A local electrostatic change is the cause of the large-scale protein conformation shift in bacteriorhodopsin

During light-driven proton transport bacteriorhodopsin shuttles between two protein conformations. A large-scale structural change similar to that in the photochemical cycle is produced in the D85N mutant upon raising the pH, even without illumination. We report here that (i) the pKa values for the change in crystallographic parameters and for deprotonation of the retinal Schiff base are the same, (ii) the retinal isomeric configuration is nearly unaffected by the protein conformation, and (iii) preventing rotation of the C13—C14 double bond by replacing the retinal with an all-trans locked analogue makes little difference to the Schiff base pKa. We conclude that the direct cause of the conformational shift is destabilization of the structure upon loss of interaction of the positively charged Schiff base with anionic residues that form its counter-ion.

A genetic record of population isolation in pocket gophers during Holocene climatic change

A long-standing question in Quaternary paleontology is whether climate-induced, population-level phenotypic change is a result of large-scale migration or evolution in isolation. To directly measure genetic variation through time, ancient DNA and morphologic variation was measured over 2,400 years in a Holocene sequence of pocket gophers (Thomomys talpoides) from Lamar Cave, Yellowstone National Park, Wyoming. Ancient specimens and modern samples collected near Lamar Cave share mitochondrial cytochrome b sequences that are absent from adjacent localities, suggesting that the population was isolated for the entire period. In contrast, diastemal length, a morphologic character correlated with body size and nutritional level, changed predictably in response to climatic change. Our results demonstrate that small mammal populations can experience the long-term isolation assumed by many theoretical models of microevolutionary change.

Characteristics of the deep ocean carbon system during the past 150,000 years: ΣCO2 distributions, deep water flow patterns, and abrupt climate change

Studies of carbon isotopes and cadmium in bottom-dwelling foraminifera from ocean sediment cores have advanced our knowledge of ocean chemical distributions during the late Pleistocene. Last Glacial Maximum data are consistent with a persistent high-ΣCO2 state for eastern Pacific deep water. Both tracers indicate that the mid-depth North and tropical Atlantic Ocean almost always has lower ΣCO2 levels than those in the Pacific. Upper waters of the Last Glacial Maximum Atlantic are more ΣCO2-depleted and deep waters are ΣCO2-enriched compared with the waters of the present. In the northern Indian Ocean, δ13C and Cd data are consistent with upper water ΣCO2 depletion relative to the present. There is no evident proximate source of this ΣCO2-depleted water, so I suggest that ΣCO2-depleted North Atlantic intermediate/deep water turns northward around the southern tip of Africa and moves toward the equator as a western boundary current. At long periods (>15,000 years), Milankovitch cycle variability is evident in paleochemical time series. But rapid millennial-scale variability can be seen in cores from high accumulation rate series. Atlantic deep water chemical properties are seen to change in as little as a few hundred years or less. An extraordinary new 52.7-m-long core from the Bermuda Rise contains a faithful record of climate variability with century-scale resolution. Sediment composition can be linked in detail with the isotope stage 3 interstadials recorded in Greenland ice cores. This new record shows at least 12 major climate fluctuations within marine isotope stage 5 (about 70,000–130,000 years before the present).

Long-term change in the organization of inventive activity

Relying on a quantitative analysis of the patenting and assignment behavior of inventors, we highlight the evolution of institutions that encouraged trade in technology and a growing division of labor between those who invented new technologies and those who exploited them commercially over the nineteenth and early-twentieth centuries. At the heart of this change in the organization of inventive activity was a set of familiar developments which had significant consequences for the supply and demand of inventions. On the supply side, the growing complexity and capital intensity of technology raised the amount of human and physical capital required for effective invention, making it increasingly desirable for individuals involved in this activity to specialize. On the demand side, the growing competitiveness of product markets induced firms to purchase or otherwise obtain the rights to technologies developed by others. These increasing incentives to differentiate the task of invention from that of commercializing new technologies depended for their realization upon the development of markets and other types of organizational supports for trade in technology. The evidence suggests that the necessary institutions evolved first in those regions of the country where early patenting activity had already been concentrated. A self-reinforcing process whereby high rates of inventive activity encouraged the evolution of a market for technology, which in turn encouraged greater specialization and productivity at invention as individuals found it increasingly feasible to sell and license their discoveries, appears to have been operating. This market trade in technological information was an important contributor to the achievement of a high level of specialization at invention well before the rise of large-scale research laboratories in the twentieth century.

Scale dependence in earthquake phenomena and its relevance to earthquake prediction.

The recent discovery of a low-velocity, low-Q zone with a width of 50-200 m reaching to the top of the ductile part of the crust, by observations on seismic guided waves trapped in the fault zone of the Landers earthquake of 1992, and its identification with the shear zone inferred from the distribution of tension cracks observed on the surface support the existence of a characteristic scale length of the order of 100 m affecting various earthquake phenomena in southern California, as evidenced earlier by the kink in the magnitude-frequency relation at about M3, the constant corner frequency for earthquakes with M below about 3, and the sourcecontrolled fmax of 5-10 Hz for major earthquakes. The temporal correlation between coda Q-1 and the fractional rate of occurrence of earthquakes in the magnitude range 3-3.5, the geographical similarity of coda Q-1 and seismic velocity at a depth of 20 km, and the simultaneous change of coda Q-1 and conductivity at the lower crust support the hypotheses that coda Q-1 may represent the activity of creep fracture in the ductile part of the lithosphere occurring over cracks with a characteristic size of the order of 100 m. The existence of such a characteristic scale length cannot be consistent with the overall self-similarity of earthquakes unless we postulate a discrete hierarchy of such characteristic scale lengths. The discrete hierarchy of characteristic scale lengths is consistent with recently observed logarithmic periodicity in precursory seismicity.