Discriminating stromatolite formation modes using rare earth element geochemistry: Trapping and binding versus in situ precipitation of stromatolites from the Neoproterozoic Bitter Springs Formation, Northern Territory, Australia

Stromatolites consist primarily of trapped and bound ambient sediment and/or authigenic mineral precipitates, but discrimination of the two constituents is difficult where stromatolites have a fine texture. We used laser ablation-inductively coupled plasma-mass spectrometry to measure trace element (rare earth element – REE, Y and Th) concentrations in both stromatolites (domical and branched) and closely associated particulate carbonate sediment in interspaces (spaces between columns or branches) from bioherms within the Neoproterozoic Bitter Springs Formation, central Australia. Our high resolution sampling allows discrimination of shale-normalised REE patterns between carbonate in stromatolites and immediately adjacent, fine-grained ambient particulate carbonate sediment from interspaces. Whereas all samples show similar negative La and Ce anomalies, positive Gd anomalies and chondritic Y/Ho ratios, the stromatolites and non-stromatolite sediment are distinguishable on the basis of consistently elevated light REEs (LREEs) in the stromatolitic laminae and relatively depleted LREEs in the particulate sediment samples. Additionally, concentrations of the lithophile element Th are higher in ambient sediment samples than in stromatolites, consistent with accumulation of some fine siliciclastic detrital material in the ambient sediment but a near absence in the stromatolites. These findings are consistent with the stromatolites consisting dominantly of in situ carbonate precipitates rather than trapped and bound ambient sediment. Hence, high resolution trace element (REE + Y, Th) geochemistry can discriminate fine-grained carbonates in these stromatolites from coeval non-stromatolitic carbonate sediment and demonstrates that the sampled stromatolites formed primarily from in situ precipitation, presumably within microbial mats/biofilms, rather than by trapping and binding of ambient sediment. Identification of the source of fine carbonate in stromatolites is significant, because if it is not too heavily contaminated by trapped ambient sediment, it may contain geochemical biosignatures and/or direct evidence of the local water chemistry in which the precipitates formed.

Identification of vitronectin as a novel insulin-like growth factor-II binding protein

We have previously reported the presence of a 70 kDa insulin-like growth factor (IGF)-II-specific binding protein in chicken serum using Western ligand blotting approaches. In order to ascertain the identity of this 70 kDa IGF-II binding species, the protein has been purified from chicken serum using a combination of ion-exchange and gel-permeation chromatography. Interestingly, amino acid sequencing of the purified protein revealed that it has the same N-terminal sequence as chicken vitronectin (VN). The protein has the ability to specifically bind IGF-II and not IGF-I as determined by ligand blotting, cross-linking and competitive binding assay approaches. In addition, the protein binds 125I-des(l-6)-IGF-II, suggesting that the interaction with IGF-II is different to those with other characterized IGF-binding proteins. Importantly, we have ascertained that both human and bovine VN also specifically bind IGF-II. These results are particularly relevant in the light of the recent report that the urokinase-type plasminogen activator receptor, a protein that also binds VN, has been shown to associate with the cation-independent mannose-6-phosphate/GF-II receptor and suggest a possible role for IGF-II in cell adhesion and invasion.

The "free-factor" impact on value in health services

Purpose - This paper seeks to understand the impact of financial cost on customer value in health prevention services by comparing free government services with private fee-charging providers. This is important as there is a common belief that a free health service is of lower quality and thus lower value than a paid service. However there is no evidence to verify this notion. Design / Methodology / Approach - A large-scale online survey was administered nationwide to Australian women. The respondents were asked about the functional and emotional value derived from their service experiences. Findings - Structural equation modelling (SEM) revealed non significant relationships between fee/free services and functional and emotional value (FV/EV). The non-significant relationship with FV is contrary to the theory of price quality relationship in services. This could be attributed to consumer perceptions that the technical quality of health professionals is comparable across free and paid services. The non-significant relationship with EV could be explained by the indicators used to reflect EV. These indicators were reflective of breast screening behaviour, not breast screening services. Subsequently, it may be posited that the act of having a breast screen is sufficient for consumers to derive emotional value, regardless of the financial cost. Originality / Value - This research fills an important gap in the literature by investigating the impact of financial cost on a service that consumers use proactively(prevention), rather than reactively (treatment). Insights are provided into the impact of cost on customer value in preventive health services, which are valuable to social marketing academics, health practitioners, and governments

The adenine-rich tract in the 5ʹ-end of the hepatitis C virus ORF encodes a peptide regulating the binding of the C protein to RNA

Hepatitis C virus (HCV ) core (C) protein is thought to bind to viral RNA before it undergoes oligomerization leading to RNA encapsidation. Details of these events are so far unknown. The 5ʹ-terminal C protein coding sequence that includes an adenine (A)-rich tract is a part of an internal ribosome entry site(IRES). This nucleotide sequence but not the corresponding protein sequence is needed for proper initiation of translation of viral RNA by an IRES-dependent mechanism. In this study, we examined the importance of this sequence for the ability of the C protein to bind to viral RNA. Serially truncated C proteins with deletions from 10 up to 45 N-terminal amino acids were expressed in Escherichia coli, purified and tested for binding to viral RNA by a gel shift assay. The results showed that truncation of the C protein from its N-terminus by more than 10 amino acids abolished almost completely its expression in E. coli. The latter could be restored by adding a tag to the N-terminus of the protein. The tagged proteins truncated by 15 or more amino acids showed an anomalous migration in SDS-PAGE. Truncation by more than 20 amino acids resulted in a complete loss of ability of tagged C protein to bind to viral RNA. These results provide clues to the early events in the C protein - RNA interactions leading to C protein oligomerization, RNA encapsidation and virion assembly.

Pedigree-free animal models : the relatedness matrix reloaded

Animal models typically require a known genetic pedigree to estimate quantitative genetic parameters. Here we test whether animal models can alternatively be based on estimates of relatedness derived entirely from molecular marker data. Our case study is the morphology of a wild bird population, for which we report estimates of the genetic variance-covariance matrices (G) of six morphological traits using three methods: the traditional animal model; a molecular marker-based approach to estimate heritability based on Ritland's pairwise regression method; and a new approach using a molecular genealogy arranged in a relatedness matrix (R) to replace the pedigree in an animal model. Using the traditional animal model, we found significant genetic variance for all six traits and positive genetic covariance among traits. The pairwise regression method did not return reliable estimates of quantitative genetic parameters in this population, with estimates of genetic variance and covariance typically being very small or negative. In contrast, we found mixed evidence for the use of the pedigree-free animal model. Similar to the pairwise regression method, the pedigree-free approach performed poorly when the full-rank R matrix based on the molecular genealogy was employed. However, performance improved substantially when we reduced the dimensionality of the R matrix in order to maximize the signal to noise ratio. Using reduced-rank R matrices generated estimates of genetic variance that were much closer to those from the traditional model. Nevertheless, this method was less reliable at estimating covariances, which were often estimated to be negative. Taken together, these results suggest that pedigree-free animal models can recover quantitative genetic information, although the signal remains relatively weak. It remains to be determined whether this problem can be overcome by the use of a more powerful battery of molecular markers and improved methods for reconstructing genealogies.

A variable-stepsize Jacobian-free exponential integrator for simulating transport in heterogeneous porous media : application to wood drying

A Jacobian-free variable-stepsize method is developed for the numerical integration of the large, stiff systems of differential equations encountered when simulating transport in heterogeneous porous media. Our method utilises the exponential Rosenbrock-Euler method, which is explicit in nature and requires a matrix-vector product involving the exponential of the Jacobian matrix at each step of the integration process. These products can be approximated using Krylov subspace methods, which permit a large integration stepsize to be utilised without having to precondition the iterations. This means that our method is truly "Jacobian-free" - the Jacobian need never be formed or factored during the simulation. We assess the performance of the new algorithm for simulating the drying of softwood. Numerical experiments conducted for both low and high temperature drying demonstrates that the new approach outperforms (in terms of accuracy and efficiency) existing simulation codes that utilise the backward Euler method via a preconditioned Newton-Krylov strategy.

The active site residue V266 of Chlamydial HtrA is critical for substrate binding during both in vitro and in vivo conditions

HtrA is a complex, multimeric chaperone and serine protease important for the virulence and survival of many bacteria. Chlamydia trachomatis is an obligate, intracellular bacterial pathogen that is responsible for severe disease pathology. C. trachomatis HtrA (CtHtrA) has been shown to be highly expressed in laboratory models of disease. In this study, molecular modelling of CtHtrA protein active site structure identified putative S1-S3 subsite residues I242, I265, and V266. These residues were altered by site-directed mutagenesis, and these changes were shown to considerably reduce protease activity on known substrates and resulted in a narrower and distinct range of substrates compared to wild type. Bacterial two-hybrid analysis revealed that CtHtrA is able to interact in vivo with a broad range of protein sequences with high affinity. Notably, however, the interaction was significantly altered in 35 out of 69 clones when residue V266 was mutated, indicating that this residue has an important function during substrate binding.

A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR-Rep binding

Geminivirus infectivity is thought to depend on interactions between the virus replication-associated proteins Rep or RepA and host retinoblastoma-related proteins (pRBR), which control cell-cycle progression. It was determined that the substitution of two amino acids in the Maize streak virus (MSV) RepA pRBR-interaction motif (LLCNE to LLCLK) abolished detectable RepA-pRBR interaction in yeast without abolishing infectivity in maize. Although the mutant virus was infectious in maize, it induced less severe symptoms than the wild-type virus. Sequence analysis of progeny viral DNA isolated from infected maize enabled detection of a high-frequency single-nucleotide reversion of C(601)A in the 3 nt mutated sequence of the Rep gene. Although it did not restore RepA-pRBR interaction in yeast, sequence-specific PCR showed that, in five out of eight plants, the C(601)A reversion appeared by day 10 post-inoculation. In all plants, the C(601)A revertant eventually completely replaced the original mutant population, indicating a high selection pressure for the single-nucleotide reversion. Apart from potentially revealing an alternative or possibly additional function for the stretch of DNA that encodes the apparently non-essential pRBR-interaction motif of MSV Rep, the consistent emergence and eventual dominance of the C(601)A revertant population might provide a useful tool for investigating aspects of MSV biology, such as replication, mutation and evolution rates, and complex population phenomena, such as competition between quasispecies and population turnover. © 2005 SGM.

Comparing measures of fat-free mass in overweight older adults using three different bioelectrical impedance devices and three prediction equations

Objectives: To compare measures of fat-free mass (FFM) by three different bioelectrical impedance analysis (BIA) devices and to assess the agreement between three different equations validated in older adult and/or overweight populations. Design: Cross-sectional study. Setting: Orthopaedics ward of Brisbane public hospital, Australia. Participants: Twenty-two overweight, older Australians (72 yr ± 6.4, BMI 34 kg/m2 ± 5.5) with knee osteoarthritis. Measurements: Body composition was measured using three BIA devices: Tanita 300-GS (foot-to-foot), Impedimed DF50 (hand-to-foot) and Impedimed SFB7 (bioelectrical impedance spectroscopy (BIS)). Three equations for predicting FFM were selected based on their ability to be applied to an older adult and/ or overweight population. Impedance values were extracted from the hand-to-foot BIA device and included in the equations to estimate FFM. Results: The mean FFM measured by BIS (57.6 kg ± 9.1) differed significantly from those measured by foot-to-foot (54.6 kg ± 8.7) and hand-to-foot BIA (53.2 kg ± 10.5) (P < 0.001). The mean ± SD FFM predicted by three equations using raw data from hand-to-foot BIA were 54.7 kg ± 8.9, 54.7 kg ± 7.9 and 52.9 kg ± 11.05 respectively. These results did not differ from the FFM predicted by the hand-to-foot device (F = 2.66, P = 0.118). Conclusions: Our results suggest that foot-to-foot and hand-to-foot BIA may be used interchangeably in overweight older adults at the group level but due to the large limits of agreement may lead to unacceptable error in individuals. There was no difference between the three prediction equations however these results should be confirmed within a larger sample and against a reference standard.

Natural improvements of geochemical conditions of acid sulfate soils caused by free tidal inundation and its effects on the mangrove seedlings

Acid sulfate soils (ASS) are one of the stressor factors that cause many mangrove restoration projects to fail. Achieving successful rehabilitation in an ASS affected area requires an understanding of the geochemical conditions that influence the establishment and growth of mangrove seedlings. This study evaluated the effect of tidal inundation on geochemical conditions on sub layer to better understand their impacts on the density, establishment, and growth of mangrove seedlings. This study also examined the geochemical conditions under which mangrove seedlings can establish naturally, and/or be replanted in abandoned aquaculture ponds. The study area was in an area of abandoned aquaculture ponds situated in the Mare District, adjacent to Bone Bay, South Sulawesi, Indonesia.The pH, pHfox, redox potential, organic content, water soluble sulfate, SKCl, SPOS, and grain size of the soil from the sediment core at + 10 - 15 cm depth near roots were measured using. Pyrite analysis were conducted for the top and sub sediments. The density, establishment, and the relative root growth of Rhizophoraceae were also determined. Free tidal inundation at abandoned pond sites improved the sediment quality. The high density, establishment, and growth of mangrove seedlings were characterized by freely drained areas with a higher pH (field and oxidisable), lower organic content, and high proportion of silt/clay. Higher density and growth also correlated to reduced environments. Sulfur species did not influence the density, establishment, and growth of the seedlings directly. The supply of propagules from the mangrove stands, or access from good waterways were also important for seedlings to establish naturally.

Markers of cutaneous human papillomavirus infection in individuals with tumor-free skin, actinic keratoses, and squamous cell carcinoma

Separately, actinic keratosis (AK) and cutaneous squamous cell carcinoma (SCC) have been associated with cutaneous human papillomavirus (HPV) infections. To further explore the association between HPV infection and SCC development, we determined markers of cutaneous HPV infection within a single population in persons with precursor lesions (AK), cancerous lesions (SCC), and without. Serum and plucked eyebrow hairs were collected from 57 tumor-free controls, 126 AK, and 64 SCC cases. Presence of HPV L1 and E6 seroreactivity and viral DNA were determined for HPV types 5, 8, 15, 16, 20, 24, and 38. Significant positive associations with increasing severity of the lesions (controls, AK, and SCC, respectively) were observed for overall HPV L1 seropositivity (13%, 26%, and 37%) and for HPV8 (4%, 17%, and 30%). In parallel, the proportion of L1 seropositive individuals against multiple HPV types increased from 14% to 39% and 45%. The overall E6 seroreactivity, however, tended to decline with AK and SCC, especially for HPV8 (21%, 11%, and 2%). HPV DNA positivity was most prevalent in the AK cases (54%) compared with the SCC cases (44%) and the tumor-free controls (40%). Among all participants, there was a positive trend between overall HPV DNA positivity and L1 seropositivity, but not E6 seropositivity. Taken together, our data suggest that cutaneous HPV infections accompanied by detectable HPV DNA in eyebrow hairs and HPV L1 seropositivity, but not E6 seropositivity, are associated with an increased risk of AK and SCC.

Exponential asymptotics of free surface flow due to a line source

The steady problem of free surface flow due to a submerged line source is revisited for the case in which the fluid depth is finite and there is a stagnation point on the free surface directly above the source. Both the strength of the source and the fluid speed in the far field are measured by a dimensionless parameter, the Froude number. By applying techniques in exponential asymptotics, it is shown that there is a train of periodic waves on the surface of the fluid with an amplitude which is exponentially small in the limit that the Froude number vanishes. This study clarifies that periodic waves do form for flows due to a source, contrary to a suggestion by Chapman & Vanden-Broeck (2006, J. Fluid Mech., 567, 299--326). The exponentially small nature of the waves means they appear beyond all orders of the original power series expansion; this result explains why attempts at describing these flows using a finite number of terms in an algebraic power series incorrectly predict a flat free surface in the far field.

First-principles prediction of metal-free magnetism and intrinsic half-metallicity in graphitic carbon nitride

Transition metal-free magnetism and half-metallicity recently has been the subject of intense research activity due to its potential in spintronics application. Here we, for the first time, demonstrate via density functional theory that the most recently experimentally realized graphitic carbon nitride (g-C4N3) displays a ferromagnetic ground state. Furthermore, this novel material is predicted to possess an intrinsic half-metallicity never reported to date. Our results highlight a new promising material toward realistic metal-free spintronics application.