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Biomedical subjects

K Samejima

Publications and source records attributed to K Samejima.

At least 19 recordsLinked to original sources
PubMed2001

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.

Animals↗
PubMed2001

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].

Algorithms↗
PubMed2001

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.

Bacteria↗
PubMed2000

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.

Animals↗
PubMed2000

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.

Biological Transport↗
PubMed2000

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.

Alternative Splicing↗
PubMed2000

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.

Magnetic Resonance Spectroscopy↗
PubMed2000

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.

Apoptosis↗
PubMed2000

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.

Animals↗
PubMed2000

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.

Amino Acids↗
PubMed1999

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.

Animals↗
PubMed1999

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.

Aminoacyltransferases↗
PubMed1999

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.

Animals↗
PubMed1999

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.

Journal Article↗
PubMed1999

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.

Aminoacyltransferases↗
PubMed1999

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.

Acetylation↗