Developmentally regulated extinction of Ly-49 receptor expression permits maturation and selection of NK1.1+ T cells.

Clonally distributed inhibitory receptors negatively regulate natural killer (NK) cell function via specific interactions with allelic forms of major histocompatibility complex (MHC) class I molecules. In the mouse, the Ly-49 family of inhibitory receptors is found not only on NK cells but also on a minor (NK1.1+) T cell subset. Using Ly-49 transgenic mice, we show here that the development of NK1.1+ T cells, in contrast to NK or conventional T cells, is impaired when their Ly-49 receptors engage self-MHC class I molecules. Impaired NK1.1+ T cell development in transgenic mice is associated with a failure to select the appropriate CD1-reactive T cell receptor repertoire. In normal mice, NK1.1+ T cell maturation is accompanied by extinction of Ly-49 receptor expression. Collectively, our data imply that developmentally regulated extinction of inhibitory MHC-specific receptors is required for normal NK1.1+ T cell maturation and selection.

Homeodomain binding motifs modulate the probability of odorant receptor gene choice in transgenic mice.

Odorant receptor (OR) genes constitute with 1200 members the largest gene family in the mouse genome. A mature olfactory sensory neuron (OSN) is thought to express just one OR gene, and from one allele. The cell bodies of OSNs that express a given OR gene display a mosaic pattern within a particular region of the main olfactory epithelium. The mechanisms and cis-acting DNA elements that regulate the expression of one OR gene per OSN - OR gene choice - remain poorly understood. Here, we describe a reporter assay to identify minimal promoters for OR genes in transgenic mice, which are produced by the conventional method of pronuclear injection of DNA. The promoter transgenes are devoid of an OR coding sequence, and instead drive expression of the axonal marker tau-β-galactosidase. For four mouse OR genes (M71, M72, MOR23, and P3) and one human OR gene (hM72), a mosaic, OSN-specific pattern of reporter expression can be obtained in transgenic mice with contiguous DNA segments of only ~300 bp that are centered around the transcription start site (TSS). The ~150bp region upstream of the TSS contains three conserved sequence motifs, including homeodomain (HD) binding sites. Such HD binding sites are also present in the H and P elements, DNA sequences that are known to strongly influence OR gene expression. When a 19mer encompassing a HD binding site from the P element is multimerized nine times and added upstream of a MOR23 minigene that contains the MOR23 coding region, we observe a dramatic increase in the number of transgene-expressing founders and lines and in the number of labeled OSNs. By contrast, a nine times multimerized 19mer with a mutant HD binding site does not have these effects. We hypothesize that HD binding sites in the H and P elements and in OR promoters modulate the probability of OR gene choice.

Free inertial processes driven by Gaussian noise: Probability distributions, anomalous diffusion and fractal behavior

We study the motion of an unbound particle under the influence of a random force modeled as Gaussian colored noise with an arbitrary correlation function. We derive exact equations for the joint and marginal probability density functions and find the associated solutions. We analyze in detail anomalous diffusion behaviors along with the fractal structure of the trajectories of the particle and explore possible connections between dynamical exponents of the variance and the fractal dimension of the trajectories.

Generalized Langevin equations: Anomalous diffusion and probability distributions

We study the motion of a particle governed by a generalized Langevin equation. We show that, when no fluctuation-dissipation relation holds, the long-time behavior of the particle may be from stationary to superdiffusive, along with subdiffusive and diffusive. When the random force is Gaussian, we derive the exact equations for the joint and marginal probability density functions for the position and velocity of the particle and find their solutions.

Extinction debt of high-mountain plants under 21st-century climate change

Quantitative estimates of the range loss of mountain plants under climate change have so far mostly relied on static geographical projections of species' habitat shifts(1-3). Here, we use a hybrid model(4) that combines such projections with simulations of demography and seed dispersal to forecast the climate-driven spatio-temporal dynamics of 150 high-mountain plant species across the European Alps. This model predicts average range size reductions of 44-50% by the end of the twenty-first century, which is similar to projections from the most 'optimistic' static model (49%). However, the hybrid model also indicates that population dynamics will lag behind climatic trends and that an average of 40% of the range still occupied at the end of the twenty-first century will have become climatically unsuitable for the respective species, creating an extinction debt(5,6). Alarmingly, species endemic to the Alps seem to face the highest range losses. These results caution against optimistic conclusions from moderate range size reductions observed during the twenty-first century as they are likely to belie more severe longer-term effects of climate warming on mountain plants.

A global marine sedimentary response to the end-Permian mass extinction: Examples from southern Turkey and the western United States

The end-Permian mass extinction greatly diminished marine diversity and brought about a whole-scale restructuring of marine ecosystems; these ecosystem changes also profoundly affected the sedimentary record. Data presented here, attained through facies analyses of strata deposited during the immediate aftermath of the end-Permian mass extinction (southern Turkey) and at the close of the Early Triassic (southwestern United States), in combination with a literature review, show that sedimentary systems were profoundly affected by: (1) a reduction in biotic diversity and abundance and (2) long-term environmental fluctuations that resulted from the end-Permian crisis. Lower Triassic strata display widespread microbialite and carbonate seafloor fan development and contain indicators of suppressed infaunal bioturbation such as flat-pebble conglomerates and wrinkle structures (facies considered unusual in post-Cambrian subtidal deposits). Our observations suggest that depositional systems, too, respond to biotic crises, and that certain facies may act as barometers of ecologic and environmental change independent of fossil assemblage analyses. Close investigation of facies changes during other critical times in Earth history may serve as an important tool in interpreting the ecology of metazoans and their environment.

The protracted Permo-Triassic crisis and multi-episode extinction around the Permian-Triassic boundary

The Permo-Triassic crisis was a major turning point in geological history. Following the end-Guadalupian extinction phase, the Palaeozoic biota underwent a steady decline through the Lopingian (Late Permian), resulting in their decimation at the level that is adopted as the Permian-Triassic boundary (PTB). This trend coincided with the greatest Phanerozoic regression. The extinction at the end of the Guadalupian and that marking the end of the Permian are therefore related. The subsequent recovery of the biota occupied the whole of the Early Triassic. Several phases of perturbations in [delta]13Ccarb occurred through a similar period, from the late Wuchiapingian to the end of the Early Triassic. Therefore, the Permian-Triassic crisis was protracted, and spanned Late Permian and Early Triassic time. The extinction associated with the PTB occurred in two episodes, the main act with a prelude and the epilogue. The prelude commenced prior to beds 25 and 26 at Meishan and coincided with the end-Permian regression. The main act itself happened in beds 25 and 26 at Meishan. The epilogue occurred in the late Griesbachian and coincided with the second volcanogenic layer (bed 28) at Meishan. The temporal distribution of these episodes constrains the interpretation of mechanisms responsible for the greatest Phanerozoic mass extinction, particularly the significance of a postulated bolide impact that to our view may have occurred about 50,000[no-break space]Myr after the prelude. The prolonged and multi-phase nature of the Permo-Triassic crisis favours the mechanisms of the Earth's intrinsic evolution rather than extraterrestrial catastrophe. The most significant regression in the Phanerozoic, the palaeomagnetic disturbance of the Permo-Triassic Mixed Superchron, widespread extensive volcanism, and other events, may all be related, through deep-seated processes that occurred during the integration of Pangea. These combined processes could be responsible for the profound changes in marine, terrestrial and atmospheric environments that resulted in the end-Permian mass extinction. Bolide impact is possible but is neither an adequate nor a necessary explanation for these changes.

Deccan volcanism linked to the Cretaceous-Tertiary boundary mass extinction: New evidence from ONGC wells in the Krishna-Godavari basin

A scientific challenge is to assess the role of Deccan volcanism in the Cretaceous-Tertiary boundary (KTB) mass extinction. Here we report on the stratigraphy and biologic effects of Deccan volcanism in eleven deep wells from the Krishna-Godavari (K-G) Basin, Andhra Pradesh, India. In these wells, two phases of Deccan volcanism record the world's largest and longest lava mega-flows interbedded in marine sediments in the K-G Basin about 1500 km from the main Deccan volcanic province. The main phase-2 eruptions (similar to 80% of total Deccan Traps) began in C29r and ended at or near the KTB, an interval that spans planktic foraminiferal zones CF1-CF2 and most of the nannofossil Micula prinsii zone, and is correlative with the rapid global warming and subsequent cooling near the end of the Maastrichtian. The mass extinction began in phase-2 preceding the first of four mega-flows. Planktic foraminifera suffered a 50% drop in species richness. Survivors suffered another 50% drop after the first mega-flow, leaving just 7 to 8 survivor species. No recovery occurred between the next three mega-flows and the mass extinction was complete with the last phase-2 mega-flow at the KTB. The mass extinction was likely the consequence of rapid and massive volcanic CO(2) and SO(2) gas emissions, leading to high continental weathering rates, global warming, cooling, acid rains, ocean acidification and a carbon crisis in the marine environment. Deccan volcanism phase-3 began in the early Danian near the C29R/C29n boundary correlative with the planktic foraminiferal zone P1a/P1b boundary and accounts for similar to 14% of the total volume of Deccan eruptions, including four of Earth's longest and largest mega-flows. No major faunal changes are observed in the intertrappeans of zone P1b, which suggests that environmental conditions remained tolerable, volcanic eruptions were less intense and/or separated by longer time intervals thus preventing runaway effects. Alternatively, early Danian assemblages evolved in adaptation to high-stress conditions in the aftermath of the mass extinction and therefore survived phase-3 volcanism. Full marine biotic recovery did not occur until after Deccan phase-3. These data suggest that the catastrophic effects of phase-2 Deccan volcanism upon the Cretaceous planktic foraminifera were a function of both the rapid and massive volcanic eruptions and the highly specialized faunal assemblages prone to extinction in a changing environment. Data from the K-G Basin indicates that Deccan phase-2 alone could have caused the KTB mass extinction and that impacts may have had secondary effects.

Letter to the Editor : on the value of probability for evaluating results of comparative pattern analyses

This letter to the Editor comments on the article Practical relevance of pattern uniqueness in forensic science by P.T. Jayaprakash (Forensic Science International, in press).

Good genes and good luck: Ammonoid diversity and the end-Permian mass extinction

The end-Permian mass extinction removed more than 80% of marine genera. Ammonoid cephalopods were among the organisms most affected by this crisis. The analysis of a global diversity data set of ammonoid genera covering about 106 million years centered on the Permian-Triassic boundary (PTB) shows that Triassic ammonoids actually reached levels of diversity higher than in the Permian less than 2 million years after the PTB. The data favor a hierarchical rather than logistic model of diversification coupled with a niche incumbency hypothesis. This explosive and nondelayed diversification contrasts with the slow and delayed character of the Triassic biotic recovery as currently illustrated for other, mainly benthic groups such as bivalves and gastropods.