JExample: Exploiting Dependencies Between Tests to Improve Defect Localization

To quickly localize defects, we want our attention to be focussed on relevant failing tests. We propose to improve defect localization by exploiting dependencies between tests, using a JUnit extension called JExample. In a case study, a monolithic white-box test suite for a complex algorithm is refactored into two traditional JUnit style tests and to JExample. Of the three refactorings, JExample reports five times fewer defect locations and slightly better performance (-8-12\%), while having similar maintenance characteristics. Compared to the original implementation, JExample greatly improves maintainability due the improved factorization following the accepted test quality guidelines. As such, JExample combines the benefits of test chains with test quality aspects of JUnit style testing.

A Drosophila XPD model links cell cycle coordination with neuro-development and suggests links to cancer

XPD functions in transcription, DNA repair and in cell cycle control. Mutations in human XPD (also known as ERCC2) mainly cause three clinical phenotypes: xeroderma pigmentosum (XP), Cockayne syndrome (XP/CS) and trichothiodystrophy (TTD), and only XP patients have a high predisposition to developing cancer. Hence, we developed a fly model to obtain novel insights into the defects caused by individual hypomorphic alleles identified in human XP-D patients. This model revealed that the mutations that displayed the greatest in vivo UV sensitivity in Drosophila did not correlate with those that led to tumor formation in humans. Immunoprecipitations followed by targeted quantitative MS/MS analysis showed how different xpd mutations affected the formation or stability of different transcription factor IIH (TFIIH) subcomplexes. The XP mutants most clearly linked to high cancer risk, Xpd R683W and R601L, showed a reduced interaction with the core TFIIH and also an abnormal interaction with the Cdk-activating kinase (CAK) complex. Interestingly, these two XP alleles additionally displayed high levels of chromatin loss and free centrosomes during the rapid nuclear division phase of the Drosophila embryo. Finally, the xpd mutations showing defects in the coordination of cell cycle timing during the Drosophila embryonic divisions correlated with those human mutations that cause the neurodevelopmental abnormalities and developmental growth defects observed in XP/CS and TTD patients.

Concentrations and carbon isotopic compositions of organic and inorganic compounds in sediment porewaters at IODP Site U1329

Ocean drilling has revealed the existence of vast microbial populations in the deep subseafloor, but to date little is known about their metabolic activities. To better understand the biogeochemical processes in the deep biosphere, we investigate the stable carbon isotope chemistry of acetate and other carbon-bearing metabolites in sediment pore-waters. Acetate is a key metabolite in the cycling of carbon in anoxic sediments. Its stable carbon isotopic composition provides information on the metabolic processes dominating acetate turnover in situ. This study reports our findings for a methane-rich site at the northern Cascadia Margin (NE Pacific) where Expedition 311 of the Integrated Ocean Drilling Program (IODP) sampled the upper 190 m of sediment. At Site U1329, d13C values of acetate span a wide range from -46.0 per mill to -11.0 per mill vs. VPDB and change systematically with sediment depth. In contrast, d13C values of both the bulk dissolved organic carbon (DOC) (-21.6 ± 1.3 per mill vs. VPDB) and the low-molecular-weight compound lactate (-20.9 ± 1.8 per mill vs. VPDB) show little variability. These species are interpreted to represent the carbon isotopic composition of fermentation products. Relative to DOC, acetate is up to 23.1 per mill depleted and up to 9.1 per mill enriched in 13C. Broadly, 13C-depletions of acetate relative to DOC indicate flux of carbon from acetogenesis into the acetate pool while 13C-enrichments of pore-water acetate relative to DOC suggest consumption of acetate by acetoclastic methanogenesis. Isotopic relationships between acetate and lactate or DOC provide new information on the carbon flow and the presence and activity of specific functional microbial communities in distinct biogeochemical horizons of the sediment. In particular, they suggest that acetogenic CO2-reduction can coexist with methanogenic CO2-reduction, a notion contrary to the hypothesis that hydrogen levels are controlled by the thermodynamically most favorable electron-accepting process. Further, the isotopic relationship suggests a relative increase in acetate flow to acetoclastic methanogenesis with depth although its contribution to total methanogenesis is probably small. Our study demonstrates how the stable carbon isotope biogeochemistry of acetate can be used to identify pathways of microbial carbon turnover in subsurface environments. Our observations also raise new questions regarding the factors controlling acetate turnover in marine sediments.

(Figure 2) Organic carbon content, stable isotope ratios, TEX86 index and sea surface temperature reconstruction for the early Aptian of ODP Hole 198-1207B

The Cretaceous has long been recognized as a time when greenhouse conditions were fueled by elevated atmospheric CO2 and accompanied by perturbations of the global carbon cycle described as oceanic anoxic events (OAEs). Yet, the magnitude and frequency of temperature change during this interval of warm and equable climate are poorly constrained. Here we present a high-resolution record of sea-surface temperatures (SSTs) reconstructed using the TEX86 paleothermometer for a sequence of early Aptian organic-rich sediments deposited during the first Cretaceous OAE (OAE1a) at Shatsky Rise in the tropical Pacific. SSTs range from ~30 to ~36 °C and include two prominent cooling episodes of ~4 °C. The cooler temperatures reflect significant temperature instability in the tropics likely triggered by changes in carbon cycling induced by enhanced burial of organic matter. SST instability recorded during the early Aptian in the Pacific is comparable to that reported for the late Albian-early Cenomanian in the Atlantic, suggesting that such climate perturbations may have recurred during the Cretaceous with concomitant consequences for biota and the marine environment.

Element contents, sulfur and oxygen isotopes, and molecular biomarkers of phosphatic crust samples from the Chimbote Platform of the shelf off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01' S and 10°24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS2) and sphalerite (ZnS). Low d34Spyrite values (average -28.8 per mill) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C15:0, i/ai-C17:0 and 10MeC16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

Marine diatoms in deep sea sediments

Long-term evolution is thought to take opportunities that arise as a consequence of mass extinction (as argued, for example, by Gould, 2002) and the following biotic recovery, but there is absolutely no evidence for this being the case. However, our study shows that eutrophication by oceanic mixing also played a part in the enhancement of several evolutionary events amongst marine organisms, and these results could indicate that the rates of oceanic biodiversification may be slowed if upwelling becomes weakened by future global warming. This paper defines three distinct evolutionary events of resting spores of the marine diatom genus Chaetoceros, to reconstruct past upwelling through the analysis of several DSDP, ODP and land-based successions from the North, South and equatorial Pacific as well as the Atlantic Ocean during the past 40 million years. The Atlantic Chaetoceros Explosion (ACE) event occurred across the E/O boundary in the North Atlantic, and is characterized by resting spore diversification that occurred as a consequence of the onset of upwelling following changes in thermohaline circulation through global cooling in the early Oligocene. Pacific Chaetoceros Explosion events-1 and -2 (PACE-1 and PACE-2) are characterized by relatively higher occurrences of iron input following the Himalayan uplift and aridification at 8.5 Ma and ca. 2.5 Ma in the North Pacific region. These events not only enhanced the diversification and increased abundance of primary producers, including that of Chaetoceros, other diatoms and seaweeds, but also stimulated the evolution of zooplankton and larger predators, such as copepods and marine mammals, which ate these phytoplankton and plants. Current thinking suggests new evolutionary niches open up after a mass extinction, but our study finds that eutrophication can also stimulate evolutionary diversification. Moreover, in the opposite fashion, our results show that as thermohaline circulation abates, global warming progresses and the ocean surface becomes warmer, many marine organisms will be affected by the environmental degradation.

Benthic foraminifera across the Cretaceous/Paleogene boundary in the Southern Ocean

The impact of an asteroid at the Cretaceous/Paleogene (K/Pg) boundary triggered dramatic biotic, biogeochemical and sedimentological changes in the oceans that have been intensively studied. Paleo-biogeographical differences in the biotic response to the impact and its environmental consequences, however, have been less well documented. We present a high-resolution analysis of benthic foraminiferal assemblages at Southern Ocean ODP Site 690 (Maud Rise, Weddell Sea, Antarctica). At this high latitude site, late Maastrichtian environmental variability was high, but benthic foraminiferal assemblages were not less diverse than at lower latitudes, in contrast to those of planktic calcifiers. Also in contrast to planktic calcifiers, benthic foraminifera did not suffer significant extinction at the K/Pg boundary, but show transient assemblage changes and decreased diversity. At Site 690, the extinction rate was even lower (~3%) than at other sites. The benthic foraminiferal accumulation rate varied little across the K/Pg boundary, indicating that food supply to the sea floor was affected to a lesser extent than at lower latitude sites. Compared to Maastrichtian assemblages, Danian assemblages have a lower diversity and greater relative abundance of heavily calcified taxa such as Stensioeina beccariiformis and Paralabamina lunata. This change in benthic foraminiferal assemblages could reflect post-extinction proliferation of different photosynthesizers (thus food for the benthos) than those dominant during the Late Cretaceous, therefore changes in the nature rather than in the amount of the organic matter supplied to the seafloor. However, severe extinction of pelagic calcifiers caused carbonate supersaturation in the oceans, thus might have given competitive advantage to species with large, heavily calcified tests. This indirect effect of the K/Pg impact thus may have influenced the deep-sea dwellers, documenting the complexity of the effects of major environmental disturbance.

Methane concentration profiles and isotopic composition of sediment cores from the Black Sea

We present high resolution profiles for the methane concentration and the carbon isotope composition of methane from surface sediments and from the sediment-water transition in the Black Sea. At shallow water sites methane migrates from the sediment into the water column, and the magnitude of this upward migrating flux depends on the depth of the sulfate-methane transition (SMT) in the sediment. The isotope data reveal that the sediments at shallow water sites are a source for methane depleted in 13C relative to the isotope composition of methane in the water column. At deep water sites the methane concentration first decreases with depth in the sediment to reach lowest values at the Unit I to Unit II transition. Below this transition the concentration increases again. Numerical modeling of methane concentration and isotope data shows that high methane oxidation rates occur in the surface sediment layer, indicating that the removal of methane in the surface sediments is not related to the anaerobic oxidation of methane coupled to sulfate reduction that occurs a few meters deep in the sediment, at the SMT. Instead, near-surface methane consumption in the euxinic Black Sea sediments appears to be related to lithological stratification. Furthermore, a map of the diffusive methane fluxes in the Black Sea surface sediments indicates that approximately half of the Black Sea seafloor acts as a sink for methane and thus limits the flux of methane to the atmosphere.

Nannofossil and stable isotope record across the Paleocene/Eocene Thermal Maximum in ODP Hole 183-1135A

The Paleocene/Eocene Thermal Maximum (PETM, ca. 55 Ma) is an abrupt, profound perturbation of climate and the carbon cycle associated with a massive injection of isotopically light carbon into the ocean-atmosphere system. As such, it provides an analogue for understanding the interplay between phytoplankton and climate under modern anthropogenic global-warming conditions. However, the accompanying enhanced dissolution poses uncertainty on the reconstruction of the affected ecology and productivity. We present a high-resolution record of bulk isotopes and nannofossil absolute abundance from Ocean Drilling Program (ODP) Site 1135 on the Kerguelen Plateau, Southern Indian Ocean to quantitatively constrain for the first time the influence of dissolution on paleoecological reconstruction. Our bulk-carbonate isotope record closely resembles that of the classic PETM site at ODP Site 690 on the opposite side of the Antarctic continent, and its correlation with those from ODP Sites 690, 1262 and 1263 records allows recognition of 14 precessional cycles upsection from the onset of the carbon isotopic excursion (CIE). This, together with a full range of common Discoasteraraneus and an abundance crossover between Fasciculithus and Zygrhablithusbijugatus, indicates the presence of the PETM at Site 1135, a poorly known record with calcareous fossils throughout the interval. The strong correlation between the absolute abundances of Chiasmolithus and coccolith assemblages reveals a dominant paleoecological signal in the poorly preserved fossil assemblages, while the influence of dissolution is only strong during the CIE. This suggests that r-selected taxa can preserve faithful ecological information even in the severely-altered assemblages studied here, and therefore provide a strong case for the application of nannofossils to paleoecological studies in better-preserved PETM sections. The inferred nannoplankton productivity drops abruptly at the CIE onset, but rapidly increases after the CIE peak, both of which may be driven by nutrient availability related to ocean stratification and vertical mixing due to changed sea-surface temperatures.

Distribution and stable isotopic compositions of hydrogen and carbon of plant-wax derived n-C29 and -C31 alkanes in terrestrial, coastal and offshore surface sediments

Reconstructing terrestrial water budgets is of prime importance for understanding past climate and environment. To shed more light on how plant-wax derived n-alkanes may be used for this purpose we investigated the distribution and stable isotopic compositions of hydrogen (dD) and carbon (d13C) of plant-wax derived n-C29 and -C31 alkanes in terrestrial, coastal and offshore surface sediments in relation to hydrology along a NW-SE transect east of the Italian Apennines from the Po River to the Eastern Gulf of Taranto. The plant wax average chain length increases southward and may relate to increasing temperature and/or aridity. The plant wax dD of the terrestrial and coastal samples also increases southward and mainly reflects changes in the dD of precipitation. The d13C of plant waxes is primarily interpreted in terms of C3 vegetation changes rather than varying contributions by C4 plants. The plant wax d13C-dD composition of the Po River and Apennine rivers differs considerably from that in southern Italy, and suggests a mainly southern source for plant waxes in marine sediments of the Gulf of Taranto. This calibration provides a basis for the reconstruction of past changes in the Italian water balance and n-alkane source areas.

Lead isotopic ratios of Barremian-Aptian marine sediments

We present initial isotopic ratios of lead for Early Cretaceous (Barremian-Aptian) sections from Shatsky Rise (Pacific) and Gorgo a Cerbara (Italy). Our Pb isotopic data track an interval representing Oceanic Anoxic Event (OAE)-1a, which is characterized by quasi-global deposition of organic carbon-rich black shale. Pb isotopic compositions of sediments from Shatsky Rise decrease at the end of Barremian time, from radiogenic continental values to unradiogenic values, and subsequently remained less radiogenic until the end of early Aptian time. We explain the isotopic shift by a significant increase in supply rate of unradiogenic Pb, most likely due to massive volcanism. In contrast, the Pb isotopic compositions from the Italian section, which was situated at the western end of Tethys, are mostly identical to those of upper continental crust, showing no significant change in supply rate of unradiogenic Pb. The discrepancy between two sites is attributed to quiescent deep-submarine eruptions of Pacific large igneous provinces (LIPs) such as the Ontong Java Plateau (OJP), which severely limited dispersion of Pb-carrying particles out of the Pacific Ocean. Published Os isotopic data from the Italian section indicate two episodes of massive eruptions of OJP or contemporaneous Manihiki and Hikurangi plateaus starting from earliest Aptian time, slightly later than that indicated by the sedimentary Pb isotopic record from Shatsky Rise. Differences in isotopic variations between Pb and Os likely reflect differences in their chemical behaviors in the oceans, i.e., Pb isotopic compositions would have varied in response to local or regional changes in sediment provenances, whereas large-scale changes in Os inputs are required to explain variations in seawater Os isotopic compositions. Our Pb isotopic data, together with the published Os isotopic record, provide new evidence for the eruptive history of OJP together with contemporaneous Pacific plateaus and its environmental consequences, starting from end-Barremian time and extending through early Aptian time.