A novel strategy for selection of allosteric ribozymes yields RiboReporter sensors for caffeine and aspartame

We have utilized in vitro selection technology to develop allosteric ribozyme sensors that are specific for the small molecule analytes caffeine or aspartame. Caffeine- or aspartame-responsive ribozymes were converted into fluorescence-based RiboReporter™ sensor systems that were able to detect caffeine or aspartame in solution over a concentration range from 0.5 to 5 mM. With read-times as short as 5 min, these caffeine- or aspartame-dependent ribozymes function as highly specific and facile molecular sensors. Interestingly, successful isolation of allosteric ribozymes for the analytes described here was enabled by a novel selection strategy that incorporated elements of both modular design and activity-based selection methods typically used for generation of catalytic nucleic acids.     

The first known neonate Ichthyosaurus communis skeleton: a rediscovered specimen from the Lower Jurassic,UK

Numerous specimens of Ichthyosaurus are known, but only very few small examples (total length of <1 m) have been assigned beyond Ichthyosaurus sp. Here, we report on a very small specimen (preflexural length of 560 mm) that can be unequivocally assigned to Ichthyosaurus communis due to possessing a unique combination of diagnostic skull and postcranial characters that are found in larger examples of the species. Furthermore, the specimen is identified as a neonate because of the small size, large sclerotic ring relative to the orbital region, and poorly ossified (highly cancellous) bones of the skull and postcranium. It is not an embryo as it is not preserved within an adult specimen and stomach contents are clearly evident. This is therefore the first neonate Ichthyosaurus communis skeleton to be described. The specimen, in the Lapworth Museum of Geology, University of Birmingham, has no provenance data associated with it. A microfossil analysis of the matrix in which the ichthyosaur skeleton is preserved strongly suggests a stratigraphic range of uppermost Hettangian to lowermost Sinemurian age (Lower Jurassic), but does not provide any geographical information.     

黄瓜花叶病毒香蕉株系(CMV-Xb)RNA3 cDNA的克隆和序列分析

通过RT-PCR方法,设计两对引物,克隆了黄瓜花叶病毒香蕉株系(CMV-Xb)RNA3,并进行了核苷酸和蛋白质水平上的分析.结果表明Xb株系RNA3全长2205nt,具有两个蛋白编码阅读框架(ORF),其中5'端(97～936nt)编码一个279aa的3a蛋白;3'端(1225～1871nt)编码一个218aa的CP蛋白.5'非编码区域为96nt;基因间隔区(IR)长288nt;3'NR含有324nt.通过与亚组Ⅱ其它株系RNA3核苷酸和所编码产物推导的氨基酸序列分析发现,亚组Ⅱ株系无论在编码区还是非编码区的核苷酸同源性都相对较高;亚组Ⅱ株系在进化过程中具有连续性.     

Accumulating evidence in ecology: Once is not enough

Many published studies in ecological science are viewed as stand‐alone investigations that purport to provide new insights into how ecological systems behave based on single analyses. But it is rare for results of single studies to provide definitive results, as evidenced in current discussions of the “reproducibility crisis” in science. The key step in science is the comparison of hypothesis‐based predictions with observations, where the predictions are typically generated by hypothesis‐specific models. Repeating this step allows us to gain confidence in the predictive ability of a model, and its corresponding hypothesis, and thus to accumulate evidence and eventually knowledge. This accumulation may occur via an ad hoc approach, via meta‐analyses, or via a more systematic approach based on the anticipated evolution of an information state. We argue the merits of this latter approach, provide an example, and discuss implications for designing sequences of studies focused on a particular question. We conclude by discussing current data collection programs that are preadapted to use this approach and argue that expanded use would increase the rate of learning in ecology, as well as our confidence in what is learned.     

Groundwater-induced redox-gradients control soil properties and phosphorus availability across four headwater wetlands, New York, USA

Hydrochemical patterns across groundwater-fed wetlands, especially carbonate and redox gradients, can influence phosphorus (P) availability by controlling its distribution among different soil pools. We explored these linkages by comparing shallow (5–20 cm) soil properties along groundwater flowpaths in two rich fens, a marl fen, and a poor fen. Organic matter content, bulk density, and total elemental content varied more with depth to underlying drift materials than with water table fluctuation, but also were influenced by groundwater discharge, which stabilized water table elevations and controlled redox conditions. Total sulfur and calcium content increased where pore-water chemistry indicated active iron and sulfate reduction. Calcium mineral dynamics, however, did not appear to influence P availability: first, calcium carbonate (CaCO₃) accounted for <2% of the soil composition, except in the marl fen where it accounted for 20–25% of the soil composition. Second, Ca-bound P pools, determined from hydrochloric extraction of wet soil samples, accounted for <25% of the inorganic soil P pool. In contrast, iron-bound P determined from bicarbonate-buffered dithionite solution, accounted for 50–80% of the inorganic soil P, and increased where there was evidence of groundwater mixing, as did P release rates inferred from incubated anion resin bags. The total carbon and phosphorus content of organic-rich soils as well as available and labile P pools were strongly correlated with pore-water iron and alkalinity concentrations. Groundwater discharge and resulting hydrochemical gradients explained significant variation in soil composition and P availability across each site. Results highlight the importance of conducting biogeochemical studies in the context of a site’s shallow geologic setting and suggest mechanisms supporting the diverse plant species unique to groundwater wetlands.     

Spatially explicit dynamic N-mixture models

Population Ecology - Knowledge of demographic parameters such as survival, reproduction, emigration, and immigration is essential to understand metapopulation dynamics. Traditionally the estimation...     

Synthesis of acid-labile diplasmenyl lipids for drug and gene delivery applications.

The low pH environments characteristic of endosomal compartments and ischemic tissues provide an intrinsic pathway for triggering site-specific contents release from appropriately designed delivery vehicles. Accordingly, research in this group has focused on the design, synthesis and application of novel acid-sensitive lipids that will undergo facile lamellar (L alpha) to hexagonal (HII) phase transitions within these acidic sites. Previously, it has been demonstrated that plasmenylcholine-type lipids have excellent acid hydrolysis and contents release kinetics (Gerasimov et al., Biochim. Biophys. Acta. 1324 (1997) 200-214; Rui et al., J. Am. Chem. Soc. 120 (1998) 11213-11218). This paper describes the synthesis of three new acid sensitive lipids, based on a chiral 1,2-di-O-(1Z',9Z'-octadecadienyl)-sn-glycerol (6) platform, displaying phosphocholine (7), poly(ethyleneoxide) (8), and O-carbamoyl-N-diethylen-etriamine (10) headgroups. Intermediate 6 was obtained in 28% overall yield via a six step synthesis from (S)-(+)-2,2-dimethyl-1,2-dioxolane-4-methanol. Subsequent conversion to the final products was acheived in moderate (7 and 10) to excellent yields (8).