Type-specific proactive interference in patients with semantic and phonological STM deficits

Prior neuropsychological evidence suggests that semantic and phonological components of short-term memory (STM) are functionally and neurologically distinct. The current paper examines proactive interference (PI) from semantic and phonological information in two STM-impaired patients, DS (semantic STM deficit) and AK (phonological STM deficit). In Experiment 1 probe recognition tasks with open and closed sets of stimuli were used. Phonological PI was assessed using nonword items, and semantic and phonological PI was assessed using words. In Experiment 2 phonological and semantic PI was elicited by an item recognition probe test with stimuli that bore phonological and semantic relations to the probes. The data suggested heightened phonological PI for the semantic STM patient, and exaggerated effects of semantic PI in the phonological STM case. The findings are consistent with an account of extremely rapid decay of activated type-specific representations in cases of severely impaired phonological and semantic STM.

Gramene 2013: comparative plant genomics resources

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

Abstract TP105: Increaed GABA A Mediated Synaptic Activity and Structural Remodeling in Peri-infarct Cortex Layer 5 in the Post-stroke Rodent Brain

Introduction: The mechanisms of functional recovery after stroke are thought to be based on structural and functional changes in brain circuits adjacent to or connected with the stroke site. Deciphering these changes at the synaptic level is key to understanding the re-organization of the synaptic circuitry. Here we use a combined approach of i) array tomography to determine the composition of GABA synapses in the post-stroke mouse brain, with ii) electrophysiology to determine whether stroke leads to functional changes in GABA A receptor-mediated neurotransmission.

Methods: A cortical lesion was induced in 12-week-old C57BL/6J male mice using the distal middle cerebral artery occlusion model of ischemia. For array tomography, small tissue was removed from the peri-infarct cortex and ribbons of serial ultrathin sections were obtained. Ribbons were stained with antibodies for synaptic markers. Analysis of the resultant staining pattern was used to quantify GABAergic synapses. In addition, whole-cell patch clamp recordings from acute neocortical brain slices were performed to evaluate GABA-mediated synaptic signaling in the peri-infarct cortex. Behavior was evaluated weekly.

Results: At 1 week post-stroke, the array tomography data revealed an increase in the density and proportion of alpha1 subunit-containing GABAergic synapses in layer 5 of the peri-infarct cortex (Density: 0.064 vs 0.036 synapses/μm3. Proportion: 15.3 vs 9.1 %, p<0.05, n=6); no changes were observed in layer2/3. Changes in GABA synapses were transient and returned to basal levels by 1 month. Electrophysiological recordings at 1 week post-stroke showed that GABA A receptor-mediated currents were enhanced in layer 5, but not in layer 2/3. These changes were specific to the pyramidal neurons. Behavioral impairment after stroke was observed only at 1 week compared to sham mice (p<0.05, n=10).

Conclusion: Our results suggest that stroke leads to an increased expression of functional GABA A receptors in peri-infarct neocortex and that these changes are layer- and cell type-specific. These synaptic changes may represent a mechanism of post-stroke functional recovery and remapping of surviving circuits.

Rehabilitation of spelling in a participant with a graphemic buffer impairment: the role of orthographic neighbourhood in remediating the serial position effect

Graphemic Output Buffer (GOB) disorder is defined as difficulty with the serial output of a sequence of letters in the output stage of the spelling process. In their rehabilitation study with a GOB patient, Sage and Ellis ( 2006 ) found that improvement on treated words generalised to untreated words from the same orthographic neighbourhoods as treated items, but not to other unrelated words. GOB patients frequently show a bow-shaped accuracy curve across letter positions, where letters at the middle positions are most error-prone. It may be that consistent letters at these middle letter positions across neighbourhoods modulate this effect. Spelling was treated using an Anagram and Copy Treatment (ACT) and generalisation to three untreated sets was examined: (1) neighbours of treated words with shared middle letters (e.g., clock-block), (2) neighbours with different medial position letters (e.g., clock-click), and (3) unrelated words (e.g., clock-puppy). Improvement was found for untreated neighbours with shared middle letters. There was no effect of training on the unrelated word set, and a negative impact on untreated neighbours with changed middle letters after the treatment. We attribute these results to top-down support from learned lexical representations, which facilitate spelling of untreated neighbours with shared middle letters but impede neighbours with changed middle letters. This latter result is attributed to interference from neighbours in the trained set strengthening competing letter representations at middle positions.

Constant Versus Rhythmic Muscle Tension in Applied Tension

The research aimed to examine ways in which applied tension for blood-injury phobia may be improved. The effect on blood pressure of two forms of muscle tension under three different rates of breathing is reported. Forty-five participants were randomly assigned to use either constant or rhythmic muscle tension under three different breathing rates (i.e., fast, slow, and normal). The effects on systolic and diastolic blood pressure were measured. Results indicated that both constant and rhythmic forms of muscle tension increased systolic and diastolic blood pressure. However, rhythmic tension was significantly more effective than constant tension at raising diastolic blood pressure. Breathing rate had no differential effects on blood pressure. Suggestions are made about modifications of Applied Tension in the treatment of blood-injury phobia.

Abstract 116: Single-synapse Analysis Of Synaptic Remodeling In The Post-stroke Rodent Brain

Introduction: The mechanisms of functional recovery after stroke are thought to be based on structural and functional changes in brain circuits adjacent to or connected with the stroke site. Deciphering these changes at the synaptic level is key to understanding the re-organization of the synaptic circuitry (i.e. the connectome). Quantitative information about such synapse rearrangements after stroke has been inadequate however, due to the technical limitations of available methodologies. Here we describe the use of array tomography, a new high-resolution proteomic imaging method, to determine the composition of glutamate and GABA synapses in the post-stroke mouse brain.

Methods: A cortical lesion was induced in 12-week-old C57BL/6J male mice using the distal middle cerebral artery occlusion model of ischemia. Small tissue sections were removed from the peri-infarct cortex and ribbons of serial ultrathin (70 nm) sections were obtained using an ultramicrotome. Ribbons were stained with antibodies for the synaptic markers SynapsinI, VGlut1, VGlut2, PSD-95, GAD, VGAT. Analysis of the resultant staining pattern was used to identify subtypes of glutamatergic and GABAergic synapses.

Results: At 1 week post-stroke, an increase in GABAergic synapses was observed in layer 5 of the peri-infarct cortex. A sub-analysis of the type of inhibitory interneurons (e.g. parvalbumin, somatostatin) expressing these synapses is pending. In addition, a trend for an increase of VGlut1+2 synapses was also observed. However, there were no detectable differences in total synapse number between stroke-injured and naïve animals, thus suggesting that VGluT2 expression may be upregulated in existing glutamatergic VGluT1 synapses after stroke. Further analysis will be extended to cortical layers 2/3 and 4.

Conclusion: These results provide new information about the organization of synaptic circuitry and its plasticity after stroke. Furthermore, it demonstrates how array tomography enables a previously unobtainable level of volumetric visualization and quantification of synapses.

Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization

Insulators or chromatin boundary elements are defined by their ability to block transcriptional activation by an enhancer and to prevent the spread of active or silenced chromatin. Recent studies have increasingly suggested that insulator proteins play a role in large-scale genome organization. To better understand insulator function on the global scale, we conducted a genome-wide analysis of the binding sites for the insulator protein CTCF in Drosophila by Chromatin Immunoprecipitation (ChIP) followed by a tiling-array analysis. The analysis revealed CTCF binding to many known domain boundaries within the Abd-B gene of the BX-C including previously characterized Fab-8 and MCP insulators, and the Fab-6 region. Based on this finding, we characterized the Fab-6 insulator element. In genome-wide analysis, we found that dCTCF-binding sites are often situated between closely positioned gene promoters, consistent with the role of CTCF as an insulator protein. Importantly, CTCF tends to bind gene promoters just upstream of transcription start sites, in contrast to the predicted binding sites of the insulator protein Su(Hw). These findings suggest that CTCF plays more active roles in regulating gene activity and it functions differently from other insulator proteins in organizing the Drosophila genome.

Binding synergy and cooperativity in dihydrodipicolinate reductase: implications for mechanism and the design of biligand inhibitors

Dihydrodipicolinate reductase (DHPR) is a homotetramer that catalyzes reduction of dihydrodipicolinate (DHP). We recently reported a biligand inhibitor ( K i = 100 nM) of DHPR, comprised of fragments that bind in the NADH (CRAA = catechol rhodanine acetic acid) and DHP (PDC = pyridine dicarboxylate) binding sites. Herein, we characterize binding synergy and cooperativity for ligand binding to Escherichia coli DHPR: NADH or CRAA and PDC (stable analog of DHP). While K d values indicate little synergy between NADH and PDC, (1)H- (15)N HSQC chemical shift perturbation and saturation transfer difference (STD) titrations indicate that PDC induces a more dramatic conformational change than NADH, consistent with a role in domain closure. PDC binds cooperatively (Hill coefficient = 2), while NADH does not, based on STD titrations that monitor only fast exchange processes. However, HSQC titrations monitoring Trp253 (located between monomers) indicate that NADH binds in two steps, with high affinity binding to only one of the monomers. Therefore, DHPR binds cofactor via a sequential model, with negative cooperativity. These results, interpreted in light of steady-state data, suggest that DHPR activity requires NADH binding at only one of the four monomers. Implications of our results for fragment assembly are discussed, using CRAA tethering to PDC as a model biligand: (a) if one fragment (ex. PDC) must induce a large structural change before the other fragment is brought proximal, this must be screened for upfront, and (b) cooperative or synergistic interactions between binding sites can lead to unexpected and misleading effects in NMR-based screening.

Immunoproteomics strategy for automation of chemoresistance and chemosensitivity array

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Background: Chemotherapy sensitivity and resistance assays (CSRAs) often guide therapeutic regimen selection based on patient cancer cells response to chemotherapeutics in culture. Current CSRAs rely on highly time- and skill- dependent biochemical and microscopic endpoint assays of apoptosis. Instead, the assay under development uses immunoproteomic array readout of biomarkers. Such automation may broaden the use of CSRAs for guiding clinical use of increasingly costly chemotherapeutic options. Methods: Specimens from 30 ovarian cancer patients were cultured with and without cisplatinum according to established CSRA procedures (http://weisenthal.org/w_ovarian_cp.pdf). Cells pelleted and fixed at experimental points (0 and 96 hrs cisplatin, and 96 hrs non-treated) were paraffin embedded for construction of immunoproteomic microarrays. A panel of 57 NIH cancer cell lines was similarly arrayed. Protein profiling is performed with monospecific antibodies for 35 select markers of cell cycle, apoptosis, cell signalling, and transcription. Immunostaining results, including rate of cell death and marker expression level are quantitated manually (immunoscore assigned for cell core) and automatically (algorithm by Aperio, Inc). Results: Evaluation of readouts differentiates responders from non-responders aiming to predict clinical chemotherapy outcome. For a subset of imunoproteomic markers, observed expression corresponds to either induced apoptosis or to cisplatin resistance. Selected markers were subjected to cytologic analysis and time line westerns; results corroborate protein profiling data. Correspondence to the results of the classic CSRAs and individual patient therapeutic response will be unblinded. Conclusions: Use of immunoproteomic arrays to replicate classic CSRAs by establishing concordant results may allow automated guidance for chemotherapeutic choices.

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RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs

Use of RNA interference (RNAi) in forward genetic screens is proliferating. Currently, short-interfering RNAs (siRNAs) and short-hairpin RNAs (shRNAs) are being used to silence genes to tease out functional information. It is becoming easier to harness RNAi to silence specific genes, owing to the development of libraries of readymade shRNA and siRNA gene-silencing constructs by using a variety of sources. RNAi Codex, which consists of a database of shRNA related information and an associated website, has been developed as a portal for publicly available shRNA resources and is accessible at . RNAi Codex currently holds data from the Hannon–Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available. We will describe features of RNAi Codex and explain the use of the tool.

Bridging expressed sequence alignments through targeted cDNA sequencing

One of the major challenges in genome research is the identification of the complete set of genes in a genome. Alignments of expressed sequences (RNA and EST) with genomic sequences have been used to characterize genes. However, the number of alignments far exceeds the likely number of genes in a genome, suggesting that, for many genes, two or more alignments can be joined through overlapping sequences to yield accurate gene structures. High-throughput EST sequencing becomes less efficient in closing those alignment gaps due to its nonselective nature. We sought to bridge these alignments through a novel approach: targeted cDNA sequencing. Human expressed sequences from GenBank version 124 were aligned with the genomic sequence from NCBI build 24 using LEADS, Compugen's EST and RNA clustering and assembly software system. Nine hundred forty-eight pairs of alignments were selected based on EST clone information and/or their homology to the same known proteins. Reverse transcriptase PCR and sequencing yielded sequences for 363 of those pairs. These sequences helped characterize over 60 novel or otherwise incomplete genes in the recent UniGene build 153, which included over 1 million additional ESTs. These results indicate that this integrated and targeted strategy, combining computational prediction and experimental cDNA sequencing, can efficiently generate the overlapping sequences and enable the full characterization of genomes. Additional information about the contig pairs, the resultant overlapping sequences, tissue sources, and tissue profiles are available in a supplemental file.

Consequences of immunogenicity to the therapeutic monoclonal antibodies ReoPro and Remicade

The clinical consequences of immune antibodies generated to abciximab (ReoPro) and infliximab (Remicade) are described. Abciximab, a chimaeric Fab fragment that binds to the beta3 integrin of the GPIIb/IIIa and alphavbeta3 receptors on human platelets, is approved in the US and Europe for use in percutaneous coronary intervention (PCI) to prevent cardiac ischaemic complications. The effects of induced antibodies upon the safety and efficacy of repeat administration of abciximab have been evaluated in the ReoPro Re-administration Registry Study, in which 5.7% of patients were HACA positive before re-treatment. An interim evaluation of 1000 patients has indicated that re-administration of abciximab can be accomplished in the setting of PCI with an acceptable safety and efficacy profile. Infliximab is a chimaeric IgG1 antibody specific for human TNFalpha, and is approved in the US and Europe for the acute treatment of the signs and symptoms of Crohn's disease and for the chronic treatment of rheumatoid arthritis (RA). The incidence of antibodies to infliximab is reported to be approximately 10%; however, an inverse dose-immunogenicity relationship was observed, indicating that higher doses of infliximab (> or = 3 to 10 mg/kg) could reduce the incidence of immune antibodies. The induction of immune antibodies could also be reduced by concomitant administration of low-dose methotrexate and other immunosuppressant agents. Although antibodies to infliximab appeared to be associated with lower serum infliximab concentrations and a slightly higher incidence of infusion reactions, these immune antibodies were generally not associated with a reduction in clinical efficacy. In addition, the antibodies induced to infliximab are specific for infliximab, and do not cross-react with other currently available therapeutic antibodies.