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Neural representation of interval encoding and decision making.

Our perception of time depends on multiple psychological processes that allow us to anticipate events. In this study, we used event-related functional magnetic resonance imaging (fMRI) to differentiate neural systems involved in formulating representations of time from processes associated with making decisions about their duration. A time perception task consisting of two randomly presented standard intervals was used to ensure that intervals were encoded on each trial and to enhance memory requirements. During the encoding phase of a trial, activation was observed in the right caudate nucleus, right inferior parietal cortex and left cerebellum. Activation in these regions correlated with timing sensitivity (coefficient of variation). In contrast, encoding-related activity in the right parahippocampus and hippocampus correlated with the bisection point and right precuneus activation was associated with a measure of memory distortion. Decision processes were studied by examining brain activation during the decision phase of a trial that was associated with the difficulty of interval discriminations. Activation in the right parahippocampus was greater for easier than harder discriminations. In contrast, activation was greater for harder than easier discriminations in systems involved in working memory (left middle-frontal and parietal cortex) and auditory rehearsal (left inferior-frontal and superior-temporal cortex). Activity in the auditory rehearsal network correlated with memory distortion. Our results support the independence of systems that mediate interval encoding and decision processes. The results also suggest that distortions in memory for time may be due to strategic processing in cortical systems involved in either encoding or rehearsal.

Acoustic Stimulation↗

fMRI evidence of word frequency and strength effects during episodic memory encoding.

Word frequency (WF) and strength effects are two important phenomena associated with episodic memory. The former refers to the superior hit-rate (HR) for low (LF) compared to high frequency (HF) words in recognition memory, while the latter describes the incremental effect(s) upon HRs associated with repeating an item at study. Using the "subsequent memory" method with event-related fMRI, we tested the attention-at-encoding (AE) [M. Glanzer, J.K. Adams, The mirror effect in recognition memory: data and theory, J. Exp. Psychol.: Learn Mem. Cogn. 16 (1990) 5-16] explanation of the WF effect. In addition to investigating encoding strength, we addressed if study involves accessing prior representations of repeated items via the same mechanism as that at test [J.L. McClelland, M. Chappell, Familiarity breeds differentiation: a subjective-likelihood approach to the effects of experience in recognition memory, Psychol. Rev. 105 (1998) 724-760], entailing recollection [K.J. Malmberg, J.E. Holden, R.M. Shiffrin, Modeling the effects of repetitions, similarity, and normative word frequency on judgments of frequency and recognition memory, J. Exp. Psychol.: Learn Mem. Cogn. 30 (2004) 319-331] and whether less processing effort is entailed for encoding each repetition [M. Cary, L.M. Reder, A dual-process account of the list-length and strength-based mirror effects in recognition, J. Mem. Lang. 49 (2003) 231-248]. The increased BOLD responses observed in the left inferior prefrontal cortex (LIPC) for the WF effect provide support for an AE account. Less effort does appear to be required for encoding each repetition of an item, as reduced BOLD responses were observed in the LIPC and left lateral temporal cortex; both regions demonstrated increased responses in the conventional subsequent memory analysis. At test, a left lateral parietal BOLD response was observed for studied versus unstudied items, while only medial parietal activity was observed for repeated items at study, indicating that accessing prior representations at encoding does not necessarily occur via the same mechanism as that at test, and is unlikely to involve a conscious recall-like process such as recollection. This information may prove useful for constraining cognitive theories of episodic memory.

Adult↗

Age-related reorganization of encoding networks directly influences subsequent recognition memory.

Functional magnetic resonance imaging was used to link performance-related brain activity during two word encoding tasks to subsequent recognition for those words in young and older adults. There were no significant group differences in performance during encoding, but the young subjects performed better than the older at the recognition task. Performance-related brain networks strongly differed between the two groups. In young subjects, there were two networks associated with performance, one related to encoding (mainly involving premotor and parietal brain regions) and the other to recognition (involving middle frontal, and lateral and medial temporal regions), whereas the network for older subjects (including prefrontal, premotor, lateral and medial temporal regions) was associated both with encoding and recognition. Areas in this network strongly overlapped with those supporting recognition in the young subjects (e.g., medial temporal lobe), suggesting that older subjects may have recruited these areas to maintain performance during encoding. However, this reorganization of brain networks appears to have come at the cost of subsequent recognition.

Adult↗

Maturation of medial temporal lobe response and connectivity during memory encoding.

The medial temporal lobe (MTL) plays an important role in memory encoding. The development and maturation of MTL and other brain regions involved in memory encoding are, however, poorly understood. We used functional magnetic resonance imaging to examine activation and effective connectivity of the MTL in children and adolescents during encoding of outdoor visual scenes. Here, we show that MTL response decreases with age whereas its connectivity with the left dorsolateral prefrontal cortex (PFC) increases with age. Our findings provide evidence for dissociable maturation of local and distributed memory encoding processes involving the MTL and furthermore suggest that increased functional interactions between the MTL and the PFC may underlie the development of more effective memory encoding strategies.

Adolescent↗

Systematic screening of nuclear encoded proteins involved in the splicing metabolism of group II introns in yeast mitochondria.

Studies of yeast, algae and plants have provided genetic and biochemical evidence that the splicing reaction of organellar localized group II introns either depends on proteins encoded by the introns themselves ('maturases') or encoded by other genes of the host organisms. However, only a few of those proteins have been identified to date and characterized in more detail. In order to find new nuclear encoded proteins that assist group II splicing, we screened a complete knockout library of Saccharomyces cerevisiae strain BY4741 consisting of 4878 viable haploid clones. The strain contains a rho+ mitochondrial genome with a set of 13 introns including the three group II introns (aI1, aI2, aI5gamma) in the gene encoding cytochrome-c-oxidase subunit 1 (COX1) and the single group II intron (bI1) in the gene encoding cytochrome b (CYTB). In our screen and initial molecular analysis, we focus on intron aI5gamma, the last intron in the COX1 gene.

Cell Nucleus↗

Cytomegalovirus-encoded homologs of G protein-coupled receptors and chemokines.

BACKGROUND: Cytomegaloviruses (CMVs) have developed various sophisticated strategies to manipulate and evade the defense mechanisms of their hosts. Among the CMV genes that are predicted to be involved in these strategies are genes that encode mimics of cellular proteins, such as G protein-coupled receptors (GPCRs) and chemokines (CKs). These genes may have been pirated from the host genome during the long co-evolution of virus and host. OBJECTIVES: In this report, the putative functions of the CMV-encoded homologs of GPCRs and CKs in the pathogenesis of infection will be discussed. STUDY DESIGN: In order to present an overview of the current state of knowledge, the literature on the CMV-encoded homologs of GPCRs and CKs was reviewed. RESULTS: The GPCR and CK homologs that are encoded by the CMVs represent immunomodulatory proteins with crucial roles in the pathogenesis of infection. CONCLUSIONS: In light of their function as well as accessibility on the cell surface, the CMV-encoded GPCR homologs are attractive targets for the development of new anti-viral therapies.

Chemokines↗

Plasmid-encoded antirestriction protein ArdA can discriminate between type I methyltransferase and complete restriction-modification system.

Many promiscuous plasmids encode the antirestriction proteins ArdA (alleviation of restriction of DNA) that specifically affect the restriction activity of heterooligomeric type I restriction-modification (R-M) systems in Escherichia coli cells. In addition, a lot of the putative ardA genes encoded by plasmids and bacterial chromosomes are found as a result of sequencing of complete genomic sequences, suggesting that ArdA proteins and type I R-M systems that seem to be widespread among bacteria may be involved in the regulation of gene transfer among bacterial genomes. Here, the mechanism of antirestriction action of ArdA encoded by IncI plasmid ColIb-P9 has been investigated in comparison with that of well-studied T7 phage-encoded antirestriction protein Ocr using the mutational analysis, retardation assay and His-tag affinity chromatography. Like Ocr, ArdA protein was shown to be able to efficiently interact with EcoKI R-M complex and affect its in vivo and in vitro restriction activity by preventing its interaction with specific DNA. However, unlike Ocr, ArdA protein has a low binding affinity to EcoKI Mtase and the additional C-terminal tail region (VF-motif) is needed for ArdA to efficiently interact with the type I R-M enzymes. It seems likely that this ArdA feature is a basis for its ability to discriminate between activities of EcoKI Mtase (modification) and complete R-M system (restriction) which may interact with unmodified DNA in the cells independently. These findings suggest that ArdA may provide a very effective and delicate control for the restriction and modification activities of type I systems and its ability to discriminate against DNA restriction in favour of the specific modification of DNA may give some advantage for efficient transmission of the ardA-encoding promiscuous plasmids among different bacterial populations.

Amino Acid Sequence↗

Ultrafast 2D NMR spectroscopy using a continuous spatial encoding of the spin interactions.

A new protocol for acquiring multidimensional NMR spectra within a single scan is introduced and illustrated. The approach relies on applying a pair of frequency-chirped excitation and storage pulses in combination with echoing magnetic field gradients, in order to impart the kind of linear spatial encoding of the NMR interactions that is required by ultrafast 2D NMR spectroscopy. It is found that when dealing with 2D NMR experiments involving a t1 amplitude-modulation of the spin evolution, such continuous encoding scheme presents a number of advantages over alternatives employing discrete excitation pulses. From an experimental standpoint this is mainly reflected by the use of a single pair of bipolar gradients during the course of the indirect-domain encoding, as opposed to the numerous (and more intense) gradient echoes required so far. In terms of the spectral outcome, main advantages of the continuous spatial encoding scheme are the avoidance of "ghost peaks" and of "enveloping effects" associated to the discrete excitation mode. The principles underlying this new spatial encoding protocol are derived, and its applicability is demonstrated with homo- and heteronuclear 2D ultrafast NMR applications on small molecule and on protein samples.

Carbon Isotopes↗

A continuous phase-modulated approach to spatial encoding in ultrafast 2D NMR spectroscopy.

Ultrafast 2D NMR replaces the time-domain parametrization usually employed to monitor the indirect-domain spin evolution, with an equivalent encoding along a spatial geometry. When coupled to a gradient-assisted decoding during the acquisition, this enables the collection of complete 2D spectra within a single transient. We have presented elsewhere two strategies for carrying out the spatial encoding underlying ultrafast NMR: a discrete excitation protocol capable of imparting a phase-modulated encoding of the interactions, and a continuous protocol yielding amplitude-modulated signals. The former is general but has associated with it a number of practical complications; the latter is easier to implement but unsuitable for certain 2D NMR acquisitions. The present communication discusses a new protocol that incorporates attractive attributes from both alternatives, imparting a continuous spatial encoding of the interactions yet yielding a phase modulation of the signal. This in turn enables a number of basic experiments that have shown particularly useful in the context of in vivo 2D NMR, including 2D J-resolved and 2D H,H-COSY spectroscopies. It also provides a route to achieving sensitivity-enhanced acquisitions for other homonuclear correlation experiments, such as ultrafast 2D TOCSY. The main features underlying this new spatial encoding protocol are derived, and its potential demonstrated with a series of phase-modulated homonuclear single-scan 2D NMR examples.

Algorithms↗

Encoding to the longitudinal magnetization for MR imaging and flow velocity mapping.

Phase-encoding to the longitudinal magnetization is implemented by adding encoding gradient pulses in the evolution period tau of the NMR pulse sequence 90 degrees+x-tau-90 degrees-x. This work focuses on the effect of the spin-lattice relaxation and its removal and on the constraint that the 90 degrees-x pulse can only transform the phase of the transverse magnetization partially to the longitudinal magnetization. Theoretical analysis shows that the encoded phase information and the spin-lattice relaxation effect are separable and the latter is identical in each repetition in collecting phase-encoding data. Thus the relaxation effect can be eliminated by subtracting a second data set whose phase information is inverted or by alternating the polarity of the relaxation contribution. From data with partial phase information, Fourier-transform image reconstruction results in mirror aliasing in which the two halves of the Fourier spectrum of positive and negative coordinates overlap. Removal of mirror aliasing requires imaging data of the orthogonal component. Nevertheless mirror aliasing is not necessarily a problem, depending on the subject of study. Phase-encoding to the longitudinal magnetization for spatial MRI and flow velocity mapping are demonstrated using the rotating ultra-fast imaging sequence (RUFIS).

Algorithms↗

Identification of Francisella tularensis genes encoding exported membrane-associated proteins using TnphoA mutagenesis of a genomic library.

Francisella tularensis, the causative agent of tularemia, is a highly infectious pathogen of humans and animals, yet little is known about the surface proteins of this organism that mediate mechanisms of pathogenicity. lambdaTnphoA was used to generate random alkaline phosphatase gene fusions in a F. tularensis subsp. tularensis (strain Schu S4) genomic library to identify genes encoding exported extracytoplasmic proteins. Eleven genes encoding membrane-associated proteins were identified by this method and their respective signal peptides were characterized. Three of the genes encoded conserved 'housekeeping' enzymes, while the other eight genes were unique to F. tularensis, encoding proteins with molecular masses ranging from 11 to 78kDa as deduced from the amino acid sequences. Two genes putatively encoded lipoproteins based on the presence of characteristic signal peptidase II cleavage sites. Four selected proteins were found associated with outer membranes from Schu S4 and LVS strains by Western blotting. Indirect immunofluorescence of strain Schu S4 cells also showed evidence of protein localization to the outer membrane. Protein database searches produced significant alignments with proteins from other bacteria involved in carbohydrate transport, lipid metabolism, and cell envelope biogenesis, thereby providing clues for putative functions. These findings demonstrated that TnphoA mutagenesis can be used in conjunction with F. tularensis genome sequence data to provide a foundation for studies to identify and define cellular surface protein virulence factors of this pathogen.

Alkaline Phosphatase↗

Enhancing the acquisition efficiency of fast magnetic resonance imaging via broadband encoding of signal content.

Current efficient magnetic resonance imaging (MRI) methods such as parallel-imaging and k-t methods encode MR signals using a set of effective encoding functions other than the Fourier basis. This work revisits the proposition of directly manipulating the set of effective encoding functions at the radiofrequency excitation step in order to increase MRI efficiency. This approach, often termed "broadband encoding," enables the application of algebraic matrix factorization technologies to extract efficiency by representing and encoding MR signal content in a compacted form. Broadband imaging equivalents of fast multiecho, parallel and k-t MRI are developed and analyzed. The potential of these techniques to increase the time efficiency of data acquisition is experimentally verified on a commercial MRI scanner using simple spin-echo imaging. A three-dimensional gradient-echo dynamic imaging application that demonstrates the potential benefits of this approach compared to the present state of the art for certain applications is also presented.

Fourier Analysis↗

The three beta-1,3-glucanases from Acremonium blochii strain C59 appear to be encoded by separate genes.

Three exocellular beta-1,3-glucanases from Acremonium blochii strain C59, BGN3.2, BGN3.3 and BGN3.4, were purified. Two, BGN3.2 and BGN3.4 appeared to act as exo-enzymes against laminarin from Laminaria digitata, while BGN3.3 displayed an endo-mode of action. The N-terminal amino acid sequence data for BGN3.2 and BGN3.4 suggested these two enzymes may be encoded by different genes. The gene encoding the BGN3.2 glucanase was fully sequenced, and its deduced amino acid sequence was similar to those for all other sequenced fungal exo-beta-1,3-glucanases. This BGN3.2 gene consists of an uninterrupted ORF of 2349 bp encoding 783 amino acids possibly with two cleavage sites for the potential removal of a pre- and pro-protein, respectively. A DNA fragment encoding a portion of the BGN3.4 gene was amplified by PCR, and the nucleotide sequence of this fragment confirmed that BGN3.2 and BGN3.4 are encoded by different genes. The internal peptide sequences of BGN3.3 were not present in the amino acid sequence deduced from the BGN3.2 gene, reinforcing the view that BGN3.3 is also genetically different to BGN3.2. Genetic differences between multiple forms of fungal beta-1,3-glucanases from a single fungus have not been reported previously.

Acremonium↗

Immunization of Alzheimer model mice with adenovirus vectors encoding amyloid beta-protein and GM-CSF reduces amyloid load in the brain.

Induction of anti-amyloid beta-protein (Abeta) antibodies in transgenic mouse models of Alzheimer disease (AD) by repeated injection of synthetic Abeta was shown to be effective in preventing and removing deposition of Abeta aggregates in the brain. Here, we have tested a non-invasive modality whereby a replication-defective adenovirus vector encoding Abeta was intranasally administered to mice to elicit immune responses against Abeta. Intranasal immunization only with the adenovirus vector failed to induce significant immune responses. When an adenovirus vector encoding granulocyte/macrophage-colony stimulating factor (GM-CSF) was used as an adjuvant in conjunction with the adenovirus encoding Abeta, a marked immune response was elicited against Abeta. Immunoglobulin isotyping revealed that the induced anti-Abeta antibodies are predominantly of the IgG2b and IgG1 isotypes, suggesting a Th-2 anti-inflammatory type. Furthermore, amyloid load in the brain of AD model mice (Tg2576) vaccinated with adenovirus vectors encoding Abeta and GM-CSF was much smaller than that in control Tg2576 mice. Thus, intranasal administration of adenovirus vectors encoding Abeta and GM-CSF may be effective in prevention and treatment of AD.

Adenoviridae↗

Brain activation during encoding and recognition of verbal and figural information in older adults.

Positron emission tomography (PET) patterns of cerebral blood flow associated with verbal and figural memory are described in relation to their value as functional probes for studying longitudinal changes that occur in the aging brain. Relative to a matching control task, verbal and figural encoding increase blood flow in prefrontal cortex (PFC), anterior cingulate, insular, lateral and medial temporal, occipital cortex and the cerebellum. Additionally, medial temporal regions exhibited greater activity during figural encoding relative to verbal encoding. During recognition, blood flow increases in prefrontal, cingulate, insular, and lateral temporal and Broca's areas. Analysis of hemispheric asymmetry reveals that the prefrontal cortex exhibits regionally dependent results. Prefrontal region BA 10 demonstrates more bilateral activation during encoding and retrieval, whereas BA 46 shows right greater than left activation during both encoding and retrieval. Overall, the two tasks activate diverse regions within the frontal, temporal and occipital lobes of the brain, including areas that show age-related structural changes, proving their usefulness in the longitudinal assessment of brain function in the elderly.

Aged↗

Age differences in neural correlates of route encoding and route recognition.

Spatial memory deficits are core features of aging-related changes in cognitive abilities. The neural correlates of these deficits are largely unknown. In the present study, we investigated the neural underpinnings of age-related differences in spatial memory by functional MRI using a navigational memory task with route encoding and route recognition conditions. We investigated 20 healthy young (18-29 years old) and 20 healthy old adults (53-78 years old) in a random effects analysis. Old subjects showed slightly poorer performance than young subjects. Compared to the control condition, route encoding and route recognition showed activation of the dorsal and ventral visual processing streams and the frontal eye fields in both groups of subjects. Compared to old adults, young subjects showed during route encoding stronger activations in the dorsal and the ventral visual processing stream (supramarginal gyrus and posterior fusiform/parahippocampal areas). In addition, young subjects showed weaker anterior parahippocampal activity during route recognition compared to the old group. In contrast, old compared to young subjects showed less suppressed activity in the left perisylvian region and the anterior cingulate cortex during route encoding. Our findings suggest that age-related navigational memory deficits might be caused by less effective route encoding based on reduced posterior fusiform/parahippocampal and parietal functionality combined with diminished inhibition of perisylvian and anterior cingulate cortices correlated with less effective suppression of task-irrelevant information. In contrast, age differences in neural correlates of route recognition seem to be rather subtle. Old subjects might show a diminished familiarity signal during route recognition in the anterior parahippocampal region.

Adolescent↗

When less means more: deactivations during encoding that predict subsequent memory.

In event-related functional MRI (fMRI) studies, greater activity for items that are subsequently remembered (R-items) than for items that are subsequently forgotten (F-items), or Dm effect (Difference in memory), has been attributed to successful encoding operations. In contrast, regions showing a reverse DM effect (revDM = F-items > R-items) have been linked to detrimental processes leading to forgetting. Yet, revDMs may reflect not only activations for F-items (aFs) but also deactivations for R-items (dRs), and the latter alternative is more likely to reflect beneficial rather than detrimental encoding processes. To investigate this issue, we used a paradigm that included a fixation baseline and could distinguish between the two types of revDMs (aF vs. dR). Participants were scanned while encoding semantic associations between words or perceptual associations between words and fonts, and their memory was measured with associative recognition tests. For both semantic and perceptual encoding, dR effects were found in dorsolateral prefrontal, temporoparietal, and posterior midline regions. In contrast with a prior study that attributed revDMs in these regions to detrimental processes, the present results suggest that these effects reflect beneficial processes, that is, the efficient reallocation of neurocognitive resources. At the same time, aF effects were found in other regions, such as the insula, and these are more consistent with an interpretation in terms of detrimental processes. Whereas most fMRI studies of encoding have focused on activation increases, the present study indicates that activation decreases are also critical for successful learning of new information.

Adult↗

Coherent theta-band EEG activity predicts item-context binding during encoding.

Episodic memories consist of semantic information coupled with a rich array of contextual detail. Here, we investigate the neural processes by which information about the sensory context of a learning event is "bound" to the semantic representation of the to-be-encoded item. We present evidence that item-context binding during encoding is mediated by frontoposterior electroencephalographic (EEG) phase locking within and between hemispheres in the theta (4-8 Hz) band. During a task in which subjects encoded words in different font colors, later memory for the word was associated with sustained frontal theta activity and frontoposterior theta-band coherence, primarily within the left hemisphere. When the word-color association was later successfully retrieved, however, neurons synchronized their theta-band responses bilaterally in a more sustained fashion, particularly during the latter part of the stimulus epoch (>800 ms). Our results confirm the importance of functional coupling between frontal and posterior regions for successful encoding. One interpretation of these data is hemispheric contributions to item and context encoding may be asymmetric, with left hemisphere coherence facilitating semantic processing of an item and right hemisphere coherence facilitating processing of sensory context. Theta-band coherence may be an important mechanism by which brain networks exchange information during learning.

Adult↗