Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs

For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT-AG and GC-AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5' splice sites (5'ss) and 3' splice sites (3'ss). As a result, differential frequencies of nucleotides at the first 5'ss in both the GT-AG and GC-AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5'ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC-AG introns, the tendency to have a weak consensus sequence at 5'ss is different between H. sapiens and M. musculus pre-mRNAs.     

RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family

The receptor activator of NF-κB (RANK) is a member of the tumor necrosis factor (TNF) receptor family and acts to cause osteoclastgenesis through the interaction with its ligand, RANKL. We isolated RNA aptamers with high affinity to human RANK by SELEX. Sequence and mutational analysis revealed that the selected RNAs form a G-quartet conformation that is crucial for binding to RANK. When the aptamer binding to RANK was challenged by RANKL, there was no competition between the aptamer and RANKL. Instead, the formation of a ternary complex, aptamer–RANK–RANKL, was detected by a spin down assay and by BIAcore surface plasmon resonance analysis. Moreover, the selected aptamer efficiently bound to other TNF receptor family proteins, such as TRAIL-R2, CD30, NGFR as well as osteoprotegerin, a decoy receptor for RANK. These results suggest that the selected aptamer recognizes not the ligand-binding site, but rather a common structure conserved in the TNF receptor family proteins.     

Tree growth and competition in a Betula platyphylla-Larix cajanderi post-fire forest in central Kamchatka

BACKGROUND AND AIMS: Fire is the dominant disturbance in central Kamchatka boreal forests, yet patterns and mechanisms of stand recovery have not been investigated. METHODS: Measurements were made of 1433 stems > or =1.3 m height and annual radial increments of 225 randomly selected trees in a 0.4-ha plot of a 53-year-old fire-origin mixed-species stand to examine the spatio-temporal variation in establishment, growth, size inequality and the mode of competition among individual trees. Growth variations were related to tree size, age and local interference with neighbours. KEY RESULTS: Betula platyphylla formed the main canopy following a fire in 1947, with Larix cajanderi and Pinus pumila progressively reinvading the lower tree and shrub stratum. Most B. platyphylla originated from sprouts in small patches (polycormons) during the first 15 post-fire years. Betula platyphylla had normal distributions of diameter and age classes, but negatively skewed height distribution, as expected from shade-intolerant, pioneer species. Larix cajanderi had fewer tall and many short individuals. The smaller and younger B. platyphylla grew disproportionately more in diameter than larger trees from 1950 to 1975, and hence stem size inequalities decreased. The reverse trend was observed from 1995 to 2000: larger trees grew more, indicating an increasing asymmetry of competition for light. Betula platyphylla had steady diameter growth in the first 25 post-fire years, after which the growth declined in smaller trees. Neighbourhood analysis showed that the decline resulted from increased competition from taller neighbours. CONCLUSIONS: The observed growth patterns suggest that mode of interactions altered during stand development from early stages of weak competition for soil resources released by fire to later stages of asymmetric competition for light. Asymmetric crown competition started later than reported in other studies, which can be attributed to the lower stem density leaving much space for individual growth, greater relative importance of below-ground competition in this site of nutrient-poor volcanic soil, and the vegetative origin of B. platyphylla. Larix cajanderi growing under B. platyphylla had steady diameter growth during the first 20 years, after which growth declined. It is suggested that early succession fits the tolerance model of succession, while inhibition dominates in later stages.     

Model of bidirectional modulated parasystole as a mechanism for cyclic bursts of ventricular premature contractions

Cyclic bursts of ventricular premature contractions (VPC) coming at minute-order intervals have been discerned by analyzing ambulatory ECG recordings, and their mechanism has not been clarified. The present study simulates this phenomenon by constructing a bidirectional modulated parasystole model. With Ts and Te as the intrinsic periods of the sinus and ectopic pacemakers, there are distinct and initial condition-dependent solutions in the model with Ts/Te values close to 1, 1/2, 1/4, etc. Typically, two distinct stable solutions are found existing together around Ts/Te = 1/2. We have verified theoretically the coexistence of different solutions and their dependence on the model parameters. The solution presented switches between those by a premature stimulus and those by fluctuations in the model parameters such as Ts. Patterns of RR intervals were generated by simulation with randomly fluctuating Ts. They included cyclic bursts of bigeminy of the flat type and the dome type reported by Takayanagi et al. (1999) and other transient types with Wenckebach or reverse Wenckebach rhythm of coupling intervals. This model provides a mathematical representation of the atrioventricular feedback mechanism and enables the modulated parasystole hypothesis to be applied to wider classes of VPCs.     

Alterations in the Function of Cerebral Dopaminergic and Serotonergic Systems Following Electroacupuncture and Moxibustion Applications: Possible Correlates with Their Antistress and Psychosomatic Actions

Alterations in cerebral monoamines following application of electroacupuncture were investigated using conscious rats with and without application of restraining stress. The dopamine and serotonin levels were significantly decreased in the nucleus accumbens, caudate putamen, and lateral hypothalamus and increased in the dorsal raphe nucleus by restraining stress. On the other hand, application of electroacupuncture on the lumbar and hindlimb segments eliminated the above changes in dopamine, while the changes in serotonin were attenuated by lumbar and hindlimb electroacupuncture. However, the effects of hindlimb electroacupuncture were greater than those of lumbar electroacupuncture. These results clearly indicate that lumbar and hindlimb electroacupuncture stimulations have differential effects on brain monoaminergic neurons in rats exposed to restraining stress. Moxa burning stimulation was applied to the lumbar and hindlimb segments of rats without restraining stress. The dopamine level was significantly increased in the midbrain substantia nigra-ventrotegmental area by hindlimb moxibusion. On the other hand, the serotonin levels were significantly increased in the nucleus amygdala by lumber moxibusion and decreased in the nucleus accumbens by hindlimb moxibusion. The present results indicate that electroacupuncture applied to the lumbar and hindlimb segments has an antistress effect, while the application of moxibustion to the lumbar and hindlimb segments was likely to stimulate the functions of mesocortical and mesolimbic dopaminergic and serotonergic neurons. We suggest that functional alterations in cerebral dopaminergic and serotonergic neurons are involved in the clinical efficacy of electroacupuncture and moxibustion, especially because of their antistress and psychosomatic actions.     

X-ray structures of NADPH-dependent carbonyl reductase from Sporobolomyces salmonicolor provide insights into stereoselective reductions of carbonyl compounds

The X-ray structures of red yeast Sporobolomyces salmonicolor carbonyl reductase (SSCR) and its complex with a coenzyme, NADPH, have been determined at a resolution of 1.8A and 1.6A, respectively. SSCR was crystallized in an orthorhombic system with the space group P2(1)2(1)2(1) and cell dimensions of a=54.86 A, b=83.49 A, and c=148.72 A. On its cocrystallization with NADPH, isomorphous crystals of the SSCR/NADPH complex were obtained. The structure of SSCR was solved by a single wavelength anomalous diffraction measurement using a selenomethionine-substituted enzyme, and that of the SSCR/NADPH complex was solved by a molecular replacement method using the solved structure of SSCR. The structures of SSCR and the SSCR/NADPH complex were refined to an R-factor of 0.193 (R(free)=0.233) and 0.211 (R(free)=0.238), respectively. SSCR has two domains, an NADPH-binding domain and a substrate-binding domain, and belongs to the short-chain dehydrogenases/reductases family. The structure of the NADPH-binding domain and the interaction between the enzyme and NADPH are very similar to those found in other structure-solved enzymes belonging to the short-chain dehydrogenases/reductases family, while the structure of the substrate-binding domain is unique. SSCR has stereoselectivity in its catalytic reaction, giving rise to excessive production of (S)-alcohols from ethyl 4-chloro-3-oxobutanoate. The X-ray structure of the SSCR/NADPH complex and preliminary modeling show that the formation of the hydrophobic channel induced by the binding of NADPH is closely related to the stereoselective reduction by SSCR.     

Tubulin and CRMP-2 complex is transported via Kinesin-1

The transport of tubulin and microtubules in a growing axon is essential for axonal growth and maintenance. However, the molecular mechanism underlying the linkage of tubulin and microtubules to motor proteins is not yet clear. Collapsin response mediator protein-2 (CRMP-2) is enriched at the distal part of growing axons in primary hippocampal neurons and plays a critical role in axon differentiation through its interaction with tubulin dimer and Numb. In this study, we show that CRMP-2 regulates tubulin transport by linking tubulin and Kinesin-1. The C-terminal region of CRMP-2 directly binds to the tetratricopeptide repeat domain of kinesin light chain 1 (KLC1). Soluble tubulin binds to the middle of CRMP-2 and forms a trimeric complex with CRMP-2/KLC1. Furthermore, the movement of GFP-tubulin in the photobleached area is weakened by knockdown of KLCs or CRMP-2. These results indicate that the CRMP-2/Kinesin-1 complex regulates soluble tubulin transport to the distal part of the growing axon.     

Preferential cell death of CD8+ effector memory (CCR7-CD45RA-) T cells by hydrogen peroxide-induced oxidative stress

T cells are used in many cell-based cancer treatments. However, oxidative stress that is induced during various chronic inflammatory conditions, such as cancer, can impair the immune system and have detrimental effects on T cell function. In this study, we have investigated the sensitivity of different human T cell subsets to H(2)O(2)-induced oxidative stress. We showed that central memory (CD45RA(-)CCR7(+)) and effector memory (CD45RA(-)CCR7(-)) T cells are more sensitive to H(2)O(2) as compared with naive (CD45RA(+)CCR7(+)) T cells. Furthermore, the study showed that CD8(+) effector memory T cells are more sensitive to low levels of H(2)O(2) (5 microM) compared with other types of T cells investigated. H(2)O(2)-exposed CD45RO(+) T cells showed mitochondrial depolarization prior to caspase 3 activity. Moreover, the pan-caspase inhibitor z-Val-Ala-Asp(OMe)-fluoromethylketone rescued cells from death. These experiments suggest that H(2)O(2)-induced cell death of CD45RO(+) T cells acts via the mitochondrial pathway and that caspase involvement is needed. This study suggests that oxidative stress in cancer patients can be disadvantageous for T cell-based adoptive cell transfer therapies, since effector memory T cells are the primary phenotype of the cells administered.     

Stat3 in resident macrophages as a repressor protein of inflammatory response

Inflammation is counterbalanced by anti-inflammatory cytokines such as IL-10, in which Stat3 mediates the signaling pathway. In this study, we demonstrate that resident macrophages, but not other cell types, are important targets of IL-10 in a murine model of acute peritonitis. Injection of thioglycollate i.p. induced a considerable number of neutrophils and macrophages in the peritoneum, which was significantly augmented in mice with a cell-type specific disruption of the Stat3 gene in macrophages and neutrophils (LysMcre/Stat3flox/- mice). The augmented leukocyte infiltration was accompanied by increased peritoneal levels of TNF-alpha, MIP-2, KC chemokine (KC), and MCP-1/CCL2. Stat3 was tyrosine phosphorylated in peritoneal resident macrophages as well as infiltrating leukocytes in the littermate controls, suggesting that Stat3 in either or both of these cells might play a regulatory role in inflammation. The peritoneal levels of TNF-alpha, MIP-2, KC, and MCP-1 were similarly elevated in LysMcre/Stat3flox/- mice rendered leukopenic by cyclophosphamide treatment as compared with the controls. Adoptive transfer of resident macrophages from LysMcre/Stat3flox/- mice into the control littermates resulted in increases in the peritoneal level of TNF-alpha, MIP-2, KC, and MCP-1 after i.p. injection of thioglycollate. Under these conditions, control littermates harboring LysMcre/Stat3flox/- macrophages exhibited an augmented leukocyte infiltration relative to those received control macrophages. Taken together, these data provide evidence that resident macrophages, but not other cell types, play a regulatory role in inflammation through a Stat3 signaling pathway. Stat3 in resident macrophages appears to function as a repressor protein in this model of acute inflammation.     

New series of potent delta-opioid antagonists containing the H-Dmt-Tic-NH-hexyl-NH-R motif

Heterodimeric compounds H-Dmt-Tic-NH-hexyl-NH-R (R = Dmt, Tic, and Phe) exhibited high affinity to δ- (K_iδ = 0.13–0.89 nM) and μ-opioid receptors (K_iμ = 0.38–2.81 nM) with extraordinary potent δ antagonism (pA₂ = 10.2–10.4). These compounds represent the prototype for a new class of structural homologues lacking μ-opioid receptor-associated agonism (IC₅₀ = 1.6–5.8 μM) based on the framework of bis-[H-Dmt-NH]-alkyl (Okada, Y.; Tsuda, Y.; Fujita, Y.; Yokoi, T.; Sasaki, Y.; Ambo, A.; Konishi, R.; Nagata, M.; Salvadori, S.; Jinsmaa, Y.; Bryant, S. D.; Lazarus, L. H. J. Med. Chem. 2003, 46, 3201), which exhibited both high μ affinity and bioactivity.