Aquatic parameters and life history observations of the Great Basin spadefoot toad in Utah

The distribution and breeding habitats of the Great Basin spadefoot toad ( Scaphiopus intermontanus ) were investigated in the Bonneville Basin of western Utah. The permanent springs and man-made reservoirs used for breeding were largely found below the 1600 m elevation. The pH's ranged between 7.2 and 10.4 and the total dissolved solids between 170 and 4800 mg/l. The springs were less alkaline than the rain-filled reservoirs. The lack of aquatic vegetation was a common feature of the reservoirs and most of the springs. Observations of breeding without rain are noted as well as the lack of breeding with rain. The snout – vent lengths of adult spadefoots are greater in the Bonneville Basin than in other parts of the Great Basin. Utilization of permanent water sources and stimuli for emergence and breeding, as well as the larger adult size of S. intermontanus in the Bonneville Basin, are discussed in relation to the diverse precipitation patterns, the sparseness of the water sources, and the Holocene history of the Great Basin.      

Factors affecting selection of winter food and roosting resources by porcupines in Utah

Ecological and phytochemical factors potentially affecting winter dietary discrimination by porcupines ( Erethizon dorsatum ) in the mountain brush zone of Utah were studied. Porcupines utilized gambel oak ( Quercus gambelii ) as their primary winter food and roosting resource. Big-tooth maple ( Acer grandidentatum ) was the most common tree species in the study area but was rarely utilized by porcupines. Conifer species were used as a food and roosting resource significantly less often than they occurred in the study area, despite thermal advantages provided by their relatively dense canopies. Oak feed trees were successfully separated from conifer feed trees by discriminant analysis 100% of the time. Oak trees were correctly classified as feed and nonfeed trees 71% of the time. Gambel oak contained higher amounts of crude protein, fiber, and tannins, but was lower in either extract fractions and fatty acid content than conifers. A layer of adipose tissue used as an energy reserve by porcupines may have relaxed energy intake demands sufficiently to permit them to concentrate on a diet of oak tissue, which is high in protein, rather than a high-fat conifer diet. A diet relatively high in protein may have facilitated digestion of food material high in fiber. Temperature did not affect selection of tree species for roosting. Rock and snow caves were utilized infrequently and the study population ranged widely. Three of 15 study animals were eaten by predators.     

Modular and predictable assembly of porous organic molecular crystals

Nanoporous molecular frameworks are important in applications such as separation, storage and catalysis. Empirical rules exist for their assembly but it is still challenging to place and segregate functionality in three-dimensional porous solids in a predictable way. Indeed, recent studies of mixed crystalline frameworks suggest a preference for the statistical distribution of functionalities throughout the pores rather than, for example, the functional group localization found in the reactive sites of enzymes. This is a potential limitation for 'one-pot' chemical syntheses of porous frameworks from simple starting materials. An alternative strategy is to prepare porous solids from synthetically preorganized molecular pores. In principle, functional organic pore modules could be covalently prefabricated and then assembled to produce materials with specific properties. However, this vision of mix-and-match assembly is far from being realized, not least because of the challenge in reliably predicting three-dimensional structures for molecular crystals, which lack the strong directional bonding found in networks. Here we show that highly porous crystalline solids can be produced by mixing different organic cage modules that self-assemble by means of chiral recognition. The structures of the resulting materials can be predicted computationally, allowing in silico materials design strategies. The constituent pore modules are synthesized in high yields on gram scales in a one-step reaction. Assembly of the porous co-crystals is as simple as combining the modules in solution and removing the solvent. In some cases, the chiral recognition between modules can be exploited to produce porous organic nanoparticles. We show that the method is valid for four different cage modules and can in principle be generalized in a computationally predictable manner based on a lock-and-key assembly between modules.     

Seeking Allies: Modelling How Listeners Choose Their Musical Friends

In this paper we describe in some detail a formal computer model of inferential discourse based on a belief system. The key issue is that a logical model in a computer, based on rational sets, can usefully model a human situation based on irrational sets. The background of this work is explained elsewhere, as is the issue of rational and irrational sets (Billinge and Addis, in: Magnani and Dossena (eds.), Computing, philosophy and cognition, 2004; Stepney et al., Journey: Non-classical philosophy—socially sensitive computing in journeys non-classical computation: A grand challenge for computing research, 2004). The model is based on the Belief System (Addis and Gooding, Proceedings of the AISB’99 Symposium on Scientific Creativity, 1999) and it provides a mechanism for choosing queries based on a range of belief. We explain how it provides a way to update the belief based on query results, thus modelling others’ experience by inference. We also demonstrate that for the same internal experience, different models can be built for different actors.

A loss-of-function RNA interference screen for molecular targets in cancer

The pursuit of novel therapeutic agents in cancer relies on the identification and validation of molecular targets. Hallmarks of cancer include self-sufficiency in growth signals and evasion from apoptosis; genes that regulate these processes may be optimal for therapeutic attack. Here we describe a loss-of-function screen for genes required for the proliferation and survival of cancer cells using an RNA interference library. We used a doxycycline-inducible retroviral vector for the expression of small hairpin RNAs (shRNAs) to construct a library targeting 2,500 human genes. We used retroviral pools from this library to infect cell lines representing two distinct molecular subgroups of diffuse large B-cell lymphoma (DLBCL), termed activated B-cell-like DLBCL and germinal centre B-cell-like DLBCL. Each vector was engineered to contain a unique 60-base-pair 'bar code', allowing the abundance of an individual shRNA vector within a population of transduced cells to be measured using microarrays of the bar-code sequences. We observed that a subset of shRNA vectors was depleted from the transduced cells after three weeks in culture only if shRNA expression was induced. In activated B-cell-like DLBCL cells, but not germinal centre B-cell-like DLBCL cells, shRNAs targeting the NF-kappaB pathway were depleted, in keeping with the essential role of this pathway in the survival of activated B-cell-like DLBCL. This screen uncovered CARD11 as a key upstream signalling component responsible for the constitutive IkappaB kinase activity in activated B-cell-like DLBCL. The methodology that we describe can be used to establish a functional taxonomy of cancer and help reveal new classes of therapeutic targets distinct from known oncogenes.