Recovering the contents of consciousness in the noise of neuroimaging

A classical approach in the neurosciences is to study neural activity modulations induced by a stimulus, a task, etc. This approach is anchored in a behaviourist culture and has proven informative within certain limits. The present paper shows that this approach nonetheless neglects aspects of neural activity that can also contribute important information about brain function. Over the last years, the contributions with the strongest impact on progress in cognitive neuroscience have used other approaches that exploit a spatial or temporal variability of neural activity that standard analyses consider as noise and hence do not take into account. By applying multi-variate analyses, spatial variability of evoked responses has permitted decoding sensory and cognitive representations in the brain. Temporal variability of ongoing neural activity influences how stimuli are perceived trial by trial as well as the associated evoked responses which points out the importance of spontaneous brain activity for cognition. We describe these two kind of approaches based on experiments using functional neuroimaging but the conclusions generalize to other techniques applied in the neurosciences.     

Immunophilin AtFKBP13 sustains all peptidyl-prolyl isomerase activity in the thylakoid lumen from Arabidopsis thaliana deficient in AtCYP20-2

The physiological roles of immunophilins are unclear, but many possess peptidyl-prolyl isomerase (PPIase) activity, and they have been found in all organisms examined to date, implying that they are involved in fundamental, protein-folding processes. The chloroplast thylakoid lumen of the higher plant Arabidopsis thaliana contains up to 16 immunophilins (five cyclophilins and 11 FKBPs), but only two of them, AtCYP20-2 and AtFKBP13, have been found to be active PPIases, indicating that the other immunophilins in this cellular compartment may have lost their putative PPIase activities. To assess this possibility, we characterized two independent Arabidopsis knockout lines lacking AtCYP20-2 in enzymological and quantitative proteomic analyses. The PPIase activity in thylakoid lumen preparations of both mutants was equal to that of corresponding wild-type preparations, and comparative two-dimensional difference gel electrophoresis analyses of the lumenal proteins of the mutants and wild type showed that none of the potential PPIases was more abundant in the AtCYP20-2 deficient plants. Enzymatic analyses established that all PPIase activity in the mutant thylakoid lumen was attributable to AtFKBP13, and oxidative activation of this enzyme compensated for the lack of AtCYP20-2. Accordingly, sequence analyses of the potential catalytic domains of lumenal cyclophilins and FKBPs demonstrated that only AtCYP20-2 and AtFKBP13 possess all of the amino acid residues found to be essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. Thus, none of the immunophilins in the chloroplast thylakoid lumen of Arabidopsis except AtCYP20-2 and AtFKBP13 appear to possess prolyl isomerase activity toward peptide substrates.     

Leucocyte alkaline phosphatase in the Mongolian gerbil and other species: a comparative view

Cytochemical analyses performed on peripheral blood smears of the Mongolian gerbil reveal the presence of variable amounts of leucocyte alkaline phosphatase (LAP) activity in the neutrophil of this species. Levels of activity in individual cells ranged from 1 to 4+. Cells completely devoid of activity were rarely encountered. Immature neutrophils residing in the bone marrow also displayed moderate amounts of enzymatic activity. The results of a semiquantitative assessment of overall LAP activity in this rodent, expressed as a mean LAP score, were compared with similar analyses carried out on a diverse sample of vertebrates. Intermediate levels of activity were recorded for the gerbil (means = 241). This score was comparable to that obtained for the rat (means = 199) and significantly higher than that seen in man (means = 79). A wide range of LAP scores were noted for closely related species, as well as phylogenetically distant species.     

A comparative ultracytochemical and biochemical study of the ATPases of the choroid plexus in aging]

A complex study was undertaken on the ATPase and an ouabain-sensitive potassium-dependent p-nitrophenylphosphatase part of the Na, K-ATPase complex at the ultrastructural level, in addition to a biochemical assay of the total ATPase activity and activity of Na, K-ATPase of the choroid plexus (CP) of brain ventricles in adult (6-8 mo) and old (26-28 mo) rats. A correlation between the results of cytochemical and biochemical analyses was noted pointing to an age-related decrease in ATPase activity of the CP. Especially marked was the decrease in Na, K-ATPase activity that evidenced for the reduced level of liquor production in the CP during aging. Identified were the sites of a predominant localization of enzymes on the plasma membranes and intracellular organelles of the CP epitheliocytes. The latter fact was associated with their involvement in the processes of energy transformation and transport of substances. The data of the ultracytochemical and biochemical analyses, together with the results of the ultrastructural investigation, indicate an age-related decrease in the functional activity of the CP that represents one of the essential links in the mechanism of brain aging.     

Advances in quantification and characterization of telomerase activity by the telomeric repeat amplification protocol (TRAP).

The telomeric repeat amplification protocol (TRAP) assay has been used to test telomerase activity in numerous cancer specimens. We describe primers, controls and quantification methods for the TRAP assay to accurately measure the level of telomerase activity in clinical samples. The assay is reliable and reproducible in routine analyses and can be used to estimate the processivity of telomerase activity.     

Activation of extracellular signal-regulated kinase signaling in the pedunculopontine tegmental cells is involved in the maintenance of sleep in rats

Considerable evidence suggests that receptor-mediated excitation and inhibition of brainstem pedunculopontine tegmental (PPT) neurons are critically involved in the regulation of sleep-wake states. However, the molecular mechanisms operating within the PPT-controlling sleep-wake states remain relatively unknown. This study was designed to examine sleep-wake state-associated extracellular-signal-regulated kinase 1 and 2 (ERK1/2) transduction changes in the PPT of freely moving rats. The results of this study demonstrate that the levels of ERK1/2 expression, phosphorylation, and activity in the PPT increased with increased amount of time spent in sleep. The sleep-associated increases in ERK1/2 expression, phosphorylation, and activity were not observed in the cortex, or in the immediately adjacent medial pontine reticular formation. The results of regression analyses revealed significant positive relationships between the levels of ERK1/2 expression, phosphorylation, and activity in the PPT and amounts of time spent in slow-wave sleep, rapid eye movement sleep, and total sleep. Additionally, these regression analyses revealed significant negative relationships between the levels of ERK1/2 expression, phosphorylation, and activity in the PPT and amounts of time spent in wakefulness. Collectively, these results, for the first time, suggest that the increased ERK1/2 signaling in the PPT is associated with maintenance of sleep via suppression of wakefulness.     

Cellulolytic Microbes in the Yanbaru,a Subtropical Rainforest with an Endemic Biota on Okinawa Island,Japan

Cellulolytic microbes in the soil of the Yanbaru, a subtropical forest with an endemic biota, on Okinawa Island, were isolated and characterized in a search for novel microbial strains with biotechnological potential. Soil samples of the Yanbaru were suspended in sterilized water, inoculated on mineral salt agar overlaid with a filter paper as carbon source, and cultivated aerobically at 30 °C. After 2 weeks of cultivation, emerging colonies were isolated and subjected to phylogenetic and enzyme analyses. The phylogenetic analyses revealed bacterial and fungal isolates belonging to nine and three genera respectively. All isolates possessed cellulase activity, and several strains showed strong activity comparable to Trichoderma cellulase. Many isolates also exhibited xylanase activity.     

Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Finger 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.     

Cellulolytic microbes in the Yanbaru, a subtropical rainforest with an endemic biota on Okinawa Island, Japan

Cellulolytic microbes in the soil of the Yanbaru, a subtropical forest with an endemic biota, on Okinawa Island, were isolated and characterized in a search for novel microbial strains with biotechnological potential. Soil samples of the Yanbaru were suspended in sterilized water, inoculated on mineral salt agar overlaid with a filter paper as carbon source, and cultivated aerobically at 30 °C. After 2 weeks of cultivation, emerging colonies were isolated and subjected to phylogenetic and enzyme analyses. The phylogenetic analyses revealed bacterial and fungal isolates belonging to nine and three genera respectively. All isolates possessed cellulase activity, and several strains showed strong activity comparable to Trichoderma cellulase. Many isolates also exhibited xylanase activity.     

Comparative study of in vitro methods used to analyse the activity of propolis extracts with different compositions against species of Candida

AIMS: Propolis is known for its activity against micro-organisms and different in vitro assays have been used to evaluate this activity, frequently with contradictory results. METHODS AND RESULTS: Brazilian propolis from the state of S?o Paulo was extracted by maceration using different concentrations of ethanol and water. The resultant extracts were analysed by chromatographic methods. Several microbiological methods were compared to determine which one best evaluated the activity of the propolis extracts against species of Candida, with average minimal inhibitory concentration values between 6 and 12 mg ml(-1). CONCLUSIONS: Agar dilution in plates showed the clearest results. These were in agreement with the chromatographic analyses, which also identified the active substances. SIGNIFICANCE AND IMPACT OF THE STUDY: Although the active substances identified in this sample are typical of Brazilian propolis, their activity against Candida had not been recognized previously, demonstrating the importance of standardizing the correct combination of microbiological and chromatographic analyses.     

Occurrence of Conjugated Dienoic Fatty Acids in the Cellular Lipids of Pediococcus homari

Ninety-two thiolcarbamates with various substituents at the nitrogen and sulfur atoms, and their related compounds were synthesized, and their fungicidal activity against rice blast, Piricularia oryzae, and herbicidal activity against barnyardgrass, Echinochloa crus-galli, were determined in laboratory tests. The thiolcarbamate structure was necessary for the high fungicidal and herbicidal activities. The hydrophobicity of the substituents at the nitrogen atom was shown by the adaptive least-squares (ALS) method to be favorable to the fungicidal activity. The bulkier the substituents at the nitrogen atom, the less was the fungicidal activity. However, bulkiness of the substituents at the nitrogen and sulfur atoms was unfavorable to the herbicidal activity. The existence of a hydrogen atom at the nitrogen atom was favorable to fungicidal activity, but not to herbicidal activity. Correlation analyses were made to find compounds with both fungicidal and herbicidal activities against rice pests.     

Letter to the Editors: in Defense of Visual Inspection

Cornelissen and Haus (1) are certainly correct in their assertion that computerized data collection and analysis are useful and important tools in chronobiological research. We also agree that circadian rhythm data should be subjected to multiple complementary analyses whenever possible. In fact, both of our laboratories currently employ on-line collection of behavioural activity data, as well as several different computer-assisted statistical procedures, including analyses similar to those referred to by Cornelissen and Haus in their commentary.     

A double-blind investigation of the relationship between seizure activity and the sleep EEG following EEG biofeedback training

The sleep EEGs of eight medically refractory epileptic patients were examined as part of a double-blind, ABA crossover study designed to determine the effectiveness of EEG biofeedback for the control of seizures. The patients were initially reinforced for one of three EEG criteria recorded from electrodes placed over sensorimotor cortex: (a) suppression of 3- to 7-Hz activity, (b) enhancement of 12- to 15-Hz activity, or (c) simultaneous suppression of 3- to 7-Hz and enhancement of 11- to 19-Hz activity. Reinforcement contingencies were reversed during the second or B phase, and then reinstated in their original form during the final A′ phase. All-night polysomnographic recordings were obtained at the end of each conditioning phase and were subjected to both visual and computer-based power spectral analyses. Four of the patients showed changes in their nocturnal paroxysmal activity that were either partially or totally consistent with the ABA′ contingencies of the study. The spectral data proved difficult to interpret, though two trends emerged from the analyses. Decreases in nocturnal 4- to 7-Hz activity were correlated with decreases in seizure activity, and increases in 8- to 11-Hz activity were correlated with decreases in seizure activity. These findings were shown to strengthen the hypothesis that EEG biofeedback may produce changes in the sleep EEG that are related to seizure incidence.     

Ability of the Actiwatch Accelerometer to Predict Free‐Living Energy Expenditure in Young Children

Objective: To determine whether activity counts obtained with the Actiwatch monitor are associated with total expenditure and body composition in young children. Research Methods and Procedures: Actiwatch activity monitors were tested in 29 children 4 to 6 years old under field conditions over eight days. Total energy expenditure (TEE) was assessed with the doubly labeled water (DLW) technique. Correlation analyses were used to identify variables related to energy expenditure and percentage body fat. Multiple linear regression analyses were used to examine the variance in TEE and percentage body fat explained by activity counts after adjusting for relevant covariates. Results: Both average total daily activity counts (658, 816 ± 201, 657) and the pattern of activity were highly variable among subjects. TEE was significantly related to lean body mass (r = 0.45) and age (r = 0.48; p < 0.05 for both). Activity counts alone were not associated with TEE. In multiple linear regression analyses, TEE was independently associated with only lean body mass. Percentage fat mass was independently associated with body weight, being a girl, and being white, but not with average total activity counts. Discussion: Activity counts obtained with the Actiwatch under free‐living conditions do not reflect TEE in 4‐ to 6‐year‐old children and are not correlated with percentage fat mass. Therefore, average total activity counts obtained with the Actiwatch may be of limited value in identifying children at risk for becoming obese.     

Studies on the parameters controlling the stability of the TET peptidase superstructure from Pyrococcus horikoshii revealed a crucial role of pH and catalytic metals in the oligomerization process

The TET proteases from Pyrococcus horikoshii are metallopeptidases that form large dodecameric particles with high thermal stability. The influence of various physico-chemical parameters on PhTET3 quaternary structure was investigated. Analytical ultracentrifugation and biochemical analyses showed that the PhTET3 quaternary structure and enzymatic activity are maintained in high salt and that the complex is stable under extreme acidic conditions. Under basic pH conditions the complex disassembled into a low molecular weight species that was identified as folded dimer. Metal analyses showed that the purified enzyme only contains two equivalent of zinc per monomer, corresponding to the metal ions responsible for catalytic activity. When these metals were removed by EDTA treatment, the complex dissociated into the same dimeric species as those observed at high pH. Dodecameric TET particles were obtained from the metal free dimers when 2mM of divalent ions were added to the protein samples. Most of the dimers remained assembled at high temperature. Thus, we have shown that dimers are the building units in the TET oligomerization pathway and that the active site metals are essential in this process.