A bottom-up approach to gene regulation

The ability to construct synthetic gene networks enables experimental investigations of deliberately simplified systems that can be compared to qualitative and quantitative models. If simple, well-characterized modules can be coupled together into more complex networks with behaviour that can be predicted from that of the individual components, we may begin to build an understanding of cellular regulatory processes from the 'bottom up'. Here we have engineered a promoter to allow simultaneous repression and activation of gene expression in Escherichia coli. We studied its behaviour in synthetic gene networks under increasingly complex conditions: unregulated, repressed, activated, and simultaneously repressed and activated. We develop a stochastic model that quantitatively captures the means and distributions of the expression from the engineered promoter of this modular system, and show that the model can be extended and used to accurately predict the in vivo behaviour of the network when it is expanded to include positive feedback. The model also reveals the counterintuitive prediction that noise in protein expression levels can increase upon arrest of cell growth and division, which we confirm experimentally. This work shows that the properties of regulatory subsystems can be used to predict the behaviour of larger, more complex regulatory networks, and that this bottom-up approach can provide insights into gene regulation.     

A GIS model to predict the location of fossil packrat ( Neotoma ) middens in central Nevada

Fossil packrat ( Neotoma ) middens provide an important source of paleoecologic data in the arid West. This study describes and tests a predictive GIS model that uses the eights-of-evidence method for determining areas with a high probability of containing fossil middens in central Nevada. Model variables included geology, elevation, and aspect. Geology was found to be the most important variable tested. We produced a map of 4 probability classes validated by field-checking 21 randomly selected 1-km 2 sites throughout the study area. Our high-probability category reduced the search area to only 3.5% of the total study area. Fossil middens were found on 8 of 21 sites (38%). Geologic types that contained middens were granite, limestone, and volcanic tuff. A 2nd run of the model with the new midden localities added to the training set helped narrow the total search area even further. This analysis demonstrates that the weights-of-evidence method provides an effective tool both for guiding research design and for helping locate midden sites within specific localities. With only a limited training dataset and a simple set of mapped criteria, a model can be constructed that is both predictive and testable. We intend to continue development of the model to improve our ability to predict the location of Pleistocene-age middens and to locate middens on low-probability sites. This method, designed for mineral exploration, has wide potential application within the natural sciences.     

Late Pleistocene／Holocene wetland events recorded in southeast Tengger Desert lake sediments, NW China

The area along the eastern and southeastern margins of the Tengger Desert, NW China, which is sensitive to the summer monsoon variations, was selected for studying the environmental conditions surrounding the transition between Paleolithic foragers and Neolithic farmer/pastoral-ists. Short cores were obtained from four lake basins in the southwestern Tengger using a hand-driven piston coringdevice. Proxies from these cores were supplemented by ra-diocarbon ages obtained from lake sediment cores, shoreline features and spring mound deposits. Together these records provide evidence of millennial-scale climate change eventsfrom the Pleistocene-Holocene transition to the present.Lake/wetland events, representing periods of more intensive summer monsoon, occur in the records at-12.7-11.6,-10.1, -9.3, -8.0, -5.4, -1.5, and -0.8 ka BP. They do suggest that century- to miliennial-seale climatic cycles are characteristic of the Holocene in the southeastern Tengger Desert although the chronology must be considered extremely tentative.     

Whole brain methionine-enkephalin of ethanol-avoiding and ethanol-preferring C57BL mice

Summary These experiments systematically investigated ethanol preference in both the C57Bl/6N and C57Bl/6J mice utilizing three-choice 2-bottle preference test. In addition, these sublines were evaluated for whole brain methionineenkephalin levels, which were significantly lower in C57Bl/6J mice (alcohol preferring) compared to C57Bl/6N mice (alcohol non-preferring). This finding supports the involvement of the peptidyl opiates in ethanol seeking behavior.     

Whole brain methionine-enkephalin of ethanol-avoiding and ethanol-preferring c57BL mice

These experiments systematically investigated ethanol preference in both the C57Bl/6N and C57Bl/6J mice utilizing three-choice 2-bottle preference test. In addition, these sublines were evaluated for whole brain methionine-enkephalin levels, which were significantly lower in C57Bl/6J mice (alcohol preferring) compared to C57Bl/6N mice (alcohol non-preferring). This finding supports the involvement of the peptidyl opiates in ethanol seeking behavior.