Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures

RNA structures play a fundamental role in nearly every aspect of cellular physiology and pathology. Gaining insights into the functions of RNA molecules requires accurate predictions of RNA secondary structures. However, the existing thermodynamic folding models remain less accurate than desired, even when chemical probing data, such as selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) reactivities, are used as restraints. Unlike most SHAPE-directed algorithms that only consider SHAPE restraints for base pairing, we extract two-dimensional structural features encoded in SHAPE data and establish robust relationships between characteristic SHAPE patterns and loop motifs of various types (hairpin, internal, and bulge) and lengths (2–11 nucleotides). Such characteristic SHAPE patterns are closely related to the sugar pucker conformations of loop residues. Based on these patterns, we propose a computational method, SHAPELoop, which refines the predicted results of the existing methods, thereby further improving their prediction accuracy. In addition, SHAPELoop can provide information about local or global structural rearrangements (including pseudoknots) and help researchers to easily test their hypothesized secondary structures.     

干旱对小麦幼苗诱导蛋白表达与某些生理特性的初步探讨

试验以－１．２ＭＰａＰＥＧ６０００处理动小麦种子（ＴｒｉｔｉｃｕｍａｅｓｔｌｉｖｕｍＬ．）．ＳＤＳ－ＰＡＧＥ图谱分析表明,水分胁迫诱导幼芽及整株均产生４８．４ｋＤ、４１．５ｋＤ二个蛋白质亚基。在幼根中未出现以上二个蛋白亚基。胁迫４８ｈ后,根干重／芽干重比呈上升趋势,幼芽细胞膜楔对透性增大和相对含水量降幅度均大于幼根。     

<Emphasis Type="Italic">Rubellimicrobium roseum</Emphasis> sp. nov., a Gram-negative bacterium isolated from the forest soil sample

A novel pink-coloured, non-spore-forming, non-motile, Gram-negative bacterium, designated YIM 48858^T, is described by using a polyphasic approach. The strain can grow at pH 6.5–9 (optimum at pH 7) and 25–30°C (optimum at 28°C). NaCl is not required for its growth. Positive for oxidase and catalase. Urease activity, nitrate reduction, starch and Tween 80 tests are negative reaction. 16S rRNA gene sequence similarity studies showed that strain YIM 48858^T is a member of the genus Rubellimicrobium, with similarities of 96.3, 95.7 and 95.5% to Rubellimicrobium mesophilum MSL-20^T, Rubellimicrobium aerolatum 5715S-9^T and Rubellimicrobium thermophilum DSM 16684^T, respectively. Q-10 was the predominant respiratory ubiquinone as in the other members of the genus Rubellimicrobium. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, glycolipid and the major fatty acids were C18:1 ω7c, C16:0 and C10:0 3-OH, which are very different from the valid published species. The DNA G + C content was 67.7 mol%. Both phylogenetic and chemotaxonomic evidence supports that YIM 48858^T is a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium roseum sp. nov. is proposed. The type strain is YIM 48858^T (=CCTCC AA 208029^T =KCTC 23202^T).     

Carbon accumulation and distribution in Pinus massoniana and Cunninghamia lanceolata mixed forest ecosystem in Daqingshan, Guangxi, China

Carbon accumulation and distribution were studied at three sampling plots in a 13-year-old mixed planatation of Pinus massoniana and Cunninghamia lanceolata in Daqingshan, Guangxi, China. The results showed that carbon content varied with tissues and tree species, but the total carbon content of Pinus massoniana was higher than that of Cunninghamia lanceolata. The average tissue carbon contents of Pinus massoniana were: wood (58.6%) > root (56.3%) > branch (51.2%) > bark (49.8%) > leaf (46.8%), while those of Cunninghamia lanceolata were: bark (52.2%) > leaf (51.8%) > wood (50.2%) > root (47.5%) > branch (46.7%). The carbon contents of the soil (at a depth of 60cm) ranged from 1.45% to 1.84% with an average of 1.70%. Carbon contents were higher in the surface soil (0–20cm) than in the deep layer (below 20cm). The average carbon contents were the highest for trees (51.1%), followed by litter (48.3%), shrubs (44.1%), and herbs (33.0%). The biomass of the trees in the three plots ranged from 85.35 t hm^-2 to 101.35 t hm^-2 with an average of 93.83 t hm^-2, in which 75.7%–82.6% was Pinus massoniana. The biomass of the understory was 2.10–3.95 t hm^-2 with an average of 2.72 t hm^-2, while the standing stock of ground litter was 5.49–7.91 t hm^-2 with an average of 6.75 t hm^-2. The carbon storage in the mixed plantation reached the maximum in the soil layer (69.02%), followed by vegetation (29.03%), and standing litter (1.82%). The carbon storage in the tree layer occupied 23.90% of the total ecosystem and 97.7% of the vegetation layer. Pinus massoniana accounted for 65.39% of the total carbon storage in the tree layer. Tissue carbon storage was directly related to the corresponding amount of biomass. Trunks had the highest carbon storage, accounting for 53.23% of the trees in Pinus massoniana and 55.57% in Cunninghamia lanceolata, respectively. Roots accounted for about 19.22% of the total tree carbon. The annual net productivity of the mixed plantation was 11.46 t hm^-2a^-1, and that of sequestered carbon was 5.96 t hm^-2a^-1, which was equivalent to fixing CO₂ of 21.88 t hm^-2a^-1. The plantation was found to be an important sink of atmospheric CO₂.     

The beta1 subunit enhances oxidative regulation of large-conductance calcium-activated K+ channels

Oxidative stress may alter the functions of many proteins including the Slo1 large conductance calcium-activated potassium channel (BKCa). Previous results demonstrated that in the virtual absence of Ca2+, the oxidant chloramine-T (Ch-T), without the involvement of cysteine oxidation, increases the open probability and slows the deactivation of BKCa channels formed by human Slo1 (hSlo1) alpha subunits alone. Because native BKCa channel complexes may include the auxiliary subunit beta1, we investigated whether beta1 influences the oxidative regulation of hSlo1. Oxidation by Ch-T with beta1 present shifted the half-activation voltage much further in the hyperpolarizing direction (-75 mV) as compared with that with alpha alone (-30 mV). This shift was eliminated in the presence of high [Ca2+]i, but the increase in open probability in the virtual absence of Ca2+ remained significant at physiologically relevant voltages. Furthermore, the slowing of channel deactivation after oxidation was even more dramatic in the presence of beta1. Oxidation of cysteine and methionine residues within beta1 was not involved in these potentiated effects because expression of mutant beta1 subunits lacking cysteine or methionine residues produced results similar to those with wild-type beta1. Unlike the results with alpha alone, oxidation by Ch-T caused a significant acceleration of channel activation only when beta1 was present. The beta1 M177 mutation disrupted normal channel activation and prevented the Ch-T-induced acceleration of activation. Overall, the functional effects of oxidation of the hSlo1 pore-forming alpha subunit are greatly amplified by the presence of beta1, which leads to the additional increase in channel open probability and the slowing of deactivation. Furthermore, M177 within beta1 is a critical structural determinant of channel activation and oxidative sensitivity. Together, the oxidized BKCa channel complex with beta1 has a considerable chance of being open within the physiological voltage range even at low [Ca2+]i.     

Descending vasa recta endothelium is an electrical syncytium

We examined gap junction coupling of descending vasa recta (DVR). DVR endothelial cells or pericytes were depolarized to record the associated capacitance transients. Virtually all endothelia and some pericytes exhibited prolonged transients lasting 10-30 ms. Carbenoxolone (100 microM) and 18beta-glycyrrhetinic acid (18betaGRA; 100 microM) markedly shortened the endothelial transients. Carbenoxolone and heptanol (2 mM) reduced the pericyte capacitance transients when they were prolonged. Lucifer yellow (LY; 2 mM) was dialyzed into the cytoplasm of endothelial cells and pericytes. LY spread diffusely along the endothelial monolayer, whereas in most pericytes, it was confined to a single cell. In some pericytes, complex patterns of LY spreading were observed. DVR cells were depolarized by voltage clamp as fluorescence of bis(1,3-dibarbituric acid)-trimethine oxanol [DiBAC(4)(3)] was monitored approximately 200 microm away. A 40-mV endothelial depolarization was accompanied by a 26.1 +/- 5.5-mV change in DiBAC(4)(3) fluorescence. DiBAC(4)(3) fluorescence did not change after 18betaGRA or when pericytes were depolarized. Similarly, propagated cytoplasmic Ca(2+) responses arising from mechanical perturbation of the DVR wall were attenuated by 18betaGRA or heptanol. Connexin (Cx) immunostaining showed predominant linear Cx40 and Cx43 in endothelia, whereas Cx37 stained smooth muscle actin-positive pericytes. We conclude that the DVR endothelium is an electrical syncytium and that gap junction coupling in DVR pericytes exists but is less pronounced.