioning. We demonstrate separable effects of each of the active training conditions, with SAT leading to improvements in both spatial and non-spatial aspects of attention and WMT leading to improvements only on very closely related working memory tasks. Both training groups reported improvements in everyday functioning, which were associated with improvements in attentional functions, suggesting that improving attention may be of particular importance in maximising functional recovery in this patient group.

clinical trials↗

bioRxiv2018

Hierarchical Cognition causes Task Related Deactivations but not just in Default Mode Regions

AbstractThe well-known deactivation of the Default Mode Network (DMN) during external tasks is usually thought to reflect the suppression of internally directed mental activity during external attention. In 3 experiments with human participants we organized sequences of task events identical in their attentional and control demands into larger task episodes. We found that DMN deactivation across such sequential events was never constant, but was maximum at the beginning of the episode, then decreased gradually across the episode, reaching baseline towards episode completion, with the final event of the episode eliciting an activation. Crucially, this pattern of activity was not limited to a fixed set of DMN regions but, across experiments, was shown by a variable set of regions expected to be uninvolved in processing the ongoing task. This change in deactivation across sequential but identical events showed that the deactivation cannot be related to attentional/control demands which were constant across the episode, instead it has to be related to some episode related load that was maximal at the beginning and then decreased gradually as parts of the episode got executed. We argue that this load resulted from cognitive programs through which the entire episode was hierarchically executed as one unit. At the beginning of task episodes, programs related to their entire duration is assembled, causing maximal deactivation. As execution proceeds, elements within the program related to the completed parts of the episode dismantle, thereby decreasing the program load and causing a decrease in deactivation.\n\nSignificance StatementWe prepare breakfasts and write emails, and not individually execute their many component acts. The current study suggests that cognitive entities that enable such hierarchical execution of goal-directed behavior may cause the ubiquitously seen deactivation during external task execution. Further, while this deactivation has previously been associated with a defined set of the so called default mode regions, current study demonstrates that deactivation is shown by any region not currently involved in task execution, and in certain task episodes can even include attention related fronto-parietal regions as well as primary sensory and motor regions.

neuroscience↗

bioRxiv2018

Role of the default mode network in cognitive transitions

A frequently repeated finding is that the default mode network (DMN) shows activation decreases during externally-focused tasks. This finding has led to an emphasis in DMN research on internally-focused self-relevant thought processes. A recent study, in contrast, implicates the DMN in substantial externally-focused task switches. Using functional magnetic resonance imaging, we scanned 24 participants performing a task switch experiment. Whilst replicating previous DMN task switch effects, we also found large DMN increases for brief rests as well as task restarts after rest. Our findings are difficult to explain using theories strictly linked to internal or self-directed cognition. In line with principal results from the literature, we suggest that the DMN encodes scene, episode or context, by integrating spatial, self-referential and temporal information. Context representations are strong at rest, but re-reference to context also occurs at major cognitive transitions.

neuroscience↗

bioRxiv2018

Response of the multiple-demand network during simple stimulus discriminations

The multiple-demand (MD) network is sensitive to many aspects of task difficulty, including such factors as rule complexity, memory load, attentional switching and inhibition. Many accounts link MD activity to top-down task control, raising the question of response when performance is limited by the quality of sensory input, and indeed, some prior results suggest little effect of sensory manipulations. Here we examined judgments of motion direction, manipulating difficulty by either motion coherence or salience of irrelevant dots. We manipulated each difficulty type across six levels, from very easy to very hard, and additionally manipulated whether difficulty level was blocked, and thus known in advance, or randomized. Despite the very large manipulations employed, difficulty had little effect on MD activity, especially for the coherence manipulation. Contrasting with these small or absent effects, we observed the usual increase of MD activity with increased rule complexity. We suggest that, for simple sensory discriminations, it may be impossible to compensate for reduced stimulus information by increased top-down control.

neuroscience↗

bioRxiv2017

Functional reorganisation and recovery following cortical lesions: A study in macaque monkeys

Damage following traumatic brain injury or stroke can often extend beyond the boundaries of the initial insult and can lead to maladaptive cortical reorganisation. On the other hand, beneficial cortical reorganisation leading to recovery of function can also occur. Here, we used resting state FMRI (rsFMRI) to examine how functional connectivity in the macaque brain changed across time in response to lesions to the prefrontal cortex, and how this reorganisation correlated with changes in behaviour. Two monkeys were trained to perform location-based and object-based delayed match-to-sample tasks. We also collected rsFMRI data under general anaesthesia at two pre-lesion time-points, separated by 3-4 weeks. After two cycles of testing and scanning, the animals received a principal sulcus lesion followed by an additional 4 cycles of testing and scanning. Later, the same animals received a second lesion to the opposite hemisphere and additional cycles of testing and scanning.\n\nBoth animals showed a marked behavioural impairment following the first lesion, which was associated with a decrease in functional connectivity, predominantly within frontal-frontal networks in both hemispheres. Approximately 8 weeks following the lesion, performance improved, as did functional connectivity within these networks. Following the second lesion, functional connectivity again decreased and this was associated with a marginal behavioural deficit that did not recover.\n\nOur data show that behavioural impairments reflect not just the removal of the lesioned area, but also disturbance to an extensive cortical network. This network can recover by restoring and/or strengthening pre-existing connections, leading to improvement in behaviour.

neuroscience↗