Geochemical analysis of nine sections from the Nama Group, Namibia

The first appearance of skeletal metazoans in the late Ediacaran (~550 million years ago; Ma) has been linked to the widespread development of oxygenated oceanic conditions, but a precise spatial and temporal reconstruction of their evolution has not been resolved. Here we consider the evolution of ocean chemistry from ~550 to ~541 Ma across shelf-to-basin transects in the Zaris and Witputs Sub-Basins of the Nama Group, Namibia. New carbon isotope data capture the final stages of the Shuram/Wonoka deep negative C-isotope excursion, and these are complemented with a reconstruction of water column redox dynamics utilising Fe-S-C systematics and the distribution of skeletal and soft-bodied metazoans. Combined, these inter-basinal datasets provide insight into the potential role of ocean redox chemistry during this pivotal interval of major biological innovation. The strongly negative d13C values in the lower parts of the sections reflect both a secular, global change in the C-isotopic composition of Ediacaran seawater, as well as the influence of 'local' basinal effects as shown by the most negative d13C values occurring in the transition from distal to proximal ramp settings. Critical, though, is that the transition to positive d13C values postdates the appearance of calcified metazoans, indicating that the onset of biomineralization did not occur under post-excursion conditions. Significantly, we find that anoxic and ferruginous deeper water column conditions were prevalent during and after the transition to positive d13C that marks the end of the Shuram/Wonoka excursion. Thus, if the C isotope trend reflects the transition to global-scale oxygenation in the aftermath of the oxidation of a large-scale, isotopically light organic carbon pool, it was not sufficient to fully oxygenate the deep ocean. Both sub-basins reveal highly dynamic redox structures, where shallow, inner ramp settings experienced transient oxygenation. Anoxic conditions were caused either by episodic upwelling of deeper anoxic waters or higher rates of productivity. These settings supported short-lived and monospecific skeletal metazoan communities. By contrast, microbial (thrombolite) reefs, found in deeper inner- and mid-ramp settings, supported more biodiverse communities with complex ecologies and large skeletal metazoans. These long-lived reef communities, as well as Ediacaran soft-bodied biotas, are found particularly within transgressive systems, where oxygenation was persistent. We suggest that a mid-ramp position enabled physical ventilation mechanisms for shallow water column oxygenation to operate during flooding and transgressive sea-level rise. Our data support a prominent role for oxygen, and for stable oxygenated conditions in particular, in controlling both the distribution and ecology of Ediacaran skeletal metazoan communities.

Functional analysis of DNA bending and unwinding by the high mobility group domain of LEF-1

LEF-1 (lymphoid enhancer-binding factor 1) is a cell type-specific member of the family of high mobility group (HMG) domain proteins that recognizes a specific nucleotide sequence in the T cell receptor (TCR) α enhancer. In this study, we extend the analysis of the DNA-binding properties of LEF-1 and examine their contributions to the regulation of gene expression. We find that LEF-1, like nonspecific HMG-domain proteins, can interact with irregular DNA structures such as four-way junctions, albeit with lower efficiency than with specific duplex DNA. We also show by a phasing analysis that the LEF-induced DNA bend is directed toward the major groove. In addition, we find that the interaction of LEF-1 with a specific binding site in circular DNA changes the linking number of DNA and unwinds the double helix. Finally, we identified two nucleotides in the LEF-1-binding site that are important for protein-induced DNA bending. Mutations of these nucleotides decrease both the extent of DNA bending and the transactivation of the TCRα enhancer by LEF-1, suggesting a contribution of protein-induced DNA bending to the function of TCRα enhancer.

Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: Population genetics, human serologic response, and gene transcription

Species of pathogenic microbes are composed of an array of evolutionarily distinct chromosomal genotypes characterized by diversity in gene content and sequence (allelic variation). The occurrence of substantial genetic diversity has hindered progress in developing a comprehensive understanding of the molecular basis of virulence and new therapeutics such as vaccines. To provide new information that bears on these issues, 11 genes encoding extracellular proteins in the human bacterial pathogen group A Streptococcus identified by analysis of four genomes were studied. Eight of the 11 genes encode proteins with a LPXTG(L) motif that covalently links Gram-positive virulence factors to the bacterial cell surface. Sequence analysis of the 11 genes in 37 geographically and phylogenetically diverse group A Streptococcus strains cultured from patients with different infection types found that recent horizontal gene transfer has contributed substantially to chromosomal diversity. Regions of the inferred proteins likely to interact with the host were identified by molecular population genetic analysis, and Western immunoblot analysis with sera from infected patients confirmed that they were antigenic. Real-time reverse transcriptase–PCR (TaqMan) assays found that transcription of six of the 11 genes was substantially up-regulated in the stationary phase. In addition, transcription of many genes was influenced by the covR and mga trans-acting gene regulatory loci. Multilocus investigation of putative virulence genes by the integrated approach described herein provides an important strategy to aid microbial pathogenesis research and rapidly identify new targets for therapeutics research.

The EU's Group-to-Group Dialogue with the Southern Mediterranean and ASEAN – How much have they achieved? A Comparative Analysis. EU Centre Singapore Working Paper No, 18, December 2013

Four decades of the EU's group-to-group dialogues with the Southern Mediterranean grouping of countries and with ASEAN have produced different dynamics and outcomes, despite the EU’s common strategy to use economic soft power to achieve their goals for the partnerships. Diverging conditions in the two regions created inconsistency in the EU's application of the common approach. The EU's neighbourhood security concerns forced it to relax its political stand with their Southern Mediterranean partners. For ASEAN, geographical distance dilutes the EU’s security concerns it that region and has afforded the EU to be more ideological and assertive on democracy and human rights practices. These issues have provoked disagreements in EU-ASEAN dialogues, but both sides have also tried to remain pragmatic in order to achieve some progress in the partnership. In contrast, the protracted the Arab-Israeli conflict continues to hamper the Euro-Mediterranean dialogue, resulting in little progress. Social upheavals in the Southern Mediterranean also brought their partnership to a standstill. The EU's cooperation with former authoritarian regimes like Libya and Syria have only caused damage to its credibility in the Southern Mediterranean, and future Euro-Mediterranean dialogues are likely to be affected by it.

Analysis of plant microfossils in archaeological deposits from two remote archipelagos: The Marshall Islands, Eastern Micronesia, and the Pitcairn Group, Southeast Polynesia

Pollen and starch residue analyses were conducted on 24 sediment samples from archaeological sites on Maloelap and Ebon Atolls in the Marshall Islands, eastern Micronesia, and Henderson and Pitcairn Islands in the Pitcairn Group, Southeast Polynesia. The sampled islands, two of which are mystery islands (Henderson and Pitcairn), previously occupied and abandoned before European contact, comprise three types of Pacific islands: low coral atolls, raised atolls, and volcanic islands. Pollen, starch grains, calcium oxylate crystals, and xylem cells of introduced non-Colocasia Araceae (aroids) were identified in the Marshalls and Henderson (ca. 1,900 yr B.P. and 1,200 yr B.P. at the earliest, respectively). The data provide direct evidence of prehistoric horticulture in those islands and initial fossil pollen sequences from Pitcairn Island. Combined with previous studies, the data also indicate a horticultural system on Henderson comprising both field and tree crops, with seven different cultigens, including at least two species of the Araceae. Starch grains and xylem cells of Ipomoea sp., possibly introduced 1. batatas, were identified in Pitcairn Island deposits dated to the last few centuries before European contact in 1790.

Mixed order parameters, accidental nodes and broken time reversal symmetry in organic superconductors: a group theoretical analysis

We present a group theoretical analysis of several classes of organic superconductor. We predict that highly frustrated organic superconductors, such as K-(ET)(2)Cu-2(CN)(3) (where ET is BEDT-TTF, bis(ethylenedithio) tetrathiafulvalene) and beta'-[Pd(dmit)(2)](2)X, undergo two superconducting phase transitions, the first from the normal state to a d-wave superconductor and the second to a d + id state. We show that the monoclinic distortion of K-(ET)(2)Cu(NCS)(2) means that the symmetry of its superconducting order parameter is different from that of orthorhombic-K-(ET)(2)Cu[N(CN)(2)] Br. We propose that beta'' and theta phase organic superconductors have d(xy) + s order parameters.

Simulation of glassy state relaxations in polymers: A static analysis of methyl group and methoxy group rotation in poly(vinyl methyl ether)

We show that the simple quasi-static technique, also called the adiabatic mapping technique, can be used to determine the energetics of rotation of methyl and methoxy groups in amorphous poly(vinyl methyl ether) even though the latter process is too slow to be amenable to direct molecular dynamics simulation. For the methyl group rotation, we find that the mean and standard deviation of the simulated rotational barrier heights agree well with experimental data from quasi-elastic neutron scattering. In the case of the methoxy groups we find that just 4% of the groups contribute more than 90% of the observed dielectric relaxation strength. The groups which make the most contribution are those which, by virtue of their particular conformation and local environment, have two alternative positions of similar energy.

Stage is not a reliable indicator of tumor volume in non-small cell lung cancer: a preliminary analysis of the trans-tasman radiation oncology group 99-05 database

Background: Tumor volume has been shown to be a prognostic factor for the response of some tumors to radiotherapy. TNM stage has prognostic value for patients treated surgically for non-small cell lung cancer (NSCLC), but its value is less clear for patients treated by nonsurgical means. This may be because tumor size is not a consistent determinant of T stage or stage group. As part of the preliminary analyses for the Trans-Tasman Radiation Oncology Group 99-05 study, the authors performed this analysis to determine to what extent stage reflects tumor volume. Methods: In this prospective multicenter observational study, patients had to have histologically proven NSCLC, no evidence of disease beyond the primary site or thoracic lymph nodes, and been planned for radical radiotherapy with or without chemotherapy. Tumor volume measurements were based on computed tomography-based treatment planning images. Results: Four hundred four patients were available for analysis. There was a strong correlation between (log) maximum tumor diameter and (log) tumor volume (r = 0.93, p < 0.001). Although there was a highly significant trend of increasing volume with increasing T stage and stage group, when tumors were categorized into four groups according to increasing volume, there was only 55% concordance with T stage and 67% concordance with stage group. Conclusions: There is limited correlation between tumor size and disease stage in patients with NSCLC. This justifies documentation and investigation of size as a potential prognostic factor independent of stage. Maximum tumor diameter may be an adequate substitute for volume as a measurement of size.