Large-scale latitudinal and vertical distributions of NMHCs and selected halocarbons in the troposphere over the Pacific Ocean during the March-April 1999 Pacific Exploratory Mission (PEM-Tropics B)

Nonmethane hydrocarbons (NMHCs) and selected halocarbons were measured in whole air samples collected over the remote Pacific Ocean during NASA's Global Tropospheric Experiment (GTE) Pacific Exploratory Mission-Tropics B (PEM-Tropics B) in March and early April 1999. The large-scale spatial distributions of NMHCs and C2Cl4 reveal a much more pronounced north-south interhemispheric gradient, with higher concentrations in the north and lower levels in the south, than for the late August to early October 1996 PEM-Tropics A experiment. Strong continental outflow and winter-long accumulation of pollutants led to seasonally high Northern Hemisphere trace gas levels during PEM-Tropics B. Observations of enhanced levels of Halon 1211 (from developing Asian nations such as the PRC) and CH3Cl (from SE Asian biomass burning) support a significant southern Asian influence at altitudes above 1 km and north of 10° N. By contrast, at low altitude over the North Pacific the dominance of urban/industrial tracers, combined with low levels of Halon 1211 and CH3Cl, indicate a greater influence from developed nations such as Japan, Europe, and North America. Penetration of air exhibiting aged northern hemisphere characteristics was frequently observed at low altitudes over the equatorial central and western Pacific south to ∼5° S. The relative lack of southern hemisphere biomass burning sources and the westerly position of the South Pacific convergence zone contributed to significantly lower PEM-Tropics B mixing ratios of the NMHCs and CH3Cl south of 10° S compared to PEM-Tropics A. Therefore the trace gas composition of the South Pacific troposphere was considerably more representative of minimally polluted tropospheric conditions during PEM-Tropics B. Copyright 2001 by the American Geophysical Union

Factors controlling tropospheric O3, OH, NOx, and SO2 over the tropical Pacific during PEM-Tropics B

Observations over the tropical Pacific during the Pacific Exploratory Mission (PEM)-Tropics B experiment (March-April 1999) are analyzed. Concentrations of CO and long-lived nonmethane hydrocarbons in the region are significantly enhanced due to transport of pollutants from northern industrial continents. This pollutant import also enhances moderately O3 concentrations but not NOx concentrations. It therefore tends to depress OH concentrations over the tropical Pacific. These effects contrast to the large enhancements of O3 and NOx concentrations and the moderate increase of OH concentrations due to biomass burning outflow during the PEM-Tropics A experiment (September-October 1996). Observed CH3I concentrations, as in PEM-Tropics A, indicate that convective mass outflux in the middle and upper troposphere is largely independent of altitude over the tropical Pacific. Constraining a one-dimensiohal model with CH3I observations yields a 10-day timescale for convective turnover of the free troposphere, a factor of 2 faster than during PEM-Tropics A. Model simulated HO2, CH2O, H2O2, and CH3OOH concentrations are generally in agreement with observations. However, simulated OH concentrations are lower (∼25%) than observations above 6 km. Whereas models tend to overestimate previous field measurements, simulated HNO3 concentrations during PEM-Tropics B are too low (a factor of 2-4 below 6 km) compared to observations. Budget analyses indicate that chemical production of O3 accounts for only 50% of chemical loss; significant transport of O3 into the region appears to take place within the tropics. Convective transport of CH3OOH enhances the production of HOx and O3 in the upper troposphere, but this effect is offset by HOx loss due to the scavenging of H2O2. Convective transport and scavenging of reactive nitrogen species imply a necessary source of 0.4-1 Tg yr-1 of NOx in the free troposphere (above 4 km) over the tropics. A large fraction of the source could be from marine lightning. Oxidation of DMS transported by convection from the boundary layer could explain the observed free tropospheric SO2 concentrations over the tropical Pacific. This source of DMS due to convection, however, would imply in the model free tropospheric concentrations much higher than observed. The model overestimate cannot be reconciled using recent kinetics measurements of the DMS-OH adduct reaction at low pressures and temperatures and may reflect enhanced OH oxidation of DMS during convection. Copyright 2001 by the American Geophysical Union

NMHCs and halocarbons in Asian continental outflow during the Transport and Chemical Evolution over the Pacific (TRACE-P) Field Campaign: Comparison with PEM-West B

We present an overview of the spatial distributions of nonmethane hydrocarbons (NMHCs) and halocarbons observed over the western north Pacific as part of the NASA GTE Transport and Chemical Evolution over the Pacific (TRACE‐P) airborne field campaign (February–April 2001). The TRACE‐P data are compared with earlier measurements from the Pacific Rim during the Pacific Exploratory Mission‐West B (PEM‐West B), which took place in February–March 1994, and with emission inventory data for 2000. Despite the limited spatial and temporal data coverage inherent to airborne sampling, mean levels of the longer‐lived NMHCs (including ethane, ethyne, and benzene) were remarkably similar to our results during the PEM‐West B campaign. By comparison, mixing ratios of the fire extinguisher Halon‐1211 (CF2ClBr) increased by about 50% in the period between 1994 and 2001. Southern China (south of 35°N), and particularly the Shanghai region, appears to have been a substantial source of Halon‐1211 during TRACE‐P. Our previous analysis of the PEM‐West B data employed methyl chloroform (CH3CCl3) as a useful industrial tracer. However, regulations have reduced its emissions to the extent that its mixing ratio during TRACE‐P was only one‐third of that measured in 1994. Methyl chloroform mixing ratio “hot spots,” indicating regions downwind of continuing emissions, included outflow from the vicinity of Shanghai, China, but particularly high emission ratios relative to CO were observed close to Japan and Korea. Tetrachloroethene (C2Cl4) levels have also decreased significantly, especially north of 25°N, but this gas still remains a useful indicator of northern industrial emissions. Methyl bromide (CH3Br) levels were systematically 1–2 pptv lower from 1994 to 2001, in accord with recent reports. However, air masses that had been advected over Japan and/or South Korean port cities typically exhibited elevated levels of CH3Br. As a consequence, emissions of CH3Br from Japan and Korea calculated employing CH3Br/CO ratios and scaled to CO emission inventory estimates, were almost as large as for all of south China (south of 35°N). Total east Asian emissions of CH3Br and CH3Cl were estimated to be roughly 4.7 Gg/yr and 167 Gg/yr, respectively, in 2001

Carbonyl sulfide and carbon disulfide: Large-scale distributions over the western Pacific and emissions from Asia during TRACE-P

An extensive set of carbonyl sulfide (OCS) and carbon disulfide (CS 2) observations were made as part of the NASA Transport and Chemical Evolution over the Pacific (TRACE-P) project, which took place in the early spring 2001. TRACE-P sampling focused on the western Pacific region but in total included the geographic region 110°E to 290°E longitude, 5°N to 50°N latitude, and 0-12 km altitude. Substantial OCS and CS2 enhancements were observed for a great many air masses of Chinese and Japanese origin during TRACE-P. Over the western Pacific, mean mixing ratios of long-lived OCS and shorter-lived CS2 showed a gradual decrease by about 10% and a factor of 5-10, respectively, from the surface to 8-10 km altitude, presumably because land-based sources dominated their distribution during February through April 2001. The highest mean OCS and CS 2 levels (580 and 20 pptv, respectively, based on 2.5° × 2.5° latitude bins) were observed below 2 km near the coast of Asia, at latitudes between 25°N and 35°N, where urban Asian outflow was strongest. Ratios of OCS versus CO for continental SE Asia were much lower compared to Chinese and Japanese signatures and were strongly associated with biomass burning/biofuel emissions. We present a new inventory of anthropogenic Asian emissions (including biomass burning) for OCS and CS2 and compare it to emission estimates based on regional relationships of OCS and CS 2 to CO and CO2. The OCS and CS2 results for the two methods compare well for continental SE Asia and Japan plus Korea and also for Chinese CS2 emissions. However, it appears that the inventory underestimates Chinese emissions of OCS by about 30-100%. This difference may be related to the fact that we did not include natural sources such as wetland emissions in our inventory, although the contributions from such sources are believed to be at a seasonal low during the study period. Uncertainties in OCS emissions from Chinese coal burning, which are poorly characterized, likely contribute to the discrepancy. Copyright 2004 by the American Geophysical Union

Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies

The Red Sea, Coastal Landscapes, and Hominin Dispersals

This chapter provides a critical assessment of environment, landscape and resources in the Red Sea region over the past five million years in relation to archaeological evidence of hominin settlement, and of current hypotheses about the role of the region as a pathway or obstacle to population dispersals between Africa and Asia and the possible significance of coastal colonization. The discussion assesses the impact of factors such as topography and the distribution of resources on land and on the seacoast, taking account of geographical variation and changes in geology, sea levels and palaeoclimate. The merits of northern and southern routes of movement at either end of the Red Sea are compared. All the evidence indicates that there has been no land connection at the southern end since the beginning of the Pliocene period, but that short sea crossings would have been possible at lowest sea-level stands with little or no technical aids. More important than the possibilities of crossing the southern channel is the nature of the resources available in the adjacent coastal zones. There were many climatic episodes wetter than today, and during these periods water draining from the Arabian escarpment provided productive conditions for large mammals and human populations in coastal regions and eastwards into the desert. During drier episodes the coastal region would have provided important refugia both in upland areas and on the emerged shelves exposed by lowered sea level, especially in the southern sector and on both sides of the Red Sea. Marine resources may have offered an added advantage in coastal areas, but evidence for their exploitation is very limited, and their role has been over-exaggerated in hypotheses of coastal colonization