Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation

Generally, oaks dominate the broadleaf deciduous forests in Japan. The genetic variation in 6 cpDNA regions (trnT-trnL, trnL-trnF, atpB-rbcL, and trnH-psbA speacers, trnL intron, and matK gene) with regard to the Japanese oak (Quercus mongolica var. crispula) and 3 related species in the section Prinus (Q. serrata, Q. dentata and Q. aliena) was investigated in 598 trees belonging to 44 populations distributed throughout the Japanese archipelago. Additional samples were collected from Korea, China, and Russia (Sakhalin). Thirteen haplotypes (I to XIII) were identified on the bases of 15 nucleotide substitutions and 3 indels. Haplotypes I and II were discovered in northeastern Japan, whereas haplotypes III to IX were distributed in southwestern Japan. The boundary distinguishing these 2 groups was located in central Japan coincident with the Itoigawa-Shzuoka tectonic line. Haplotype I was also found in Sakhalin, whereas haplotypes VI, VII, VIII, X, XI, XII, and XIII were found in Korea and China. Four oak species in the same location shared identical haplotypes, suggesting cpDNA introgression by occasional hybridization. Both the values of total haplotype diversity (HT) and haplotype diversity within populations (HS) in Q. mongolica var. crispula were higher in the southwestern populations than in the northeastern populations. A haplotype network indicated that haplotype VI is the ancestral haplotype. The presence of identical haplotypes in Korea, China, and Japan suggested that the haplotypes diversified on the Eurasian continent before the last glacial period. The difference in genetic structure between the northeastern and southwestern regions indicates a difference in the history of migration and recolonization in Japan during the last glacial period.     

Endemic freshwater finfish of Asia: distribution and conservation status

Freshwater finfish species richness and level of endemism in East, and South and South‐East Asia that included 17 nations were studied using available databases, and included nation‐wise distribution, habitat types, and conservation status. The number of endemic finfish species in the region was 559, belonging to 47 families. Families Cyprinidae and Balitoridae accounted for 43.5% and 16.2% of the total number of endemic species in the region, respectively, followed by Sisoridae (25), Gobiidae (20), Melanotaeniidae (19), and Bagridae (16), and the other 41 families had at least one endemic species. Nation‐wise the most number of endemic freshwater finfish species occur in India (191), followed by China (88), Indonesia (84), and Myanmar (60). In India, the endemic species accounted for 26.4% of the native freshwater fish fauna, followed by South Korea (16.9%), the Philippines, (16.3%) and Myanmar (15.7%). Statistically significant relationships discerned between the number of indigenous and endemic species richness to land area (X_la in 10³ km²) of the nations in the region were, Y_in = 218.961 Ln(X_la) – 843.1 (R² = 0.735; P < 0.001) and Y_e = 28.445 Ln X_la?134.47 (R² = 0.534; P < 0.01), respectively, and between indigenous and endemic species richness was Y_e = 0.079X_n? 1.558 (R² = 0.235; P < 0.05). The overall conservation status of endemic finfish in Asia was satisfactory in that only 92 species were in some state of vulnerability, of which 37 species (6.6%) are endangered or critically endangered. However, the bulk of these species (83.7%) were cave‐ and or lake‐dwelling fish. However, nation‐wise, the endemic freshwater finfish fauna of the Philippines and Sri Lanka, based on the imperilment index, were found to be in a highly vulnerable state. Among river basins, the Mekong Basin had the highest number of endemic species (31.3%). The discrepancies between databases are highlighted and the need to consolidate information among databases is discussed. It is suggested that the Mekong Basin be considered as a biodiversity hotspot, and appropriate management strategies be introduced in this regard.     

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling

MOTIVATION: Recent advances in cell-free protein expression systems allow specific labeling of proteins with amino acids containing stable isotopes ((15)N, (13) C and (2)H), an important feature for protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. Given this labeling ability, we present a mathematical optimization framework for designing a set of protein isotopomers, or labeling schedules, to reduce the congestion in the NMR spectra. The labeling schedules, which are derived by the optimization of a cost function, are tailored to a specific protein and NMR experiment. RESULTS: For 2D (15)N-(1)H HSQC experiments, we can produce an exact solution using a dynamic programming algorithm in under 2 h on a standard desktop machine. Applying the method to a standard benchmark protein, calmodulin, we are able to reduce the number of overlaps in the 500 MHz HSQC spectrum from 10 to 1 using four samples with a true cost function, and 10 to 4 if the cost function is derived from statistical estimates. On a set of 448 curated proteins from the BMRB database, we are able to reduce the relative percent congestion by 84.9% in their HSQC spectra using only four samples. Our method can be applied in a high-throughput manner on a proteomic scale using the server we developed. On a 100-node cluster, optimal schedules can be computed for every protein coded for in the human genome in less than a month. AVAILABILITY: A server for creating labeling schedules for (15)N-(1)H HSQC experiments as well as results for each of the individual 448 proteins used in the test set is available at http://nmr.proteomics.ics.uci.edu.     

Overexpression of phospholipase C-gamma1 inhibits NGF-induced neuronal differentiation by proliferative activity of SH3 domain

Since the biological role of phospholipase C (PLC) gamma1 in neuronal differentiation still barely understood, here, we report that overexpression of PLC gamma1 inhibits neurite outgrowth and prolonged proliferation ability of PLC gamma1 contribute to the alteration of cell cycle regulatory proteins, subsequently exiting from cell growth arrest. Deletion of the SH3 or the entire SH223 domains, but not deletion of the N-SH2 or both the N-SH2 and C-SH2 domains expressing cells abolishes the differentiation-inhibitory effects of PLC gamma1, displaying depression of PCNA and elevation of cyclin D1. Moreover, these cells declined CDK1 and CDK2 expression and increased p21WAF-1, accompanying with G2/M accumulation. Some antiproliferative reagents are able to restore neurite outgrowth in PLC gamma1 cells, showing G2/M arrest. Our findings suggest that the proliferation activity of PLC gamma1 via its SH3 domain may be coupled with the flight from growth arrest by NGF, thereby inhibiting neuronal differentiation.     

The gene expression profile of Bombyx mori silkgland

During prepupal stage, the genes expression in silkgland is considered as a model for gene expression and regulation of eukaryotes. Aiming to comprehensively interpret gene expression profile in the silkgland, we collected all currently available EST, complete cDNA and protein expression information and other gene expression testing data published before, and explored their roles in their function pathways level. With the analysis of interaction between the known proteins and putative bio-macromolecules partners in silico, we list our prediction results in the form of pathway classification and test some of their expressions by experiments.     

Fluorescence spectroscopic and (19)f NMR studies of human thymidylate synthase with its cognate RNA

In order to investigate the interaction between hTS protein and its cognate mRNA, a 29nt fragment of TS mRNA was synthesized. This region has been suggested as a putative stem-loop involved in translational autoregulation. The melting temperature of the 29ntRNA was 65 degrees C, suggesting that this region does indeed form a stem-loop. Fluorescence spectroscopy was used to monitor the RNA: hTS protein interaction [dissociation constant (K(d)) 3.9 +/- 0.8 nM; stoichiometry of binding 1dimeric hTS: 1RNA]. When hTS was titrated against FdUMP, this gave the expected stoichiometry of 1dimeric hTS: 1.7 FdUMP but in the presence of the 29ntRNA, the stoichiometry of binding changed to 1dimeric hTS: 1RNA: 1FdUMP. Experiments using methotrexate (MTX) gave a stoichiometry of 1dimeric hTS: 1MTX and in the presence of 29ntRNA, the stoichiometry was unchanged. (19)F-NMR spectra of human TS: FdUMP complexes were found to be strikingly similar to analogous NMR spectra of complexes formed by L.casei TS and mouse TS. In the presence of FdUMP, spectra exhibited two additional resonances (-1.50 ppm and -34.4 ppm). The resonance at -1.50 ppm represents non-covalently bound FdUMP, the peak at -34.4 ppm represents covalently bound FdUMP. The addition of methotrexate to the binary TS-FdUMP complex caused a displacement of the internal equilibrium, with only the covalently-bound form seen, and with a slightly disturbed (19)F chemical shift (-36.5 ppm). Similar results were found when MTX was replaced by folinic or folic acid. The addition of 29ntRNA caused no changes to the (19)F spectra of either the binary or ternary complexes.     

Orthostatic panic as a key Vietnamese reaction to traumatic events: the case of September 11, 2001

This article discusses a culturally specific response to traumatic events: orthostatic panic attacks among Vietnamese refugees. We compared the rate and severity of orthostatic panic as well as the rates and severity of associated flashbacks a month before and a month after September 11, 2001. After that date, the rate and severity of orthostatic panic greatly increased, as did the rate and severity of associated flashbacks. The central role of orthostatic panic as a response to traumatic events is illustrated through a patient's vignette. An explanation of why September 11 so profoundly influenced this population is adduced, including an explanation of why it resulted in considerable worsening of orthostatic panic.     

A novel lepidopteran sex pheromone produced by females of a Lithosiinae species, Lyclene dharma dharma, in the family of Arctiidae

Female moths of Lyclene dharma dharma (Arctiidae, Lithosiinae) produced three pheromone components (I-III), which strongly stimulated male antennae. Using GC-MS analysis and chemical derivatizations, the following structures were estimated: 6-methyl-2-octadecanone (I), 14-methyl-2-octadecanone (II), and 6,14-dimethyl-2-octadecanone (III). While the stereochemistry of the chiral centers could not be determined because it was difficult to collect a sufficient amount of the natural pheromone, the plain structures of I and II were confirmed by synthesis of the racemic mixtures starting from diols. These methyl-branched ketones have not been identified as a natural product, indicating that they constitute a new chemical group of lepidopteran female sex pheromones.     

Microalgal growth enhancement by levoglucosan isolated from the green seaweed <Emphasis Type="Italic">Monostroma nitidum</Emphasis>

Microalgal growth was enhanced by the addition of levoglucosan to the culture medium. The growth-enhancing compound levoglucosan was isolated from the green seaweed Monostroma nitidum using water extraction, molecular fractionation, DEAE-cellulose column chromatography, and high-performance liquid chromatography. Yield of the compound from seaweed powder was 5 × 10⁻³% (w/w). At 10 mM concentration, levoglucosan enhanced cell growth and the specific growth rate of all feed microalgal species tested (Chaetoceros gracilis, Chlorella ellipsoidea, Dunaliella salina, Isochrysis galbana, Nannochloris oculata, Navicula incerta, Pavlova lutheri, Tetraselmis suecica) in most culture media by approximately 150%. Cellular fatty acid profiles and cell size differed marginally between cultures with and without levoglucosan.