Domesticated nature: shaping landscapes and ecosystems for human welfare

Like all species, humans have exercised their impulse to perpetuate and propagate themselves. In doing so, we have domesticated landscapes and ecosystems in ways that enhance our food supplies, reduce exposure to predators and natural dangers, and promote commerce. On average, the net benefits to humankind of domesticated nature have been positive. We have, of course, made mistakes, causing unforeseen changes in ecosystem attributes, while leaving few, if any, truly wild places on Earth. Going into the future, scientists can help humanity to domesticate nature more wisely by quantifying the tradeoffs among ecosystem services, such as how increasing the provision of one service may decrease ecosystem resilience and the provision of other services.     

A single IGF1 allele is a major determinant of small size in dogs

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.     

Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56

Posttranslational modifications of the histone octamer play important roles in regulating responses to DNA damage. Here, we reveal that Saccharomyces cerevisiae Rtt109p promotes genome stability and resistance to DNA-damaging agents, and that it does this by functionally cooperating with the histone chaperone Asf1p to maintain normal chromatin structure. Furthermore, we show that, as for Asf1p, Rtt109p is required for histone H3 acetylation on lysine 56 (K56) in vivo. Moreover, we show that Rtt109p directly catalyzes this modification in vitro in a manner that is stimulated by Asf1p. These data establish Rtt109p as a member of a new class of histone acetyltransferases and show that its actions are critical for cell survival in the presence of DNA damage during S phase.     

Action research on alternative land tenure arrangements in Wenchi,Ghana: learning from ambiguous social dynamics and self-organized institutional innovation

This study reports on action research efforts that were aimed at developing institutional arrangements beneficial for soil fertility improvement. Three stages of action research are described and analyzed. We initially began by bringing stakeholders together in a platform to engage in a collaborative design of new arrangements. However, this effort was stymied mainly because conditions conducive for learning and negotiation were lacking. We then proceeded to support experimentation with alternative arrangements initiated by individual landowners and migrant farmers. The implementation of these arrangements too ran into difficulties due to intra-family dynamics and ambiguities regarding land tenure. Further investigations to find out how ambiguities could be tackled revealed that the local actors themselves had taken initiatives towards developing institutional innovations to reduce ambiguities. However, there is still considerable scope for further development of these self-organized innovations. The article ends with a reflection on inter-disciplinary action research, where it is argued that making “mistakes” is an inherent and necessary characteristic in action research that aims to address complex social issues.

“<Emphasis Type="Italic">Chasms</Emphasis>” in agrifood systems: rethinking how we can contribute

The reaction to conventional agriculture and food systems has generated a host of alternative social movements in the past several decades. Many progressive agrifood researchers have researched these movements, exploring their strengths, weaknesses, and failures. Most such research is abstracted from the movements themselves. This paper proposes a new way of self-organization that, while fulfilling traditional university demands on researchers, will provide research support for progressive agrifood movements by transcending the boundaries of disciplines and individual universities.

Mercury cratering record viewed from MESSENGER's first flyby

Morphologies and size-frequency distributions of impact craters on Mercury imaged during MESSENGER's first flyby elucidate the planet's geological history. Plains interior to the Caloris basin displaying color and albedo contrasts have comparable crater densities and therefore similar ages. Smooth plains exterior to Caloris exhibit a crater density approximately 40% less than on interior plains and are thus volcanic and not Caloris impact ejecta. The size distribution of smooth-plains craters matches that of lunar craters postdating the Late Heavy Bombardment, implying that the plains formed no earlier than 3.8 billion years ago (Ga). At diameters less than or equal to 8 to 10 kilometers, secondary impact craters on Mercury are more abundant than primaries; this transition diameter is much larger than that on the Moon or Mars. A low density of craters on the peak-ring basin Raditladi implies that it may be younger than 1 Ga.     

Band gap fluorescence from individual single-walled carbon nanotubes

Fluorescence has been observed directly across the band gap of semiconducting carbon nanotubes. We obtained individual nanotubes, each encased in a cylindrical micelle, by ultrasonically agitating an aqueous dispersion of raw single-walled carbon nanotubes in sodium dodecyl sulfate and then centrifuging to remove tube bundles, ropes, and residual catalyst. Aggregation of nanotubes into bundles otherwise quenches the fluorescence through interactions with metallic tubes and substantially broadens the absorption spectra. At pH less than 5, the absorption and emission spectra of individual nanotubes show evidence of band gap-selective protonation of the side walls of the tube. This protonation is readily reversed by treatment with base or ultraviolet light.     

Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine

In mammalian cells, repair of DNA double-strand breaks (DSBs) by nonhomologous end-joining (NHEJ) is critical for genome stability. Although the end-bridging and ligation steps of NHEJ have been reconstituted in vitro, little is known about the end-processing reactions that occur before ligation. Recently, functionally homologous end-bridging and ligation activities have been identified in prokarya. Consistent with its homology to polymerases and nucleases, we demonstrate that DNA ligase D from Mycobacterium tuberculosis (Mt-Lig) possesses a unique variety of nucleotidyl transferase activities, including gap-filling polymerase, terminal transferase, and primase, and is also a 3' to 5' exonuclease. These enzyme activities allow the Mt-Ku and Mt-Lig proteins to join incompatible DSB ends in vitro, as well as to reconstitute NHEJ in vivo in yeast. These results demonstrate that prokaryotic Ku and ligase form a bona fide NHEJ system that encodes all the recognition, processing, and ligation activities required for DSB repair.