Evaluation of meteorites as habitats for terrestrial microorganisms: results from the Nullarbor Plain, Australia, a Mars analogue site

Unambiguous identification of biosignatures on Mars requires access to well-characterized, long-lasting geochemical standards at the planet's surface that can be modified by theoretical martian life. Ordinary chondrites, which are ancient meteorites that commonly fall to the surface of Mars and Earth, have well-characterized, narrow ranges in trace element and isotope geochemistry compared to martian rocks. Given that their mineralogy is more attractive to known chemolithotrophic life than the basaltic rocks that dominate the martian surface, exogenic rocks (e.g., chondritic meteorites) may be good places to look for signs of prior life endemic to Mars. In this study, we show that ordinary chondrites, collected from the arid Australian Nullarbor Plain, are commonly colonized and inhabited by terrestrial microorganisms that are endemic to this Mars analogue site. These terrestrial endolithic and chasmolithic microbial contaminants are commonly found in close association with hygroscopic veins of gypsum and Mg-calcite, which have formed within cracks penetrating deep into the meteorites. Terrestrial bacteria are observed within corrosion cavities, where troilite (FeS) oxidation has produced jarosite [KFe(SO)(OH)]. Where terrestrial microorganisms have colonized primary silicate minerals and secondary calcite, these mineral surfaces are heavily etched. Our results show that inhabitation of meteorites by terrestrial microorganisms in arid environments relies upon humidity and pH regulation by minerals. Furthermore, microbial colonization affects the weathering of meteorites and production of sulfate, carbonate, Fe-oxide and smectite minerals that can preserve chemical and isotopic biosignatures for thousands to millions of years on Earth. Meteorites are thus habitable by terrestrial microorganisms, even under highly desiccating environmental conditions of relevance to Mars. They may therefore be useful as chemical and isotopic “standards” that preserve evidence of life, thereby providing the possibility of universal context for recognition of microbial biosignatures on Earth, Mars and throughout the solar system

Proteolysis-inducing factor core peptide mediates dermcidin-induced proliferation of hepatic cells through multiple signalling networks

Dermcidin is a candidate oncogene capable of increasing the number of cultured neuronal, breast cancer and prostate cancer cells and improving the survival of hepatic cells. The dermcidin gene encodes the proteolysis-inducing factor core peptide (PIF-CP) and the skin antimicrobial peptide DCD-1. The peptide responsible for inducing proliferation of cells and the mechanisms involved are unknown. In this study, we confirmed a proliferative effect of dermcidin over-expression of 20% (p<0.02) in the HuH7 human hepatic cell line. Proliferation was abrogated by prevention of PIF-CP translation or inactivation of its calcineurin-like phosphatase domain by site-directed mutagenesis. Prevention of DCD-1 translation had no effect. Treatment of cells with a 30 amino acid synthetic PIF-CP induced an analogous increase in proliferation of 14%. Microarray analysis of PIF-CP-treated cells revealed low but significant changes in 111 potential mediator genes. Pathway analysis revealed several gene networks involved in the cellular response to the peptide, one with VEGFB as a hub and two other networks converging on FOS and MYC. Quantitative PCR confirmed direct upregula-tion of VEGFB. These data reveal PIF-CP as the key mediator of dermcidin-induced proliferation and demonstrate induction of key oncogenic pathways

Structural biology and regulation of protein import into the nucleus

Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g. importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g. importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals (cNLSs), recognized by the adaptor importin-α, and the PY-NLSs, recognized by transportin-1. Post-translational modifications, in particular phosphorylation, constitute key regulatory mechanisms operating in these pathways

Binding of Transcription Factor GabR to DNA Requires Recognition of DNA Shape at a Location Distinct from its Cognate Binding Site

Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR–DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR–DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites

A 'combined framework' approach to developing a patient decision aid: the PANDAs model

Background There is a lack of practical research frameworks to guide the development of patient decision aids [PtDAs]. This paper described how a PtDA was developed using the International Patient Decision Aids (IPDAS) guideline and UK Medical Research Council (UKMRC) frameworks to support patients when making treatment decisions in type 2 diabetes mellitus. Methods This study used mixed methods to develop a PtDA for use in a UK general practice setting. A 10-member expert panel was convened to guide development and patients and clinicians were also interviewed individually using semi-structured interview guides to identify their decisional needs. Current literature was reviewed systematically to determine the best available evidence. The Ottawa Decision Support Framework was used to guide the presentation of the information and value clarification exercise. An iterative draft-review-revise process by the research team and review panel was conducted until the PtDA reached content and format `saturation’. The PtDA was then pilot-tested by users in actual consultations to assess its acceptability and feasibility. The IPDAS and UKMRC frameworks were used throughout to inform the development process. Results The PANDAs PtDA was developed systematically and iteratively. Patients and clinicians highlighted the needs for information, decisional, emotional and social support, which were incorporated into the PtDA. The literature review identified gaps in high quality evidence and variations in patient outcome reporting. The PtDA comprised five components: background of the treatment options; pros and cons of each treatment option; value clarification exercise; support needs; and readiness to decide. Conclusions This study has demonstrated the feasibility of combining the IPDAS and the UKMRC frameworks for the development and evaluation of a PtDA. Future studies should test this model for developing PtDAs across different decisions and healthcare contexts

Adjuvant Sorafenib for Renal Cell Carcinoma at Intermediate or High Risk of Relapse: Results From the SORCE Randomized Phase III Intergroup Trial.

PURPOSE: SORCE is an international, randomized, double-blind, three-arm trial of sorafenib after surgical excision of primary renal cell carcinoma (RCC) found to be at intermediate or high risk of recurrence. PATIENTS AND METHODS: We randomly assigned participants (2:3:3) to 3 years of placebo (arm A), 1 year of sorafenib followed by 2 years of placebo (arm B), or 3 years of sorafenib (arm C). The initial sorafenib dose was 400 mg twice per day orally, amended to 400 mg daily. The primary outcome analysis, which was revised as a result of external results, was investigator-reported disease-free survival (DFS) comparing 3 years of sorafenib versus placebo. RESULTS: Between July 2007 and April 2013, we randomly assigned 1,711 participants (430, 642, and 639 participants in arms A, B, and C, respectively). Median age was 58 years, 71% of patients were men, 84% had clear cell histology, 53% were at intermediate risk of recurrence, and 47% were at high risk of recurrence. We observed no differences in DFS or overall survival in all randomly assigned patients, patients with high risk of recurrence, or patients with clear cell RCC only. Median DFS was not reached for 3 years of sorafenib or for placebo (hazard ratio, 1.01; 95% CI, 0.83 to 1.23; P = .95). We observed nonproportional hazards; the restricted mean survival time (RMST) was 6.81 years for 3 years of sorafenib and 6.82 years for placebo (RMST difference, 0.01 year; 95% CI, -0.49 to 0.48 year; P = .99). Despite offering treatment adaptations, more than half of participants stopped treatment by 12 months. Grade 3 hand-foot skin reaction was reported in 24% of participants on sorafenib. CONCLUSION: Sorafenib should not be used as adjuvant therapy for RCC. Active surveillance remains the standard of care for patients at intermediate or high risk of recurrence after nephrectomy and is the appropriate control of our current international adjuvant RCC trial, RAMPART.CRU

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis