Progression of phosphorylated α-synuclein in Macaca fuscata

Prion‐like spreading of abnormal proteins is proposed to occur in neurodegenerative diseases, and the progression of α‐synuclein (α‐syn) deposits has been reported in the brains of animal models injected with synthetic α‐syn fibrils or pathological α‐syn prepared from patients with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). However, α‐syn transmission in nonhuman primates, which are more similar to humans, has not been fully clarified. Here, we injected synthetic human α‐syn fibrils into the left striatum of a macaque monkey (Macaca fuscata). At 3 months after the injection, we examined neurodegeneration and α‐syn pathology in the brain using α‐syn epitope‐specific antibodies, antiphosphorylated α‐syn antibodies (pSyn#64 and pSer129), anti‐ubiquitin antibodies, and anti‐p62 antibodies. Immunohistochemical examination with pSyn#64, pSer129, and α‐syn epitope‐specific antibodies revealed Lewy bodies, massive α‐syn‐positive neuronal intracytoplasmic inclusions (NCIs), and neurites in the left putamen. These inclusions were also positive for ubiquitin and p62. LB509, a human‐specific α‐syn antibody targeting amino acid residues 115–122, showed limited immunoreactivity around the injection site. The left substantia nigra (SN) and the bilateral frontal cortex also contained some NCIs and neurites. The left hemisphere, including parietal/temporal cortex presented sparse α‐syn pathology, and no immunoreactivity was seen in olfactory nerves, amygdala, hippocampus, or right parietal/temporal cortex. Neuronal loss and gliosis in regions with α‐syn pathology were mild, except for the left striatum and SN. Our results indicate that abnormal α‐syn fibrils propagate throughout the brain of M. fuscata via projection, association, and commissural fibers, though the progression of α‐syn pathology is limited.

Renal arteriolar hyalinosis, not intimal thickening in large arteries, is associated with cardiovascular events in people with biopsy-proven diabetic nephropathy

AIMS

Diabetic nephropathy, a pathologically diagnosed microvascular complication of diabetes, is a strong risk factor for cardiovascular events, which mainly involve arteries larger than those affected in diabetic nephropathy. However, the association between diabetic nephropathy pathological findings and cardiovascular events has not been well studied. We aimed to investigate whether the pathological findings in diabetic nephropathy are closely associated with cardiovascular event development.

METHODS

This retrospective cohort study analysed 377 people with type 2 diabetes and biopsy-proven diabetic nephropathy, with a median follow-up of 5.9 years (interquartile range 2.0 to 13.5). We investigated how cardiovascular events were impacted by two vascular diabetic nephropathy lesions, namely arteriolar hyalinosis and arterial intimal thickening, and by glomerular and interstitial lesions.

RESULTS

Of the 377 people with diabetic nephropathy, 331 (88%) and 295 (78%) had arteriolar hyalinosis and arterial intimal thickening, respectively. During the entire follow-up period, those with arteriolar hyalinosis had higher cardiovascular event rates in the crude Kaplan-Meier analysis than those without these lesions (P = 0.005, log-rank test). When fully adjusted for clinically relevant confounders, arteriolar hyalinosis independently predicted cardiovascular events [hazard ratio (HR) 1.99; 95% confidence interval (CI) 1.12, 3.86], but we did not find any relationship between arterial intimal thickening and cardiovascular events (HR 0.89; 95% CI 0.60, 1.37). Additionally, neither glomerular nor interstitial lesions were independently associated with cardiovascular events in the fully adjusted model.

CONCLUSIONS

Arteriolar hyalinosis, but not intimal thickening of large arteries, was strongly associated with cardiovascular events in people with diabetic nephropathy.

Neuronal Representation of Object Choice in the Striatum of the Monkey

According to a widely held view, the decision-making process can be conceptualized as a two-step process: “object choice,” which does not include physical actions, followed by “movement choice,” in which action is executed to obtain the object. Accumulating evidence in the field of decision neuroscience suggests that the cortico-basal ganglia circuits play a crucial role in decision-making. However, the underlying mechanisms of the object and movement choices remain poorly understood, mainly because the two processes occur simultaneously in most experiments. In this study, to uncover the neuronal basis of object choice in the striatum, the main input site of the basal ganglia, we designed a behavioral task in which the processes of object and movement choice were temporally separated, and recorded the single-unit activity of phasically active neurons (PANs) (n = 375) in the striatum of two monkeys. We focused our study mainly on neuronal representation during the object choice period, before movement choice, using a mutual information analysis. Population striatal activities significantly represented the information of the chosen object during the object choice period, which indicated that the monkeys actually made the object choice during the task. For the activity of each individual neuron during the object choice period, we identified offered object- and chosen object-type neurons, corresponding to pre- and post-decision signals, respectively. We also found the movement-type neurons during the movement period after the object choice. Most offered object- or chosen object-type neurons were not overlapped with movement-type neurons. The presence of object choice-related signals independent of movement signal in the striatum indicated that the striatum was part of the site where object choice was made within a cortico-basal ganglia circuit.

Distinct Functions of the Primate Putamen Direct and Indirect Pathways in Adaptive Outcome-Based Action Selection

Cortico-basal ganglia circuits are critical regulators of reward-based decision making. Reinforcement learning models posit that action reward value is encoded by the firing activity of striatal medium spiny neurons (MSNs) and updated upon changing reinforcement contingencies by dopamine (DA) signaling to these neurons. However, it remains unclear how the anatomically distinct direct and indirect pathways through the basal ganglia are involved in updating action reward value under changing contingencies. MSNs of the direct pathway predominantly express DA D1 receptors and those of the indirect pathway predominantly D2 receptors, so we tested for distinct functions in behavioral adaptation by injecting D1 and D2 receptor antagonists into the putamen of two macaque monkeys performing a free choice task for probabilistic reward. In this task, monkeys turned a handle toward either a left or right target depending on an asymmetrically assigned probability of large reward. Reward probabilities of left and right targets changed after 30–150 trials, so the monkeys were required to learn the higher-value target choice based on action–outcome history. In the control condition, the monkeys showed stable selection of the higher-value target (that more likely to yield large reward) and kept choosing the higher-value target regardless of less frequent small reward outcomes. The monkeys also made flexible changes of selection away from the high-value target when two or three small reward outcomes occurred randomly in succession. DA D1 antagonist injection significantly increased the probability of the monkey switching to the alternate target in response to successive small reward outcomes. Conversely, D2 antagonist injection significantly decreased the switching probability. These results suggest distinct functions of D1 and D2 receptor-mediated signaling processes in action selection based on action–outcome history, with D1 receptor-mediated signaling promoting the stable choice of higher-value targets and D2 receptor-mediated signaling promoting a switch in action away from small reward outcomes. Therefore, direct and indirect pathways appear to have complementary functions in maintaining optimal goal-directed action selection and updating action value, which are dependent on D1 and D2 DA receptor signaling.

Characteristics of fast-spiking neurons in the striatum of behaving monkeys

Inhibitory interneurons are the fundamental constituents of neural circuits that organize network outputs. The striatum as part of the basal ganglia is involved in reward-directed behaviors. However, the role of the inhibitory interneurons in this process remains unclear, especially in behaving monkeys. We recorded the striatal single neuron activity while monkeys performed reward-directed hand or eye movements. Presumed parvalbumin-containing GABAergic interneurons (fast-spiking neurons, FSNs) were identified based on narrow spike shapes in three independent experiments, though they were a small population (4.2%, 42/997). We found that FSNs are characterized by high-frequency and less-bursty discharges, which are distinct from the basic firing properties of the presumed projection neurons (phasically active neurons, PANs). Besides, the encoded information regarding actions and outcomes was similar between FSNs and PANs in terms of proportion of neurons, but the discharge selectivity was higher in PANs than that of FSNs. The coding of actions and outcomes in FSNs and PANs was consistently observed under various behavioral contexts in distinct parts of the striatum (caudate nucleus, putamen, and anterior striatum). Our results suggest that FSNs may enhance the discharge selectivity of postsynaptic output neurons (PANs) in encoding crucial variables for a reward-directed behavior.

Impact of stimulus uncanniness on speeded response

In the uncanny valley phenomenon, the causes of the feeling of uncanniness as well as the impact of the uncanniness on behavioral performances still remain open. The present study investigated the behavioral effects of stimulus uncanniness, particularly with respect to speeded response. Pictures of fish were used as visual stimuli. Participants engaged in direction discrimination, spatial cueing, and dot-probe tasks. The results showed that pictures rated as strongly uncanny delayed speeded response in the discrimination of the direction of the fish. In the cueing experiment, where a fish served as a task-irrelevant and unpredictable cue for a peripheral target, we again observed that the detection of a target was slowed when the cue was an uncanny fish. Conversely, the dot-probe task suggested that uncanny fish, unlike threatening stimulus, did not capture visual spatial attention. These results suggested that stimulus uncanniness resulted in the delayed response, and importantly this modulation was not mediated by the feelings of threat.

Effects of depression on reward-based decision making and variability of action in probabilistic learning

BACKGROUND AND OBJECTIVES

Depression is characterized by low reward sensitivity in behavioral studies applying signal detection theory. We examined deficits in reward-based decision making in depressed participants during a probabilistic learning task, and used a reinforcement learning model to examine learning parameters during the task.

METHODS

Thirty-six nonclinical undergraduates completed a probabilistic selection task. Participants were divided into depressed and non-depressed groups based on Center for Epidemiologic Studies-Depression (CES-D) cut scores. We then applied a reinforcement learning model to every participant's behavioral data.

RESULTS

Depressed participants showed a reward-based decision making deficit and higher levels of the learning parameter τ, which modulates variability of action selection, as compared to non-depressed participants. Highly variable action selection is more random and characterized by difficulties with selecting a specific course of action.

CONCLUSION

These results suggest that depression is characterized by deficits in reward-based decision making as well as high variability in terms of action selection.

Photosensitive-polyimide based method for fabricating various neural electrode architectures

An extensive photosensitive-polyimide (PSPI)-based method for designing and fabricating various neural electrode architectures was developed. The method aims to broaden the design flexibility and expand the fabrication capability for neural electrodes to improve the quality of recorded signals and integrate other functions. After characterizing PSPI's properties for micromachining processes, we successfully designed and fabricated various neural electrodes even on a non-flat substrate using only one PSPI as an insulation material and without the time-consuming dry etching processes. The fabricated neural electrodes were an electrocorticogram (ECoG) electrode, a mesh intracortical electrode with a unique lattice-like mesh structure to fixate neural tissue, and a guide cannula electrode with recording microelectrodes placed on the curved surface of a guide cannula as a microdialysis probe. In vivo neural recordings using anesthetized rats demonstrated that these electrodes can be used to record neural activities repeatedly without any breakage and mechanical failures, which potentially promises stable recordings for long periods of time. These successes make us believe that this PSPI-based fabrication is a powerful method, permitting flexible design, and easy optimization of electrode architectures for a variety of electrophysiological experimental research with improved neural recording performance.

Stimulus-dependent adjustment of reward prediction error in the midbrain

Previous reports have described that neural activities in midbrain dopamine areas are sensitive to unexpected reward delivery and omission. These activities are correlated with reward prediction error in reinforcement learning models, the difference between predicted reward values and the obtained reward outcome. These findings suggest that the reward prediction error signal in the brain updates reward prediction through stimulus-reward experiences. It remains unknown, however, how sensory processing of reward-predicting stimuli contributes to the computation of reward prediction error. To elucidate this issue, we examined the relation between stimulus discriminability of the reward-predicting stimuli and the reward prediction error signal in the brain using functional magnetic resonance imaging (fMRI). Before main experiments, subjects learned an association between the orientation of a perceptually salient (high-contrast) Gabor patch and a juice reward. The subjects were then presented with lower-contrast Gabor patch stimuli to predict a reward. We calculated the correlation between fMRI signals and reward prediction error in two reinforcement learning models: a model including the modulation of reward prediction by stimulus discriminability and a model excluding this modulation. Results showed that fMRI signals in the midbrain are more highly correlated with reward prediction error in the model that includes stimulus discriminability than in the model that excludes stimulus discriminability. No regions showed higher correlation with the model that excludes stimulus discriminability. Moreover, results show that the difference in correlation between the two models was significant from the first session of the experiment, suggesting that the reward computation in the midbrain was modulated based on stimulus discriminability before learning a new contingency between perceptually ambiguous stimuli and a reward. These results suggest that the human reward system can incorporate the level of the stimulus discriminability flexibly into reward computations by modulating previously acquired reward values for a typical stimulus.

Development of a BCI master switch based on single-trial detection of contingent negative variation related potentials

To control the startup/shutdown of a conventional brain-computer interface (BCI) that is always running for daily use, we proposed and developed a new BCI system called a BCI master switch. We designed it with on/off switching functions by detecting the contingent negative variation (CNV)--related potentials. We chose CNV to improve the single-trial discrimination of user intentions to switch because CNV had a high signal-to-noise ratio and needed high concentration for its elicitation. We also applied a support vector machine (SVM) to improve the single-trial detection of CNV-related potentials. As the best parameters of SVM were estimated and applied, the offline evaluation's best performance achieved a CNV detection rate of 99.3% for the intention to switch and 2.1% for the intention not to switch. Remarkably, this performance was achieved from single-trial detection, imaginary response of user's intention without physical reaction, and the data from only one recording electrode. These results suggest that our proposed BCI system might work as a master switch by single-trial detection.

Multiple representations of belief states and action values in corticobasal ganglia loops

Reward-related neural activities have been found in a variety of cortical and subcortical areas by neurophysiological and neuroimaging experiments. Here we present a unified view on how three subloops of the corticobasal ganglia network are involved in reward prediction and action selection using different types of information. The motor/premotor-posterior striatum loop is specialized for action-based value representation and movement selection. The orbitofrontal-ventral striatum loop is specialized for object-based value representation and target selection. The lateral prefrontal-anterior striatum loop is specialized for context-based value representation and context estimation. Furthermore, the medial prefrontal cortex (MPFC) coordinates these multiple value representations and actions at different levels of hierarchy by monitoring the error in predictions.

Efficient reinforcement learning: computational theories, neuroscience and robotics

Reinforcement learning algorithms have provided some of the most influential computational theories for behavioral learning that depends on reward and penalty. After briefly reviewing supporting experimental data, this paper tackles three difficult theoretical issues that remain to be explored. First, plain reinforcement learning is much too slow to be considered a plausible brain model. Second, although the temporal-difference error has an important role both in theory and in experiments, how to compute it remains an enigma. Third, function of all brain areas, including the cerebral cortex, cerebellum, brainstem and basal ganglia, seems to necessitate a new computational framework. Computational studies that emphasize meta-parameters, hierarchy, modularity and supervised learning to resolve these issues are reviewed here, together with the related experimental data.

Brain mechanism of reward prediction under predictable and unpredictable environmental dynamics

In learning goal-directed behaviors, an agent has to consider not only the reward given at each state but also the consequences of dynamic state transitions associated with action selection. To understand brain mechanisms for action learning under predictable and unpredictable environmental dynamics, we measured brain activities by functional magnetic resonance imaging (fMRI) during a Markov decision task with predictable and unpredictable state transitions. Whereas the striatum and orbitofrontal cortex (OFC) were significantly activated both under predictable and unpredictable state transition rules, the dorsolateral prefrontal cortex (DLPFC) was more strongly activated under predictable than under unpredictable state transition rules. We then modelled subjects' choice behaviours using a reinforcement learning model and a Bayesian estimation framework and found that the subjects took larger temporal discount factors under predictable state transition rules. Model-based analysis of fMRI data revealed different engagement of striatum in reward prediction under different state transition dynamics. The ventral striatum was involved in reward prediction under both unpredictable and predictable state transition rules, although the dorsal striatum was dominantly involved in reward prediction under predictable rules. These results suggest different learning systems in the cortico-striatum loops depending on the dynamics of the environment: the OFC-ventral striatum loop is involved in action learning based on the present state, while the DLPFC-dorsal striatum loop is involved in action learning based on predictable future states.

Representation of Action-Specific Reward Values in the Striatum

The estimation of the reward an action will yield is critical in decision-making. To elucidate the role of the basal ganglia in this process, we recorded striatal neurons of monkeys who chose between left and right handle turns, based on the estimated reward probabilities of the actions. During a delay period before the choices, the activity of more than one-third of striatal projection neurons was selective to the values of one of the two actions. Fewer neurons were tuned to relative values or action choice. These results suggest representation of action values in the striatum, which can guide action selection in the basal ganglia circuit.

Microbiological and chemical quality of ground beef treated with sodium lactate and sodium chloride during refrigerated storage

The effects of sodium lactate (NaL) and sodium chloride (NaCl), either alone (30 g/kg) or in combination (20+20 g/kg), on the microbiological and chemical quality of raw ground beef during vacuum-packaged storage at 2 degrees C were investigated. The results showed that addition of NaL alone or in combination with NaCl significantly delayed the proliferation of aerobic plate counts, psychrotrophic counts, lactic acid bacteria and Enterobacteriaceae and extended the shelf life of the product up to 15 and 21 days, respectively, versus 8 days only for control. Over the storage time (21 days), NaL maintained the ground beef at almost constant pH, while the pH of control or NaCl-treated samples significantly decreased. Lipid oxidation (TBA value) was not affected by addition of NaL. At storage day 21 however, TBA values of both NaL-treated (0.309) and control (0.318) samples were significantly lower than those of samples treated with NaCl (0.463). The combination of NaCl with NaL significantly reduced the oxidative changes caused by NaCl (0.384 versus 0.463). Therefore, NaL alone or in combination with NaCl could be utilized successfully to reduce the microbial growth, maintain the chemical quality, and extend the shelf life of ground beef during refrigerated storage.

Antioxidant and antimicrobial effects of garlic in chicken sausage

The antioxidant and antimicrobial effects of equivalent concentrations of fresh garlic (FG), garlic powder (GP) and garlic oil (GO) were investigated against lipid oxidation and microbial growth in raw chicken sausage during storage at 3 degrees C. The antioxidant activities were compared to that of a standard synthetic antioxidant; butylated hydroxyanisole (BHA). The initial mean levels of thiobarbituric acid (TBA) value and peroxide value (POV) were 0.140 and 6.32, respectively. However after 21 days of storage, TBA and POV ranged from 0.151 to 4.92, respectively, in FG (50 g/kg) formulated samples to 0.214 and 8.64, respectively, in GO (0.06 g/ kg) formulation. Addition of either garlic or BHA (0.1 g/kg) significantly delayed lipid oxidation when compared with control. The antioxidant activities of the various materials added followed the order FG>GP>BHA>GO. On the other hand, the initial aerobic plate count (APC) in the samples was 4.41 log(10) CFU/g. Addition of FG (30 g/kg) or GP (9 g/kg) significantly reduced the APC and, subsequently, the shelf-life of the product was extended to 21 days. However, addition of GO or BHA resulted in no significant difference in APC when compared with control. Sensory analysis indicated that FG had a significant stronger flavor than the other sausage formulations. The results suggest that fresh garlic and garlic powder, through their combined antioxidant and antimicrobial effects, are potentially useful in preserving meat products.

A neural correlate of reward-based behavioral learning in caudate nucleus: a functional magnetic resonance imaging study of a stochastic decision task

Humans can acquire appropriate behaviors that maximize rewards on a trial-and-error basis. Recent electrophysiological and imaging studies have demonstrated that neural activity in the midbrain and ventral striatum encodes the error of reward prediction. However, it is yet to be examined whether the striatum is the main locus of reward-based behavioral learning. To address this, we conducted functional magnetic resonance imaging (fMRI) of a stochastic decision task involving monetary rewards, in which subjects had to learn behaviors involving different task difficulties that were controlled by probability. We performed a correlation analysis of fMRI data by using the explanatory variables derived from subject behaviors. We found that activity in the caudate nucleus was correlated with short-term reward and, furthermore, paralleled the magnitude of a subject's behavioral change during learning. In addition, we confirmed that this parallelism between learning and activity in the caudate nucleus is robustly maintained even when we vary task difficulty by controlling the probability. These findings suggest that the caudate nucleus is one of the main loci for reward-based behavioral learning.

Inter-module credit assignment in modular reinforcement learning

Critical issues in modular or hierarchical reinforcement learning (RL) are (i) how to decompose a task into sub-tasks, (ii) how to achieve independence of learning of sub-tasks, and (iii) how to assure optimality of the composite policy for the entire task. The second and last requirements are often under trade-off. We propose a method for propagating the reward for the entire task achievement between modules. This is done in the form of a 'modular reward', which is calculated from the temporal difference of the module gating signal and the value of the succeeding module. We implement modular reward for a multiple model-based reinforcement learning (MMRL) architecture and show its effectiveness in simulations of a pursuit task with hidden states and a continuous-time non-linear control task.

Multiple model-based reinforcement learning

We propose a modular reinforcement learning architecture for nonlinear, nonstationary control tasks, which we call multiple model-based reinforcement learning (MMRL). The basic idea is to decompose a complex task into multiple domains in space and time based on the predictability of the environmental dynamics. The system is composed of multiple modules, each of which consists of a state prediction model and a reinforcement learning controller. The "responsibility signal," which is given by the softmax function of the prediction errors, is used to weight the outputs of multiple modules, as well as to gate the learning of the prediction models and the reinforcement learning controllers. We formulate MMRL for both discrete-time, finite-state case and continuous-time, continuous-state case. The performance of MMRL was demonstrated for discrete case in a nonstationary hunting task in a grid world and for continuous case in a nonlinear, nonstationary control task of swinging up a pendulum with variable physical parameters.

CAD/DFF40 nuclease is dispensable for high molecular weight DNA cleavage and stage I chromatin condensation in apoptosis

DNA degradation during apoptotic execution generally occurs at two levels: early as high molecular weight (HMW) fragments and later on as oligonucleosomal fragments. Two nucleases, CAD/CPAN/DFF40 and endonuclease G, can digest nuclear chromatin to produce the oligonucleosomal fragments, and it has been suggested that CAD might be responsible for HMW DNA cleavage. To more clearly define the role of CAD in nuclear disassembly, we have generated CAD(-/-) sublines of chicken DT40 cells in which the entire CAD open reading frame has been deleted. These cells grow normally and undergo apoptosis with kinetics essentially identical to wild type cells. However, they fail to undergo detectable oligonucleosomal fragmentation, proving that CAD is essential for this stage of DNA cleavage, at least in DT40 cells. Other aspects of nuclear disassembly, including HMW DNA cleavage and early stage apoptotic chromatin condensation against the nuclear periphery proceed normally in the absence of CAD. However, the final stages of chromatin condensation and nuclear fragmentation do not occur. Our results demonstrate that CAD is required for complete disassembly of the nucleus during apoptosis and reveal the existence of one or more as yet unidentified second factors responsible for HMW DNA cleavage and the early stages of apoptotic chromatin condensation.

Polyamines of the thermophilic eubacteria belonging to the genera Thermosipho, Thermaerobacter and Caldicellulosiruptor

Cellular polyamines of four new thermophiles located in three early branched eubacterial clades, were investigated for the chemotaxonomic significance of polyamine distribution profiles. The thermophilic anaerobic Thermosipho japonicus, belonging to the order Thermotogales, contained norspermidine, norspermine and thermospermine in addition to spermidine and spermine. The polyamine profile was identical to the polyamine composition of Thermotoga, Fervidobacterium and Petrotoga species of the order. Spermidine, norspermidine, spermine, N4-bis(aminopropyl)spermidine and agmatine were found in thermophilic aerobic Thermaerobacter marianensis. Some differences were observed in the polyamine compositions of the phylogenetically related thermophilic anaerobes, Moorella, Dictyoglomus, Thermoanaerobacterium and Thermoanaerobacter species. Thermophilic anaerobic Caldicellulosiruptor kristianssonii and Caldicellulosiruptor owensensis contained a linear penta-amine, thermopentamine, and two quaternary branched penta-amines, N4-bis(aminopropyl)spermidine and N4-bis(aminopropyl)norspermidine, as the major polyamines. A novel tertiary branched penta-amine, N4-aminopropylspermine, was found in the two Caldicellulosiruptor species.

Improved data processing for optical imaging of developing neuronal connectivity in the neonatal mouse barrel cortex

Optical recording methods using voltage-sensitive dyes have proven valuable for the analysis of neuronal networks both in vivo and in vitro. This technique detects membrane potential changes as changes in the absorption or fluorescence of voltage-sensitive dyes incorporated into the cellular plasma membranes. The reliability of the optical recording technique is dependent on the dye-related response being fast enough to follow the electrical activity and of the response being more or less proportional to the amplitude of the membrane potential change. A high spatial resolution can be achieved using an appropriate imaging system and a dye with a response of sufficiently high signal-to-noise ratio. Thus, it is now anticipated that this method will be able to shed more light on the spatio-temporal information processing of neocortical circuitry. While the FUJIX HR Deltaron 1700 optical imaging system offers a reasonably high time (0.6 ms) and space-resolution (7 microm at 10x magnification), one drawback of this system, however, is its relatively poor data processing capabilities. We have therefore developed a protocol to improve the signal-to-noise ratio by modifying the calculation algorithm of the optical data. Consequently, we characterized optical responses in thalamocortical slices to find developmental landmarks of thalamocortical and intracortical connectivity in the neonatal mouse barrel cortex. Successful application of this method has been published on the analysis of thalamocortical glutamatergic connectivity [8].

Detection of DNA cleavage in apoptotic cells

At least two discrete deoxyribonuclease activities can be detected during apoptotic death, one that generates 30- to 500-kilobase pair (kbp) domain-sized fragments and another that mediates internucleosomal DNA degradation. The latter nuclease has been identified as the caspase-activated deoxyribonuclease (CAD)/CPAN, a unique enzyme that is normally inhibited by the regulatory subunit ICAD (inhibitor of CAD)/DFF45 (DNA fragmentation factor). In this chapter, techniques widely used to detect DNA cleavage in apoptotic cells, including pulsed-field gel electrophoresis, conventional agarose gel electrophoresis, and terminal transferase-mediated dUTP nick end-labeling (TUNEL), are briefly reviewed. In addition, the use of ICAD to inhibit apoptosis-associated nuclease activity is illustrated. When properly applied, these techniques are widely applicable to the characterization of apoptotic cells.

Measurements of macromolecule-bound and ultra-filtrable polyamines in rat liver homogenized without buffer

Ultra-filtrable and macromolecule-bound polyamines in rat liver homogenates, made without buffer, were determined, using Potter-Elvehjem homogenizer and commercially available, pressure-aided ultrafiltration device with a membrane pore size that allows passage of particles of molecular weight no larger than 5000. About 90% of polyamines in the liver were shown to be equilibrated with externally added 15N-labeled polyamines, based on the difference in the ratio of the natural to 15N-labeled polyamine in the liver homogenate and the ultrafiltrate. The entire amount of ultrafiltrate in the homogenized liver, required for calculation of the amounts of ultra-filtrable and macromolecule-bound polyamines, was estimated to be about 0.25 g in one gram of the homogenate, using a limited dilution curve of spermine in the ultrafiltrate with phosphate buffered saline and distilled water. With this value, ultra-filtrable polyamines in normal rat liver homogenate were calculated as about 25%, 8%, and 2% of the total amount of putrescine, spermidine, and spermine, respectively. The method was then used to measure ultra-filtrable and macromolecule-bound polyamines in regenerating rat liver homogenates, to examine possible changes of polyamines during cell growth. The method was also applied to measure other ultra-filtrable compounds such as amino acids and inorganic ions in rat liver homogenate.

Two distinct pathways leading to nuclear apoptosis

Apaf-1(-/-) or caspase-3(-/-) cells treated with a variety of apoptosis inducers manifest apoptosis-associated alterations including the translocation of apoptosis-inducing factor (AIF) from mitochondria to nuclei, large scale DNA fragmentation, and initial chromatin condensation (stage I). However, when compared with normal control cells, Apaf-1(-/-) or caspase-3(-/-) cells fail to exhibit oligonucleosomal chromatin digestion and a more advanced pattern of chromatin condensation (stage II). Microinjection of such cells with recombinant AIF only causes peripheral chromatin condensation (stage I), whereas microinjection with activated caspase-3 or its downstream target caspase-activated DNAse (CAD) causes a more pronounced type of chromatin condensation (stage II). Similarly, when added to purified HeLa nuclei, AIF causes stage I chromatin condensation and large-scale DNA fragmentation, whereas CAD induces stage II chromatin condensation and oligonucleosomal DNA degradation. Furthermore, in a cell-free system, concomitant neutralization of AIF and CAD is required to suppress the nuclear DNA loss caused by cytoplasmic extracts from apoptotic wild-type cells. In contrast, AIF depletion alone suffices to suppress the nuclear DNA loss contained in extracts from apoptotic Apaf-1(-/-) or caspase-3(-/-) cells. As a result, at least two redundant parallel pathways may lead to chromatin processing during apoptosis. One of these pathways involves Apaf-1 and caspases, as well as CAD, and leads to oligonucleosomal DNA fragmentation and advanced chromatin condensation. The other pathway, which is caspase-independent, involves AIF and leads to large-scale DNA fragmentation and peripheral chromatin condensation.

Regulation of both apoptosis and cell survival by the v-Src oncoprotein

A number of oncogenes alter the regulation of the cell cycle and cell death, contributing to the altered growth of tumours. Expression of the v-Src oncoprotein in Rat-1 fibroblasts prevented cell cycle exit in response to growth factor withdrawal. Here we investigated whether survival of v-Src transformed cells in low serum is dependent on v-Src activity. We used a temperature sensitive v-Src to study the effect inactivating v-Src on transformed cells growing under low serum conditions. We found when we switched off v-Src the cells died by apoptosis characterised by activation of caspases and the stress-activated kinases, JNK (Jun N-terminal kinase) and p38 MAP (mitogen activated protein) kinase. We were able to prevent cell death by addition of serum or overexpression of Bcl-2. Thus v-Src transformed Rat-1 cells can be protected from apoptosis by serum, v-Src, or Bcl-2. We investigated how v-Src protects from apoptosis under these conditions. Amongst other effects, v-Src activates two kinases which have been shown to protect cells from apoptosis, phosphatidylinositol 3-kinase (PI3-K) and extracellular signal-regulated kinase (ERK1/2). We found that switching off v-Src led to a decrease in the activity of both PI3-K and ERK1/2, however, we found that adding a specific inhibitor of PI3-K (LY294002) to v-Src transformed Rat-1 cells grown in low serum induced apoptosis while a specific ERK kinase (MEK1) inhibitor (PD98059) had no effect. This suggests that v-Src protects from apoptosis under low serum conditions by activating PI3-K.

DNA topoisomerase IIalpha interacts with CAD nuclease and is involved in chromatin condensation during apoptotic execution

Apoptotic execution is characterized by dramatic changes in nuclear structure accompanied by cleavage of nuclear proteins by caspases (reviewed in [1]). Cell-free extracts have proved useful for the identification and functional characterization of activities involved in apoptotic execution [2-4] and for the identification of proteins cleaved by caspases [5]. More recent studies have suggested that nuclear disassembly is driven largely by factors activated downstream of caspases [6]. One such factor, the caspase-activated DNase, CAD/CPAN/DFF40 [4,7,8] (CAD) can induce apoptotic chromatin condensation in isolated HeLa cell nuclei in the absence of other cytosolic factors [6,8]. As chromatin condensation occurs even when CAD activity is inhibited, however, CAD cannot be the sole morphogenetic factor triggered by caspases [6]. Here we show that DNA topoisomerase IIalpha (Topo IIalpha), which is essential for both condensation and segregation of daughter chromosomes in mitosis [9], also functions during apoptotic execution. Simultaneous inhibition of Topo IIalpha and caspases completely abolishes apoptotic chromatin condensation. In addition, we show that CAD binds to Topo IIalpha, and that their association enhances the decatenation activity of Topo IIalpha in vitro.

Formation of spindle poles by dynein/dynactin-dependent transport of NuMA

NuMA is a large nuclear protein whose relocation to the spindle poles is required for bipolar mitotic spindle assembly. We show here that this process depends on directed NuMA transport toward microtubule minus ends powered by cytoplasmic dynein and its activator dynactin. Upon nuclear envelope breakdown, large cytoplasmic aggregates of green fluorescent protein (GFP)-tagged NuMA stream poleward along spindle fibers in association with the actin-related protein 1 (Arp1) protein of the dynactin complex and cytoplasmic dynein. Immunoprecipitations and gel filtration demonstrate the assembly of a reversible, mitosis-specific complex of NuMA with dynein and dynactin. NuMA transport is required for spindle pole assembly and maintenance, since disruption of the dynactin complex (by increasing the amount of the dynamitin subunit) or dynein function (with an antibody) strongly inhibits NuMA translocation and accumulation and disrupts spindle pole assembly.

Differential localization of ICAD-L and ICAD-S in cells due to removal of a C-terminal NLS from ICAD-L by alternative splicing

CAD/CPAN/DFF40 is an apoptotic nuclease that is associated with the regulatory subunit ICAD/DFF in healthy cells. ICAD has two forms, ICAD-L/DFF45 and ICAD-S/DFF35, which are transcribed from a single gene by alternative splicing. They differ at the C-terminus: 70 amino acids of ICAD-L are replaced by 4 different amino acids in ICAD-S. We previously showed that both transfected and endogenous ICAD-L are nuclear; however, the localization of ICAD and CAD remains controversial and an important issue to clarify. Here we present the evidence that ICAD-L is nuclear due to the presence of an autonomous nuclear localization signal located in the C-terminal 20 amino acids. This NLS is missing from ICAD-S, which is distributed throughout the cell. We also showed that a GFP:CAD fusion protein is located in the nucleus of transfected cells.

Probing the interaction between N(1),N(4)-dibenzylputrescine and tRNA through (15)N NMR: biological implications

NMR spectroscopy was used to characterize the binding properties of polyamines to Escherichia coli tRNA. The (15)N NMR spectra of three (15)N-enriched N-substituted putrescine derivatives (DMP, DEP and DBP) were recorded in the presence of tRNA, and the spin relaxation times of the nitrogen nuclei were measured. From these data, the activation parameters for the rotational correlation times of the (15)N nuclei were determined. The present data indicate that the nature of the amino substituents does play a relevant role in controlling the polyamine-tRNA interaction. This study also provides a rationale for the in vivo antiproliferative effect of DBP against tumoral cells.

Adaptive internal state space construction method for reinforcement learning of a real-world agent

One of the difficulties encountered in the application of the reinforcement learning to real-world problems is the construction of a discrete state space from a continuous sensory input signal. In the absence of a priori knowledge about the task, a straightforward approach to this problem is to discretize the input space into a grid, and to use a lookup table. However, this method suffers from the curse of dimensionality. Some studies use continuous function approximators such as neural networks instead of lookup tables. However, when global basis functions such as sigmoid functions are used, convergence cannot be guaranteed. To overcome this problem, we propose a method in which local basis functions are incrementally assigned depending on the task requirement. Initially, only one basis function is allocated over the entire space. The basis function is divided according to the statistical property of locally weighted temporal difference error (TD error) of the value function. We applied this method to an autonomous robot collision avoidance problem, and evaluated the validity of the algorithm in simulation. The proposed algorithm, which we call adaptive basis division (ABD) algorithm, achieved the task using a smaller number of basis functions than the conventional methods. Moreover, we applied the method to a goal-directed navigation problem of a real mobile robot. The action strategy was learned using a database of sensor data, and it was then used for navigation of a real machine. The robot reached the goal using a smaller number of internal states than with the conventional methods.

Role of factors downstream of caspases in nuclear disassembly during apoptotic execution

We used cytoplasmic extracts from chicken DU249 cells at various stages along the apoptotic pathway to analyse the events of apoptotic execution. So-called S/M extracts from morphologically normal 'committed-stage' cells induce apoptotic morphology and DNA cleavage in substrate nuclei. These apoptotic changes appear to require the function of multiple caspases (cysteine aspartases, a specialized class of proteases) acting in parallel. Extracts from 'execution-stage' apoptotic cells induce apoptotic events in added nuclei in a caspase-independent manner. Biochemical fractionation of these extracts reveals that a column fraction enriched in endogenous active caspases is unable to induce DNA fragmentation or chromatin condensation in substrate nuclei, whereas a caspase-depleted fraction induces both changes. 'Execution-stage' extracts contain an ICAD/DFF45-inhibitable nuclease resembling CAD, plus another activity that is required for the apoptotic chromatin condensation. 'Committed-stage' S/M extracts lack these downstream activities. These observations reveal that caspases act in an executive fashion, serving to activate downstream factors that disassemble the nucleus rather than disassembling it themselves. They also suggest that activation of the downstream factors (rather than the caspases) is the critical event that occurs at the transition from the latent to the execution phase of apoptosis.

Primary structure of rat spermidine synthase: an example of refining the cDNA-derived amino acid sequence

The primary structure of rat spermidine synthase having the N-terminal acetylated methionine and 98.7% homology with that of the mouse enzyme is presented using a limited amount of the homogeneous enzyme. The study strategy was principally to compare the molecular masses of liberated peptides determined by three specific cleavage methods with those expected from known cDNA-derived amino acid sequences of mouse and human enzymes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS). The cleavage methods involved two enzymatic methods using lysylendopeptidase and arginylendopeptidase, and a chemical method for cleaving at the cysteine residue using 2-nitro-5-thiocyanobenzoic acid. Their usefulness was clearly demonstrated. Column-switching semimicro reversed-phase HPLC, which permits application of the entire reaction mixture, was useful for collecting a small amount of peptides containing the N-terminal amino acid, to confirm acetylation of the N-terminal methionine by MALDI TOF-MS. It was necessary in this approach to examine the amino acid sequence of certain peptides. The Edman method was used for the sequence analysis, and this will be replaced by an improved MALDI TOF-MS now available in a few laboratories.

Arginyl-tRNA-protein transferase activities in crude supernatants of rat tissues

A fluorescent HPLC method for the assay of arginyl-tRNA-protein transferase (R-Transferase) activity was applied to obtain quantitative data of the enzyme activity in rat tissues for the first time. In this assay, the major problem was a significant hydrolysis of the substrate, N-aspartyl-N'-dansylamido-1,4-butanediamine, and the product, N-arginylaspartyl-N'-dansylamido-1,4-butanediamine (ArgAsp(4)DNS) by aminopeptidases in crude samples such as 105000g supernatants (105S) of tissue homogenates. As bestatin inhibited the hydrolysis of ArgAsp(4)DNS, a standard-addition method in the presence of bestatin, using a partially purified R-Transferase preparation from hog kidney as a standard, made it possible to measure directly R-Transferase activities in 105S with a short incubation time and sufficient reliability. It was found by the established method that of 14 tissues examined, stomach was rich in the R-Transferase activity with the highest specific activity, suggesting a target tissue for the future studies on R-Transferase to elucidate its physiological significance.

Preparation and usefulness of some fluorogenic substrates for assay of arginyl-tRNA-protein transferase by HPLC

A series of fluorescent substrates and products was prepared and evaluated for the assay of arginyl-tRNA-protein transferase (arginyltransferase) activity by HPLC. Since N-aspartyl-N'-dansylamido-1,4-butanediamine (Asp(4)DNS) was the most suitable substrate of the compounds tested, which had a three-, four-, or five-methylene-chain interval between Asp or Glu and DNS, the following enzymatic studies were focussed on Asp(4)DNS and its product, N-arginylaspartyl-N'-dansylamido-1,4-butanediamine (ArgAsp(4)DNS). The apparent Km value for Asp(4)DNS was calculated to be 30 microM using a hydroxyapatite-treated arginyltransferase preparation from hog kidney, which was free from any enzyme that might decompose the two compounds. The present HPLC method was shown to be advantageous in reliability and sensitivity compared to the available isotope paper disk method using the hydroxyapatite-treated enzyme preparation and in applicability to crude samples examined using a DEAE-treated arginyltransferase preparation and 105,000g supernatant (105S) from hog kidney. Stepwise elimination of Arg and Asp from ArgAsp(4)DNS was observed with the two crude enzyme solutions, and the elimination of Arg was suppressed by the addition of bestatin, suggesting the participation of certain aminopeptidases. Although Asp(4)DNS was decomposed significantly with 105S, an incubation-time-dependent linear elevation of ArgAsp(4)DNS was maintained for 5 min in the presence of bestatin. Furthermore, an addition-recovery test of the DEAE-treated enzyme preparation for the 105S assured accurate determination of arginyltransferase activity in the 105S under the tentatively established conditions. The present HPLC method, which permits the simultaneous determination of 4-dansylamidobutylamine, Asp(4)DNS, and ArgAsp(4)DNS, was advantageous in measuring arginyltransferase activity and detecting the presence of unfavorable enzyme(s) in samples to ensure accurate determination.

Caspase-mediated cleavage of DNA topoisomerase I at unconventional sites during apoptosis

Previous studies have demonstrated that topoisomerase I is cleaved late during apoptosis, but have not identified the proteases responsible or examined the functional consequences of this cleavage. Here, we have shown that treatment of purified topoisomerase I with caspase-3 resulted in cleavage at DDVD146 downward arrowY and EEED170 downward arrowG, whereas treatment with caspase-6 resulted in cleavage at PEDD123 downward arrowG and EEED170 downward arrowG. After treatment of Jurkat T lymphocytic leukemia cells with anti-Fas antibody or A549 lung cancer cells with topotecan, etoposide, or paclitaxel, the topoisomerase I fragment comigrated with the product that resulted from caspase-3 cleavage at DDVD146 downward arrowY. In contrast, two discrete topoisomerase I fragments that appeared to result from cleavage at DDVD146 downward arrowY and EEED170 downward arrowG were observed after treatment of MDA-MB-468 breast cancer cells with paclitaxel. Topoisomerase I cleavage did not occur in apoptotic MCF-7 cells, which lack caspase-3. Cell fractionation and band depletion studies with the topoisomerase I poison topotecan revealed that the topoisomerase I fragment remains in proximity to the chromatin and retains the ability to bind to and cleave DNA. These observations indicate that topoisomerase I is a substrate of caspase-3 and possibly caspase-6, but is cleaved at sequences that differ from those ordinarily preferred by these enzymes, thereby providing a potential explanation why topoisomerase I cleavage lags behind that of classical caspase substrates such as poly(ADP-ribose) polymerase and lamin B1.

Ionspray ionization-mass spectrometric separation and determination of heptafluorobutyryl derivatives of polyamines

We describe here an application of ionspray ionization-mass spectrometry (IS-MS) for simultaneous determination of putrescine, spermidine, and spermine without the need for coupling with other separation techniques such as high-performance liquid chromatography or capillary electrophoresis. Because it was essential to increase the mass of these compounds to eliminate contaminated low-mass ions, heptafluorobutyryl (HFB) derivatives were chosen. It was found that each HFB-polyamine appeared as a single major cation carrying an ammonium ion in a solution of 50% acetonitrile-water containing 0.5% ammonium acetate at an orifice potential of 20 V. Under these conditions, the three polyamines after addition of 15N-labeled polyamines as internal standards, followed by heptafluorobutylation, were determined simultaneously. It was shown, using a sample injection bulb set between the syringe drive and ionspray probe, that the analysis time for data acquisition was about 3 min and the sensitivity was about 10 fmol. In addition, polyamines in rat liver were determined by this method after simple fractionation with a small column of CM-cellulose with reasonable accuracy and precision. Behaviors of acetylated polyamines were also described, and the results showed that the acetylated polyamines would become additional target compounds in the present method.

Transition from caspase-dependent to caspase-independent mechanisms at the onset of apoptotic execution

We have compared cytoplasmic extracts from chicken DU249 cells at various stages along the apoptotic pathway. Extracts from morphologically normal "committed stage" cells induce apoptotic morphology and DNA cleavage in substrate nuclei but require ongoing caspase activity to do so. In contrast, extracts from frankly apoptotic cells induce apoptotic events in added nuclei in a caspase-independent manner. Biochemical fractionation of these extracts reveals that a column fraction enriched in endogenous active caspases is unable to induce DNA fragmentation or chromatin condensation in substrate nuclei, whereas a caspase-depleted fraction induces both changes. Further characterization of the "execution phase" extracts revealed the presence of an ICAD/DFF45 (inhibitor of caspase-activated DNase/DNA fragmentation factor)- inhibitable nuclease resembling CAD, plus another activity that was required for the apoptotic chromatin condensation. Despite the presence of active caspases, committed stage extracts lacked these downstream activities, suggesting that the caspases and downstream factors are segregated from one another in vivo during the latent phase. These observations not only indicate that caspases act in an executive fashion, serving to activate downstream factors that disassemble the nucleus rather than disassembling it themselves, but they also suggest that activation of the downstream factors (rather than the caspases) is the critical event that occurs at the transition from the latent to active phase of apoptosis.