Controls on the formation of microbially induced sedimentary structures and biotic recovery in the Lower Triassic of Arctic Canada

Microbially induced sedimentary structures (MISS) are reportedly widespread in the Early Triassic and their occurrence is attributed to either the extinction of marine grazers (allowing mat preservation) during the Permo-Triassic mass extinction or the suppression of grazing due to harsh, oxygen-poor conditions in its aftermath. Here we report on the abundant occurrence of MISS in the Lower Triassic Blind Fiord Formation of the Sverdrup Basin, Arctic Canada. Sedimentological analysis shows that mid-shelf settings were dominated by deposition from cohesive sand-mud flows that produced heterolithic, rippled sandstone facies that pass down dip into laminated siltstones and ultimately basinal mudrocks. The absence of storm beds and any other “event beds” points to an unusual climatic regime of humid, quiet conditions characterized by near continuous run off. Geochemical proxies for oxygenation (Mo/Al, Th/U, and pyrite framboid analysis) indicate that lower dysoxic conditions prevailed in the basin for much of the Early Triassic. The resultant lack of bioturbation allowed the development and preservation of MISS, including wrinkle structures and bubble textures. The microbial mats responsible for these structures are envisaged to have thrived, on sandy substrates, within the photic zone, in oxygen-poor conditions. The dysoxic history was punctuated by better-oxygenated phases, which coincide with the loss of MISS. Thus, Permo-Triassic boundary and Griesbachian mudrocks from the deepest-water settings have common benthos and a well-developed, tiered burrow profile dominated by Phycosiphon. The presence of the intense burrowing in the earliest Triassic contradicts the notion that bioturbation was severely suppressed at this time due to extinction losses at the end of the Permian. The notion that Early Triassic MISS preservation was caused by the extinction of mat grazers is not tenable

Mercury chemostratigraphy across the Cambrian Series 2 – Series 3 boundary: evidence for increased volcanic activity coincident with extinction?

Flood basalt volcanism represented by the Kalkarindji Province (Australia) is temporally associated with a trilobite mass extinction at the Cambrian Series 2 – Series 3 boundary, providing one of the oldest potential links between volcanism and biotic crisis in the Phanerozoic. However, the relative timing of flood basalt volcanism (Kalkarindji Province, Australia) and the trilobite extinctions, first recorded in North America, is not known. Mercury (Hg) enrichment in the sedimentary record provides a potential proxy for volcanism which may facilitate improved chronologies of eruption and extinction. Here we report mercury records for three sections from mid-shelf strata of the Great Basin (western USA) that straddle the Series 2 – Series 3 boundary. One section (Oak Springs Summit, NV) features a Hg enrichment at the start of the extinction interval, but mercury anomalies are also present at lower levels. These older anomalies may record either earlier phases of Kalkarindji volcanism, eruptions in other locations, or may be the result of sedimentary and/or diagenetic processes affecting the Hg record. In the Carrara Formation at Emigrant Pass, CA, the precise extinction horizon is not well defined, but a carbon isotope anomaly (the Redlichiid-Olenellid Extinction Carbon isotope Event; ROECE) provides a stratigraphic tie point to the Oak Springs Summit section. At Emigrant Pass, Hg enrichments precede the ROECE interval and are absent in the inferred extinction zone. The Pioche Formation at Ruin Wash, NV, lacks Hg enrichment at the extinction horizon but contains older enrichments. The inconsistent Hg records between the three sections demonstrate that factors controlling Hg accumulation and preservation in marine sedimentary environments are not yet fully understood. The effects of redox fluctuations may complicate one-to-one association of sedimentary Hg enrichments and massive volcanism at the Cambrian Series 2 – Series 3 boundary and elsewhere in the geologic record

Trilobite extinctions, facies changes and the ROECE carbon isotope excursion at the Cambrian Series 2 - 3 boundary, Great Basin, western USA

The mass extinction of the olenellid trilobites occurred around the Cambrian Series 2 - Series 3 boundary. Like many other crises, it coincided with a negative carbon isotope excursion but the associated palaeoenvironmental changes remain unclear. To investigate the causal mechanism for this event, we report facies changes, pyrite framboid petrography and carbon isotope values from Cambrian Series 2 - Series 3 (traditionally Early - Middle Cambrian) boundary strata of the Carrara 20 Formation (Death Valley region, California) and Pioche Formation (Nevada). These data reveal regionally changing water depths from high-energy, nearshore facies (oolitic grainstone) to more offshore silty marl and finer-grained carbonate mudstone. In the Carrara Formation, the series boundary occurs within a deepening succession, transitioning from high-energy, nearshore facies (oolitic grainstone and oncolitic packstone) to offshore marl, the latter of which contains pyrite framboid populations indicative of low-oxygen (dysoxic) depositional conditions. Intermittent dysoxia persisted below sub-wave base settings throughout the early and middle Cambrian, but did not intensify at the time of extinction, arguing against anoxia as a primary cause in the olenellid trilobite extinction. Within both field areas, the extinction interval coincided with a minimum in d13Ccarb values, which we interpret as the regional manifestation of the Redlichiid-Olenellid Extinction Carbon isotope Excursion (ROECE). The Series 2 - Series 3 boundary is reported to closely coincide with a large-amplitude sea-level fall that produced the Sauk I/II sequence boundary, but the placement of the Series 2 - Series 3 boundary within a transgressive interval of the Carrara Formation shows that this is not the case. The main sequence boundary in the succession occurs much lower in the succession (at the top of the Zabriskie Quartzite) and therefore precedes the extinction of the olenellids and ROECE

Functional diversity of marine ecosystems after the Late Permian mass extinction event

Article can be accessed from http://www.nature.com/ngeo/journal/v7/n3/full/ngeo2079.htmlThe Late Permian mass extinction event was the most severe such crisis of the past 500 million years and occurred during an episode of global warming. It is assumed to have had significant ecological impact, but its effects on marine ecosystem functioning are unknown and the patterns of marine recovery are debated. We analysed the fossil occurrences of all known Permian-Triassic benthic marine genera and assigned each to a functional group based on their inferred life habit. We show that despite the selective extinction of 62-74% of marine genera there was no significant loss of functional diversity at the global scale, and only one novel mode of life originated in the extinction aftermath. Early Triassic marine ecosystems were not as ecologically depauperate as widely assumed, which explains the absence of a Cambrian-style Triassic radiation in higher taxa. Functional diversity was, however, significantly reduced in particular regions and habitats, such as tropical reefs, and at these scales recovery varied spatially and temporally, probably driven by migration of surviving groups. Marine ecosystems did not return to their pre-extinction state, however, and radiation of previously subordinate groups such as motile, epifaunal grazers led to greater functional evenness by the Middle Triassic

Earliest Triassic microbialites in the South China Block and other areas; controls on their growth and distribution

Earliest Triassic microbialites (ETMs) and inorganic carbonate crystal fans formed after the end-Permian mass extinction (ca. 251.4 Ma) within the basal Triassic Hindeodus parvus conodont zone. ETMs are distinguished from rarer, and more regional, subsequent Triassic microbialites. Large differences in ETMs between northern and southern areas of the South China block suggest geographic provinces, and ETMs are most abundant throughout the equatorial Tethys Ocean with further geographic variation. ETMs occur in shallow-marine shelves in a superanoxic stratified ocean and form the only widespread Phanerozoic microbialites with structures similar to those of the Cambro-Ordovician, and briefly after the latest Ordovician, Late Silurian and Late Devonian extinctions. ETMs disappeared long before the mid-Triassic biotic recovery, but it is not clear why, if they are interpreted as disaster taxa. In general, ETM occurrence suggests that microbially mediated calcification occurred where upwelled carbonate-rich anoxic waters mixed with warm aerated surface waters, forming regional dysoxia, so that extreme carbonate supersaturation and dysoxic conditions were both required for their growth. Long-term oceanic and atmospheric changes may have contributed to a trigger for ETM formation. In equatorial western Pangea, the earliest microbialites are late Early Triassic, but it is possible that ETMs could exist in western Pangea, if well-preserved earliest Triassic facies are discovered in future work

Environmental and diagenetic controls on the morphology and calcification of the Ediacaran metazoan Cloudina

Abstract Cloudina is a globally distributed Ediacaran metazoan, with a tubular, funnel-in-funnel form built of thin laminae (ca. 1–10 μm). To what degree local environmental controlled morphology, and whether early diagenesis controlled the degree of calcification of Cloudina, is debated. Here we test these hypotheses by considering assemblages from four, coeval localities from the Upper Omkyk Member, Nama Group, Namibia, from inner ramp to mid-ramp reef across the Zaris Subbasin. We show that sinuosity of the Cloudina tube is variable between sites, as is the relative thickness of the tube wall, suggesting these features were environmentally controlled. Walls are thickest in high-energy reef settings, and thinnest in the low-energy, inner ramp. While local diagenesis controls preservation, all diagenetic expressions are consistent with the presence of weakly calcified, organic-rich laminae, and lamina thicknesses are broadly constant. Finally, internal ‘cements’ within Cloudina are found in all sites, and pre-date skeletal breakage, transport, as well as syn-sedimentary botryoidal cement precipitation. Best preservation shows these to be formed by fine, pseudomorphed aragonitic acicular crystals. Sr concentrations and Mg/Ca show no statistically significant differences between internal Cloudina cements and botryoidal cements, but we infer all internal cements to have precipitated when Cloudina was still in-situ and added considerable mechanical strength, but may have formed post-mortem or in abandoned parts of the skeleton

'I believe that the staff have reduced their closeness to patients': an exploratory study on the impact of HIV/AIDS on staff in four rural hospitals in Uganda

<p>Abstract</p> <p>Background</p> <p>Staff shortages could harm the provision and quality of health care in Uganda, so staff retention and motivation are crucial. Understanding the impact of HIV/AIDS on staff contributes to designing appropriate retention and motivation strategies. This research aimed 'to identify the influence of HIV/AIDS on staff working in general hospitals at district level in rural areas and to explore support required and offered to deal with HIV/AIDS in the workplace'. Its results were to inform strategies to mitigate the impact of HIV/AIDS on hospital staff.</p> <p>Methods</p> <p>A cross-sectional study with qualitative and quantitative components was implemented during two weeks in September 2005. Data were collected in two government and two faith-based private not-for-profit hospitals purposively selected in rural districts in Uganda's Central Region. Researchers interviewed 237 people using a structured questionnaire and held four focus group discussions and 44 in-depth interviews.</p> <p>Results</p> <p>HIV/AIDS places both physical and, to some extent, emotional demands on health workers. Eighty-six per cent of respondents reported an increased workload, with 48 per cent regularly working overtime, while 83 per cent feared infection at work, and 36 per cent reported suffering an injury in the previous year. HIV-positive staff remained in hiding, and most staff did not want to get tested as they feared stigmatization. Organizational responses were implemented haphazardly and were limited to providing protective materials and the HIV/AIDS-related services offered to patients. Although most staff felt motivated to work, not being motivated was associated with a lack of daily supervision, a lack of awareness on the availability of HIV/AIDS counselling, using antiretrovirals and working overtime. The specific hospital context influenced staff perceptions and experiences.</p> <p>Conclusion</p> <p>HIV/AIDS is a crucially important contextual factor, impacting on working conditions in various ways. Therefore, organizational responses should be integrated into responses to other problematic working conditions and adapted to the local context. Opportunities already exist, such as better use of supervision, educational sessions and staff meetings. However, exchanges on interventions to improve staff motivation and address HIV/AIDS in the health sector are urgently required, including information on results and details of the context and implementation process.</p

Oligonucleotide Sequence Motifs as Nucleosome Positioning Signals

To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach entailed the identification and analysis of 24 unique tetranucleotides that were defined by 8 consensus sequences. These consensus sequences were shown to be responsible for most if not all of the tetranucleotide and dinucleotide periodicities displayed by the entire library, demonstrating that the periodicities of dinucleotides that characterize the yeast genome are, in actuality, due primarily to the 8 consensus sequences. A novel combination of experimental and bioinformatic approaches was then used to show that these tetranucleotides are important for preferred formation of nucleosomes at specific sites along DNA in vitro. These results were then compared to tetranucleotide patterns in genome-wide in vivo libraries from yeast and C. elegans in order to assess the contributions of DNA sequence in the control of nucleosome residency in the cell. These comparisons revealed striking similarities in the tetranucleotide occurrence profiles that are likely to be involved in nucleosome positioning in both in vitro and in vivo libraries, suggesting that DNA sequence is an important factor in the control of nucleosome placement in vivo. However, the strengths of the tetranucleotide periodicities were 3–4 fold higher in the in vitro as compared to the in vivo libraries, which implies that DNA sequence plays less of a role in dictating nucleosome positions in vivo. The results of this study have important implications for models of sequence-dependent positioning since they suggest that a defined subset of tetranucleotides is involved in preferred nucleosome occupancy and that these tetranucleotides are the major source of the dinucleotide periodicities that are characteristic of positioned nucleosomes

Drilling Predation on Serpulid Polychaetes (Ditrupa arietina) from the Pliocene of the Cope Basin, Murcia Region, Southeastern Spain

We report quantitative analyses of drilling predation on the free-living, tube-dwelling serpulid polychaete Ditrupa arietina from the Cope Cabo marine succession (Pliocene, Spain). Tubes of D. arietina are abundant in the sampled units: 9 bulk samples from 5 horizons yielded ∼5925 specimens of D. arietina. Except for fragmentation, tubes were well preserved. Complete specimens ranged from 3.1 to 13.4 mm in length and displayed allometric growth patterns, with larger specimens being relatively slimmer. Drilled Ditrupa tubes were observed in all samples. Drillholes, identified as Oichnus paraboloides, were characterized by circular to elliptical outline (drillhole eccentricity increased with its diameter), parabolic vertical profile, outer diameter larger than inner diameter, penetration of one tube wall only, narrow range of drill-hole sizes, and non-random (anterior) distribution of drillholes. A total of 233 drilled specimens were identified, with drilling frequencies varying across horizons from 2.7% to 21% (3.9% for pooled data). Many tube fragments were broken across a drillhole suggesting that the reported frequencies are conservative and that biologically-facilitated (drill-hole induced) fragmentation hampers fossil preservation of complete serpulid tubes. No failed or repaired holes were observed. Multiple complete drillholes were present (3.9%). Drilled specimens were significantly smaller than undrilled specimens and tube length and drill-hole diameter were weakly correlated. The results suggest that drillholes were produced by a size-selective, site-stereotypic predatory organism of unknown affinity. The qualitative and quantitative patterns reported here are mostly consistent with previous reports on recent and fossil Ditrupa and reveal parallels with drilling patterns documented for scaphopod mollusks, a group that is ecologically and morphologically similar to Ditrupa. Consistent with previous studies, the results suggest that free-dwelling serpulid polychaetes are preyed upon by drilling predators and may provide a viable source of data on biotic interactions in the fossil record

Low Dosage of Histone H4 Leads to Growth Defects and Morphological Changes in Candida albicans

Chromatin function depends on adequate histone stoichiometry. Alterations in histone dosage affect transcription and chromosome segregation, leading to growth defects and aneuploidies. In the fungal pathogen Candida albicans, aneuploidy formation is associated with antifungal resistance and pathogenesis. Histone modifying enzymes and chromatin remodeling proteins are also required for pathogenesis. However, little is known about the mechanisms that generate aneuploidies or about the epigenetic mechanisms that shape the response of C. albicans to the host environment. Here, we determined the impact of histone H4 deficit in the growth and colony morphology of C. albicans. We found that C. albicans requires at least two of the four alleles that code for histone H4 (HHF1 and HHF22) to grow normally. Strains with only one histone H4 allele show a severe growth defect and unstable colony morphology, and produce faster-growing, morphologically stable suppressors. Segmental or whole chromosomal trisomies that increased wild-type histone H4 copy number were the preferred mechanism of suppression. This is the first study of a core nucleosomal histone in C. albicans, and constitutes the prelude to future, more detailed research on the function of histone H4 in this important fungal pathogen