de novo转录组学分析华南地区入侵植物五爪金龙代谢特征

为探究华南地区严重入侵植物五爪金龙(Ipomoea cairica)生物入侵的分子机制,对五爪金龙及其近缘种七爪金龙(I. digitata)和裂叶牵牛(I. nil)进行de novo转录组测序和组装,得到56551条unigenes,其中56522条得到注释,7815条GO注释,15615条COG注释,180201条KEGG数据库注释。转录组分析结果表明,五爪金龙氮代谢通路关键酶基因的表达高于对照。次生代谢关键酶(PAL、4CL、CAD、查耳酮合酶、苯基丙乙烯酮异构酶、槲皮黄3-O-甲基转移酶等)基因在五爪金龙与七爪金龙及裂叶牵牛中均得到协同性的差异表达,而这些代谢通路指导的产物合成对五爪金龙的抗逆境能力、生长、化感作用等均起关键作用。关键基因的RT-qPCR验证结果与转录组结果具有一致性。因此,这从分子生物学层面上对解释五爪金龙在华南地区的入侵机制提供了新的证据。     

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

Background  

The quantitative analysis of metabolic fluxes, i.e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on ¹³C substrates, (ii) ¹³C labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis.     

The appearance of monoamines in the adult and developing neurohypophysis of Gallus gallus

Summary Most of the specific monoamine fluorescence of the fowl neurohypophysis is found in the eminentia mediana and the infundibular stem. The densest accumulation of fluorescent structures is located to the zona externa and the subependymal layer, whereas generally only scattered fluorescence is demonstrable in the fiber layer. The neural lobe tissue is provided with very fine smooth fibers often difficult to distinguish. Spectrofluorimetric determinations have shown that noradrenaline is the major catecholamine in the chick neurohypophysis. From the embryological studies it is evident that the monoamine fluorescence first appears in the subependymal layer, the fiber layer and the neural lobe (after about 15 days of incubation). The zona externa fluorescence is not visible until just before hatching. 10 days after hatching the fluorescence intensity of the chick neurohypophysis is similar to that of the adult. Some comparisons are also made with the appearance of monoamines in the mouse.The authors take great pleasure in expressing their warmest thanks for laboratory facilities and good advice provided by Dr. Bengt Falck at the Institute of Histology, Lund, Sweden.This work was supported by grants from the Swedish Natural Science Research Council (project no. 99-35 and 2180-16), from the United States Public Health Service (NB-06701-02) and from the Swedish Medical Research Council (B-69-14 x -56-05 C).     

On the ultrastructure of follicles and isolated follicular granulosa cells of porcine ovary

Summary The endoplasmic reticulum in granulosa cells of primary, secondary, and small tertiary follicles of the porcine ovary is sparse and largely of the granular type.In granulosa cells of large tertiary follicles the endoplasmic reticulum shows distinct signs of proliferation. Some cells even contain whorls of endoplasmic reticulum membranes, essentially of the agranular variety.Direct continuity between endoplasmic reticulum membranes of the granular and agranular type as well as the continuous increase in agranular membranes suggest that these membranes may originate from the granular membranes.Granulosa cells isolated from large tertiary follicles by microdissection and keptin vitro show essentially the same ultrastructure as granulosa cells of intact large tertiary follicles.Some lipid droplets appear to be localized in cavities of the endoplasmic reticulum. It is suggested that the droplets contain precursor material for steroid hormone synthesis.Finally, the development of the agranular endoplasmic reticulum including the appearance of whorls in some granulosa cells of large tertiary follicles indicates that steroid synthesis may occur in such follicular granulosa cells.Read at the Meeting of the Swedish Society for Pathology in Umeå, September 25, 1965 (Bjersing, 1966).This investigation was supported by grants from the Swedish Medical Research Council (Projects No. 13 X-78-01, 12 X-78-02, and 12 X-78-03).     

The dynamics of the G protein-coupled neuropeptide Y2 receptor in monounsaturated membranes investigated by solid-state NMR spectroscopy

In contrast to the static snapshots provided by protein crystallography, G protein-coupled receptors constitute a group of proteins with highly dynamic properties, which are required in the receptors’ function as signaling molecule. Here, the human neuropeptide Y2 receptor was reconstituted into a model membrane composed of monounsaturated phospholipids and solid-state NMR was used to characterize its dynamics. Qualitative static ¹⁵N NMR spectra and quantitative determination of ¹H–¹³C order parameters through measurement of the ¹H–¹³C dipolar couplings of the CH, CH₂ and CH₃ groups revealed axially symmetric motions of the whole molecule in the membrane and molecular fluctuations of varying amplitude from all molecular segments. The molecular order parameters (S_backbone = 0.59–0.67, S_CH2 = 0.41–0.51 and S_CH3 = 0.22) obtained in directly polarized ¹³C NMR experiments demonstrate that the Y2 receptor is highly mobile in the native-like membrane. Interestingly, according to these results the receptor was found to be slightly more rigid in the membranes formed by the monounsaturated phospholipids than by saturated phospholipids as investigated previously. This could be caused by an increased chain length of the monounsaturated lipids, which may result in a higher helical content of the receptor. Furthermore, the incorporation of cholesterol, phosphatidylethanolamine, or negatively charged phosphatidylserine into the membrane did not have a significant influence on the molecular mobility of the Y2 receptor.     

Mechanisms governing B cell developmental defects in invariant chain-deficient mice

Invariant chain (Ii)-deficient mice exhibit profound B cell defects that have remained poorly understood, because they could not be simply explained by impaired Ag presentation. We found that Ii deficiency induced cell autonomous defects of two distinct B cell lineages. The life span of mature follicular (FO) B cells was reduced, accounting for their markedly decreased frequency, whereas, in contrast, marginal zone (MZ) B cells accumulated. Other Ii-expressing lineages such as B1 B cells and dendritic cells were unaffected. Surprisingly, the life span of FO B cells was fully corrected in Ii/I-Abeta doubly deficient mice, revealing that Ii-free I-Abeta chains alter FO B cell survival. In contrast, the accumulation of MZ B cells was controlled by a separate mechanism independent of I-Abeta. Interestingly, in Ii-deficient mice lacking FO B cells, the MZ B cells invaded the FO zone, suggesting that intact follicules contribute to the retention of B cells in the MZ. These findings reveal unexpected consequences of Ii deficiency on the development and organization of B cell follicles.     

Silurian (Ludlow) acastid trilobites from Gotland and Scania,Sweden

Acastid trilobites from Ludlow strata on Gotland include three stratigraphically non-overlapping species ofAcastella Reed:Acastella madidipes n. sp. (Hemse Marl and Eke Beds),A. breviceps (Angelin 1851) (Burgsvik Beds), andA. amatrix n. sp. (Hamra Beds, and probably Burgsvik Beds). Type and other material ofA. breviceps (Angelin) from the Klinta Formation, Scania, is revised. Meraspid and early holaspid material ofAcastella is described. Some characters supportAcaste and allied taxa of mostly Wenlock age as a monophyletic subfamily Acastinae.Acastella as widely recognized is a grade with Devonian species more closely related to Asteropyginae than to the Ludlow type species. Baltic Ludlow-P?00ED;dolí species previously placed inScotiella Delo form a distinct group,Ewacaste n. gen., that includes a species from the uppermost Eke Beds on Gotland.     

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma