Anthropogenic landscapes support fewer rare bee species

Landscape Ecology - The response of rare species to human land use is poorly known because rarity is difficult to study; however, it is also important because rare species compose most of...     

Suppressing drosophila circadian rhythm with dim light

Drosophila larvae were reared and allowed to pupate in continuous bright white light. The pupae were then transferred to a much dimmer blue light. In continuous blue light of intensity below 0.001 erg per square centimeter per second, adult flies emerged in pulses 24.7 hours apart, each pulse occupying about 6 hours. But in continuous light of intensity exceeding 0.1 erg per square centimeter per second, they emerged at a steady rate. This intensity range from effective darkness to effective light is roughly from starlight to moonlight. Inside this range, the emergence peaks broaden for about a week with little change of period.     

Scaling up digital circuit computation with DNA strand displacement cascades

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.     

Methodological considerations in reserve system selection: A case study of Malagasy lemurs

Although data quality and weighting decisions impact the outputs of reserve selection algorithms, these factors have not been closely studied. We examine these methodological issues in the use of reserve selection algorithms by comparing: (1) quality of input data and (2) use of different weighting methods for prioritizing among species. In 2003, the government of Madagascar, a global biodiversity hotspot, committed to tripling the size of its protected area network to protect 10% of the country’s total land area. We apply the Zonation reserve selection algorithm to distribution data for 52 lemur species to identify priority areas for the expansion of Madagascar’s reserve network. We assess the similarity of the areas selected, as well as the proportions of lemur ranges protected in the resulting areas when different forms of input data were used: extent of occurrence versus refined extent of occurrence. Low overlap between the areas selected suggests that refined extent of occurrence data are highly desirable, and to best protect lemur species, we recommend refining extent of occurrence ranges using habitat and altitude limitations. Reserve areas were also selected for protection based on three different species weighting schemes, resulting in marked variation in proportional representation of species among the IUCN Red List of Threatened Species extinction risk categories. This result demonstrates that assignment of species weights influences whether a reserve network prioritizes maximizing overall species protection or maximizing protection of the most threatened species.     

Apparent Digestion Coefficients and Metabolizable Energy of Feed Ingredients for Rainbow Trout Oncorhynchus mykiss

More than 50 feedstuffs used or of potential use in diets for rainbow trout Oncorhyndus mykiss were compared through metabolism chamber trials. Testing included determination of apparent digestibility and metabolic energy for a wide variety of ingredients, including fish and animal meals, vegetable proteins, and single cell protein products. Testing involved feeding individual 200–300-g fish contained in replicate chambers, from which feces, urine, and gill excreta were collected seg arately and analyzed for residual nitrogen and energy. For comparison, several products previously tested at this or other laboratories were re-evaluated at dietary concentrations of 25, 50, or 100%.     

Engineering entropy-driven reactions and networks catalyzed by DNA

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.     

Spiral waves of chemical activity

The Zhabotinsky-Zaikin reagent propagates waves of chemical activity. Reaction kinetics remain to be fully resolved, but certain features of wave behavior are determined by purely geometrical considerations. If a wave is broken, then spiral waves, resembling involutes of the circle, appear, persist, and eventually exclude all concentric ring waves.     

Enzyme-free nucleic acid logic circuits

Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation. We report the design and experimental implementation of DNA-based digital logic circuits. We demonstrate AND, OR, and NOT gates, signal restoration, amplification, feedback, and cascading. Gate design and circuit construction is modular. The gates use single-stranded nucleic acids as inputs and outputs, and the mechanism relies exclusively on sequence recognition and strand displacement. Biological nucleic acids such as microRNAs can serve as inputs, suggesting applications in biotechnology and bioengineering.     

Scroll-shaped waves of chemical activity in three dimensions

Ferric ions catalyze the oxidation of malonate by bromate in acid solution, sometimes at a spatially uniform, steady rate, but sometimes in a self-regenerating three-dimensional wave which resembles a rotating scroll, often with its axis closed in a ring. In cross section perpendicular to the axis, one sees an involute spiral emerging from a thin cylindrical core. This "dissipative structure" organizes reaction stages periodically in space and time everywhere except along its rotation axis, which may therefore be a thermodynamically unique locus.