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Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (−10.4 ± 0.9 eV versus −12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The "hydrophilic reactivity" quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference. [ABSTRACT FROM AUTHOR]

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from nonliving material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes -- whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call 'Pathway Complexity', that allows us not only to threshold the abiotic--biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Re-conceptualizing the origins of life'. [ABSTRACT FROM AUTHOR]

The proliferation of microbial carbon fixation is a key control on the evolution of the biosphere and global carbon cycle. Most records of these metabolisms in ancient rocks come from organic matter or fossils, which are not always preserved. Here, we present a potential proxy for microbial carbon fixation (autotrophy) based on the isotopic composition of carbonate minerals. Autotrophs influence carbonate chemistry in the cellular microenvironment by decreasing CO2 concentration and increasing the carbonate saturation state. This can induce rapid precipitation of carbonate minerals that are out of isotopic equilibrium with their environment. Recent work has identified disequilibrated dual clumped isotope compositions (∆47 and ∆48) in the skeletal fossils of marine calcifying organisms. Here we test whether the same is true of non‐skeletal carbonate fabrics associated with microbial autotrophs in modern and Eocene lakes. We found that microbial carbonate formed via autotrophic metabolism recorded lower ∆47 and higher ∆48 values (−∆47/+∆48) than predicted for thermodynamic equilibrium mineral formation. Our findings are supported by models of dual clumped isotope kinetics in the DIC system, and disequilibrium in the oxygen isotope system. We hypothesize that the inverse trajectory away from the equilibrium line (+∆47/−∆48) should be recorded by carbonates formed in association with alkalinizing heterotrophs, such as sulfate reducers. If so, carbonate dual clumped isotopes could be a powerful tool to identify the proliferation and rate of heterotrophic and autotrophic metabolisms in the carbonate rock record on Earth and (perhaps) other planets. Plain Language Summary: Primary producers have fueled the biosphere since the origin of life on Earth. The production of organic molecules by autotrophs is essential for the evolution of heterotrophic bacteria, and eventually fungi and animals. However, identifying where and when specific metabolisms were active in Earth history is challenging because we lack reliable biosignatures of these processes. Identifying the presence of ancient metabolic activity can provide context to how microorganisms steered global biogeochemical cycles and the carbon budget in ancient oceans, atmosphere, and on land. In this study, we present a potential fingerprint of microbial autotrophy (e.g., photosynthesis, methanogenesis) preserved in carbonate minerals in modern and ancient settings. Key Points: Microbial autotrophy imparts a dual clumped isotope and oxygen isotope disequilibrium signature on carbonate mineralsThis disequilibrium biosignature can be preserved in the rock record post‐burialDual clumped isotope signatures of microbially associated carbonates are differentiable from abiotic carbonates that formed from the same water and experienced the same burial history [ABSTRACT FROM AUTHOR]

In a regression model for treatment outcome in a randomized clinical trial, a treatment effect modifier is a covariate that has an interaction with the treatment variable, implying that the treatment efficacies vary across values of such a covariate. In this paper, we present a method for determining a composite variable from a set of baseline covariates, that can have a nonlinear association with the treatment outcome, and acts as a composite treatment effect modifier. We introduce a parsimonious generalization of the single-index models that targets the effect of the interaction between the treatment conditions and the vector of covariates on the outcome, a single-index model with multiple-links (SIMML) that estimates a single linear combination of the covariates(i.e., a single-index), with treatment-specific nonparametric link functions. The approach emphasizes a focus on the treatment-by-covariates interaction effects on the treatment outcome that are relevant for making optimal treatment decisions. Asymptotic results for estimator are obtained under possible model misspecification. A treatment decision rule based on the derived single-index is defined, and it is compared to other methods for estimating optimal treatment decision rules. An application to a clinical trial for the treatment of depression is presented. [ABSTRACT FROM AUTHOR]

Detection of indigenous organic matter (IOM) in rocks using molecular-laser-induced breakdown spectroscopy (LIBS) is reported. IOM refers to carbon-based compounds of variable complexity intimately associated with mineral and amorphous phases both in condensed phases and in a dispersed state spatially associated to mineral aggregates. The presence of IOM may provide valuable information in astrobiology about the possibility of past or present life on planetary bodies. Kerogen, charcoal, bitumen, and graphite are only some examples of IOM that may appear in rocks. This paper reports the detection of kerogen in oil shale (a sedimentary rock also containing dolomite, calcite, pyrite, quartz, and albite) from the LIBS study of CN and C 2 emissions under simulated Martian conditions. A set of oil shale samples with variable concentrations of total organic carbon (TOC) ranging from 2.78% to 12.74% were analyzed. A careful LIBS analysis of molecular species associated within hydrocarbons confirmed the presence of organic matter derived from kerogen. A linear correlation between the CN and C 2 emissions and the %TOC was observed. Using a simulated Martian atmosphere as surrounding gas, the limit of detection for organic matter was calculated in 0.42% TOC. Additionally, the potential interferences in geological samples for LIBS detection of molecular species were also evaluated. Results demonstrate that common elements in rocks such as Ca, Fe, K, Mg, Na and Si do not interfere with the detection of organics. In contrast, Ti at concentrations above 0.4% may induce false positive results using the CN emission at 388.34 nm. To overcome this inconvenience, the CN emission at 387.14 nm may be used which, although less sensitive, is free from titanium interference. [Display omitted] • LIBS novel detection of native organic matter through molecular emission recognition in complex sedimentary rocks. • Contribution of different carbon sources to the collected emission signal under Martian conditions. • Possible interferences in LIBS molecular detection of CN and C 2 species. • Linear correlation between intensity of CN and C 2 molecular systems and TOC content. • LIBS analysis for geological and astrobiological applications. [ABSTRACT FROM AUTHOR]

Agate geodes contain spheroidal patterns characterized by spectacularly coloured and circularly concentric laminations with radially aligned quartz crystals, yet the origin of these geometric patterns has remained enigmatic. Here, detailed comparisons are documented between these kinds of patterns in a selection of geodes and concretions and those produced by abiotic chemically oscillating reactions. We find strikingly comparable self-similar, fractal patterns in both natural volcanogenic geodes and sedimentary concretions as well as in these benchtop experiments. In addition, the mineralogical composition of patterns and associated organic matter point to the oxidation of organic compounds in both geodes and concretions. This process occurred during diagenetic or supergene alteration, and it is consistent with spontaneous and abiotic chemically oscillating reactions. It is concluded that the oxidation of organic acids was involved in the formation of these patterns and that these rocks indicate oxidation–reduction reactions involving organic carbon, which itself may be abiotic or biological in origin. Hence, agate geodes and concretions represent the abiotic biosignatures of possible biological origin in volcanic and sedimentary rocks. [ABSTRACT FROM AUTHOR]

The detection of exolife is one of the goals of very ambitious future space missions that aim to take direct images of Earth-like planets. While associations of simple molecules present in the planet’s atmosphere (O2, O3, CO2, etc.) have been identified as possible global biomarkers, this paper reviews the detectability of a signature of life from the planet’s surface, i.e. the green vegetation. The vegetation reflectance has indeed a specific spectrum, with a sharp edge around 700 nm, known as the “Vegetation Red Edge” (VRE). Moreover, vegetation covers a large surface of emerged lands, from tropical evergreen forest to shrub tundra. Thus, considering vegetation as a potential global biomarker is relevant. Earthshine allows us to observe the Earth as a distant planet, i.e. without spatial resolution. Since 2001, Earthshine observations have been used by several authors to test and quantify the detectability of the VRE in the Earth spectrum. The vegetation spectral signature is detected as a small “positive shift” of a few percentage points above the continuum, starting at 700 nm. This signature appears in most spectra, and its strength is correlated with the Earth’s phase (visible land versus visible ocean). The observations show that detecting the VRE on Earth requires a photometric relative accuracy of 1% or better. Detecting something equivalent on an Earth-like planet will therefore remain challenging, especially considering the possibility of mineral artifacts and the question of “red edge” universality in the Universe. [ABSTRACT FROM AUTHOR]

Here I pursue a deconstructive reading of astrobiology, the emerging science dedicated to a double quest: solving the mystery of life's origin and discovering life beyond Earth. Astrobiology, I argue, is organized as a response to the aporetic formulation assumed by the origin of life in modern molecular biology, where (as Derrida's argues in Life Death) it becomes the origin of textuality. Because all Earth life shares a single genetic code, astrobiologists are seeking a second; hoping that a sort of multi-planetary comparative genomics may reveal the secret to life's origin. But the aporia repeats in the figure of the biosignature, the trace of life. [ABSTRACT FROM AUTHOR]

Recent advances in automated microscopy and image analysis enables quantitative profiling of cellular phenotypes (Cell Painting). It paves the way for studying the broad effects of chemical perturbations on biological systems at large scale during lead optimization. Comparison of perturbation biosignatures with biosignatures of annotated compounds can inform on both on- and off-target effects. When building databases with phenotypic profiles of thousands of compounds, it is vital to control the quality of Cell Painting assays over time. A tool for this to our knowledge does not yet exist within the imaging community. In this paper, we introduce an automated tool to assess the quality of Cell Painting assays by quantifying the reproducibility of biosignatures of annotated reference compounds. The tool learns the biosignature of those treatments from a historical dataset, and subsequently, it builds a two-dimensional probabilistic quality control (QC) limit. The limit will then be used to detect aberrations in new Cell Painting experiments. The tool is illustrated using simulated data and further demonstrated on Cell Painting data of the A549 cell line. In general, the tool provides a sensitive, detailed and easy-to-interpret mechanism to validate the quality of Cell Painting assays.

Background: To improve tuberculosis (TB) diagnosis, the World Health Organisation (WHO) has called for a non-sputum based triage test to focus TB testing on people with a high likelihood of having active pulmonary tuberculosis (TB). Various host or pathogen biomarker-based testing devices are in design stage and require validity assessment. Host biomarkers have shown promise to accurately rule out active TB, but further research is required to determine generalisability. The TriageTB diagnostic test study aims to assess the accuracy of diagnostic test candidates, as well as field-test, finalise the design and biomarker signature, and validate a point-of-care multi-biomarker test (MBT). Methods: This observational diagnostic study will evaluate sensitivity and specificity of biomarker-based diagnostic candidates including the MBT and Xpert® TB Fingerstick cartridge compared with a gold-standard composite TB outcome classification defined by symptoms, sputum GeneXpert® Ultra, smear and culture, radiological features, response to TB therapy and presence of an alternative diagnosis. The study will be conducted in research sites in South Africa, Uganda, The Gambia and Vietnam which all have high TB prevalence. The two-phase design allows for finalisation of the MBT in Phase 1 in which candidate host proteins will be evaluated on stored serum from Asia, South Africa and South America and on fingerstick blood from 50 newly recruited participants per site. The MBT test will then be locked down and validated in Phase 2 on 250 participants per site. Discussion: By targeting confirmatory TB testing to those with a positive triage test, 75% of negative GXPU may be avoided, thereby reducing diagnostic costs and patient losses during the care cascade. This study builds on previous biomarker research and aims to identify a point-of-care test meeting or exceeding the minimum World Health Organisation target product profile of a 90% sensitivity and 70% specificity. Streamlining TB testing by identifying individuals with a high likelihood of TB should improve TB resources use and, in so doing, improve TB care. Trial registration: NCT04232618 (clinicaltrials.gov) Date of registration: 16 January 2020. [ABSTRACT FROM AUTHOR]

Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry. [ABSTRACT FROM AUTHOR]

Background: Chronic rhinosinusitis without nasal polyps (CRSsNP) represents a phenotype of CRS, whose immunological mechanisms are still unclear. So far there are neither suitable biomarkers to determine the course of the disease nor an individual therapy. Objective: The purpose of this study was to characterize the CRSsNP endotype by identifying and validating non-invasive proteomic biomarkers. Methods: A highly-multiplexed proteomic array consisting of antibodies against 2000 proteins was used to identify proteins that are differentially expressed in the nasal mucus of the CRSsNP and control groups (n = 7 per group). The proteins identified to be most differentially expressed were validated in matched nasal mucus samples using western blots and enzyme-linked immunosorbent assay (ELISA). Validation was also done in a second cohort using western blots (CRSsNP n = 25, control n = 23) and ELISA (n = 30 per group). Additionally, immunohistochemistry in CRSsNP and control tissue samples was performed to characterize the selected proteins further. Results: Out of the 2000 proteins examined, 7 from the most differentially expressed proteins were chosen to be validated. The validation results showed that 4 proteins were significantly upregulated in CRSsNP mucus, including macrophage inflammatory protein-1beta (MIP-1β), resistin, high mobility group box 1 (HMGB1), and forkhead box protein 3 (FOXP3). Cartilage acidic protein 1 (CRTAC1) was not significantly upregulated. Two proteins were significantly downregulated including scavenger receptor class F member 2 (SCARF2) and P-selectin. All proteins selected are mainly associated with inflammation, cell proliferation/differentiation, apoptosis and cell–cell or cell–matrix interaction. Conclusion: Proteomic analysis of CRSsNP and control mucus has confirmed known and revealed novel disease-associated proteins that could potentially serve as a new biosignature for CRSsNP. Analysis of the associated pathways will specify endotypes of CRSsNP and will lead to an improved understanding of the pathophysiology of CRSsNP. Furthermore, our data contribute to the development of a reproducible, non-invasive, and quantitative "liquid biopsy" for rhinosinusitis. [ABSTRACT FROM AUTHOR]

For decades, the search for potential signs of Martian life has attracted strong international interest and has led to significant planning and scientific implementation. Clearly, in order to detect potential life signals beyond Earth, fundamental questions, such as how to define such terms as “life” and “biosignature”, have been given considerable attention. Due to the high costs of direct exploration of Mars, Mars-like regions on Earth have been invaluable targets for astrobiological research, places where scientists could practice the search for “biosignatures” and refine ways to detect them. This review summarizes scientific instrumental techniques that have resulted from this work. Instruments must necessarily be our “eyes” and “hands” as we attempt to identify and quantify biosignatures on Mars. Scientific devices that can be applied in astrobiology include mass spectrometers and electromagnetic-spectrum-based spectrometers, redox potential indicators, circular dichroism polarimeters, in situ nucleic acid sequencers, life isolation/cultivation systems, and imagers. These devices and how to interpret the data they collect have been tested in Mars-analog extreme environments on Earth to validate their practicality on Mars. To anticipate the challenges of instrumental detection of biosignatures through the full evolutionary history of Mars, Terrestrial Mars analogs are divided into four major categories according to their similarities to different Martian geological periods (the Early−Middle Noachian Period, the Late Noachian−Early Hesperian Period, the Late Hesperian−Early Amazonian Period, and the Middle−Late Amazonian Period). Future missions are suggested that would focus more intensively on Mars’ Southern Hemisphere, once landing issues there are solved by advances in spacecraft engineering, since exploration of these early terrains will permit investigations covering a wider continuum of the shifting habitability of Mars through its geological history. Finally, this paper reviews practical applications of the range of scientific instruments listed above, based on the four categories of Mars analogs here on Earth. We review the selection of instruments suitable for autonomous robotic rover tests in these Mars analogs. From considerations of engineering efficiency, a Mars rover ought to be equipped with as few instrument assemblies as possible. Therefore, once candidate landing regions on Mars are defined, portable suites of instruments should be smartly devised on the basis of the known geological, geochemical, geomorphological, and chronological characteristics of each Martian landing region. Of course, if Mars sample-return missions are successful, such samples will allow experiments in laboratories on Earth that can be far more comprehensive and affordable than is likely to be practicable on Mars. To exclude false positive and false negative conclusions in the search for extraterrestrial life, multiple diverse and complementary analytical techniques must be combined, replicated, and carefully interpreted. The question of whether signatures of life can be detected on Mars is of the greatest importance. Answering that question is extremely challenging but appears to have become manageable.

Background: Host innate immune cells have been identified as key players in the early eradication of Mycobacterium tuberculosis and in the maintenance of an anti-mycobacterial immune memory, which we and others have shown are induced through epigenetic reprogramming. Studies on human tuberculosis immunity are dominated by those using peripheral blood as surrogate markers for immunity. We aimed to investigate DNA methylation patterns in immune cells of the lung compartment by obtaining induced sputum from M. tuberculosis- exposed subjects including symptom-free subjects testing positively and negatively for latent tuberculosis as well as patients diagnosed with active tuberculosis. Alveolar macrophages and alveolar T cells were isolated from the collected sputum and DNA methylome analyses performed (Illumina Infinium Human Methylation 450 k). Results: Multidimensional scaling analysis revealed that DNA methylomes of cells from the tuberculosis-exposed subjects and controls appeared as separate clusters. The numerous genes that were differentially methylated between the groups were functionally connected and overlapped with previous findings of trained immunity and tuberculosis. In addition, analysis of the interferon-gamma release assay (IGRA) status of the subjects demonstrated that the IGRA status was reflected in the DNA methylome by a unique signature. Conclusions: This pilot study suggests that M. tuberculosis induces epigenetic reprogramming in immune cells of the lung compartment, reflected as a specific DNA methylation pattern. The DNA methylation signature emerging from the comparison of IGRA-negative and IGRA-positive subjects revealed a spectrum of signature strength with the TB patients grouping together at one end of the spectrum, both in alveolar macrophages and T cells. DNA methylation-based biosignatures could be considered for further development towards a clinically useful tool for determining tuberculosis infection status and the level of tuberculosis exposure. [ABSTRACT FROM AUTHOR]

Post-acute COVID-19 syndrome (PACS) has been defined as symptoms persisting after clearance of a COVID-19 infection. We have previously demonstrated that alterations in DNA methylation (DNAm) status persist in individuals who recovered from a COVID-19 infection, but it is currently unknown if PACS is associated with epigenetic changes. We compared DNAm patterns in patients with PACS with those in controls and in healthy COVID-19 convalescents and found a unique DNAm signature in PACS patients. This signature unravelled modified pathways that regulate angiotensin II and muscarinic receptor signalling and protein–protein interaction networks that have bearings on vesicle formation and mitochondrial function. [ABSTRACT FROM AUTHOR]

For billions of years, life has continuously adapted to dynamic physical conditions near the Earth's surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth's earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as "paleosensors" for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies. [ABSTRACT FROM AUTHOR]

Priorities for the exploration of Mars involve the identification and observation of biosignatures that indicate the existence of life on the planet. The atmosphere and composition of the sediments on Mars suggest suitability for anaerobic chemolithotrophic metabolism. Carbonates are often considered as morphological biosignatures, such as stromatolites, but have not been considered as potential electron acceptors. Within the present study, hydrogenotrophic methanogen enrichments were generated from sediments that had received significant quantities of lime from industrial processes (lime kiln/steel production). These enrichments were then supplemented with calcium carbonate powder or marble chips as a sole source of carbon. These microcosms saw a release of inorganic carbon into the liquid phase, which was subsequently removed, resulting in the generation of methane, with 0.37 ± 0.09 mmoles of methane observed in the steel sediment enrichments supplemented with calcium carbonate powder. The steel sediment microcosms and lime sediments with carbonate powder enrichments were dominated by Methanobacterium sp., whilst the lime/marble enrichments were more diverse, containing varying proportions of Methanomassiliicoccus, Methanoculleus and Methanosarcina sp. In all microcosm experiments, acetic acid was detected in the liquid phase. Our results indicate that chemolithotrophic methanogenesis should be considered when determining biosignatures for life on Mars. [ABSTRACT FROM AUTHOR]

The article discusses various reports published within the issue, including a review on the relationship between all known magnetosome crystal habits and the phylogenetic affiliations of magnetotactic bacteria (MTB), articles deal with the mechanisms of magnetosome biomineralization, and papers explore the effects of environmental factors on magnetosome formation.

Cosmos has always sparked human curiosity to unveil and speculate its fascinating secrets. This curiosity has ultimately opened a window to other worlds. After years of observation, computation, and data analysis, scientists have revealed the diversity in exoplanets that have been helpful in the characterization and further investigation of biosignatures and technosignatures. This article presents some of the scientific advances made in extraterrestrial planetary science that guarantees to search through the thick clouds of the mysterious planets in the near future. [ABSTRACT FROM AUTHOR]

Limited taxonomic classification is possible for Archaean microbial mats and this is a fundamental limitation in constraining early ecosystems. Applying Fourier transform infrared spectroscopy (FTIR), a powerful tool for identifying vibrational motions attributable to specific functional groups, we characterized fossilized biopolymers in 3.5–3.3 Ga microbial mats from the Barberton greenstone belt (South Africa). Microbial mats from four Palaeoarchaean horizons exhibit significant differences in taxonomically informative aliphatic contents, despite high aromaticity. This reflects precursor biological heterogeneity since all horizons show equally exceptional preservation and underwent similar grades of metamorphism. Low methylene to end‐methyl (CH2/CH3) absorbance ratios in mats from the 3.472 Ga Middle Marker horizon signify short, highly branched n‐alkanes interpreted as isoprenoid chains forming archaeal membranes. Mats from the 3.45 Ga Hooggenoeg Chert H5c, 3.334 Ga Footbridge Chert, and 3.33 Ga Josefsdal Chert exhibit higher CH2/CH3 ratios suggesting mostly longer, unbranched fatty acids from bacterial lipid precursors. Absorbance ratios of end‐methyl to methylene (CH3/CH2) in Hooggenoeg, Josefsdal and Footbridge mats yield a range of values (0.20–0.80) suggesting mixed bacterial and archaeal architect communities based on comparison with modern examples. Higher (0.78–1.25) CH3/CH2 ratios in the Middle Marker mats identify Archaea. This exceptional preservation reflects early, rapid silicification preventing the alteration of biogeochemical signals inherited from biomass. Since silicification commenced during the lifetime of the microbial mat, FTIR signals estimate the affinities of the architect community and may be used in the reconstruction of Archaean ecosystems. Together, these results show that Bacteria and Archaea flourished together in Earth's earliest ecosystems. [ABSTRACT FROM AUTHOR]

The exploration of Mars is largely based on comparisons with Earth analog environments and processes. The up-coming NASA Mars mission 2020 and ExoMars 2020 has the explicit aim to search for signs of life on Mars. During preparations for the missions, glaring gaps in one specific field was pointed out: the lack of a fossil record in igneous and volcanic rock. Earth’s fossil record is almost exclusively based on findings in sedimentary rocks, while igneous rocks have been considered barren of life, including a fossil record of past life. Since martian volcanic rocks will be targeted in the search for biosignatures, the lack of a terrestrial analog fossil record is an obvious impediment to the scientific aim of the mission. Here we will briefly review the knowledge of microscopic life in deep rock and deep time. Focus will be on underexplored environments in subseafloor crustal rocks, and on ancient environments harboring early prokaryotic and eukaryotic lineages. We will highlight some of the aspects that need immediate attention and further investigations to meet the scientific goals of the missions. The current paper is a first step toward the long-term aim to establish an atlas of the fossil record in volcanic rocks, which can be of use for the up-coming space missions.

The formation of ooids and their use as a proxy to trace biogeochemical cycles have long been controversial. Here, we examined three beds of evaporite‐cemented ooids in the Qaidam Basin, including a layer of dolomitic ooids formed at 293 ± 4 kyr and cemented by gypsum at 266 ± 3 kyr, a layer of aragonitic ooids formed at 163 ± 1 kyr and cemented by halite at 111 ± 0.8 kyr, and another layer of aragonitic ooids formed at 38 ± 0.5 kyr and cemented by gypsum at 23 ± 0.3 kyr. The Raman spectra of organic extracts from these ooids indicate ubiquitous preservation of scytonemin, a unique cyanobacterial ultraviolet radiation (UVR)‐shielding pigment. This discovery suggests that ooids are capable of preserving biomarker from their depositional environment. Consequently, ooid may be used as a proxy for tracing biogeochemical processes and potentially applied to the search for life on Mars. Plain Language Summary: Following the later rise of the Tibetan Plateau, the Qaidam Basin to its north has developed an extremely dry climate and consequently a vast area of playas derived from salt lake deposits since the Pleistocene. From this sedimentary system similar to some observed on Mars, we discovered several outcrops of ooids cemented by evaporites in Pleistocene ages. All of these ooids preserve an ultraviolet radiation‐screening pigment, scytonemin, which can only be derived from indigenous photosynthetic cyanobacteria. The ability to preserve organic compounds from their depositional environments suggests that ooids may be a good proxy for tracing microbial activities in ancient salt lakes and potentially be a novel tool for seeking biosignatures on Mars. Key Points: Three carbonate ooids cemented by evaporites from playas in the Qaidam Basin were dated to be 38, 163, and 293 kyrCyanobacterial ultraviolet radiation‐shielding pigment scytonemin was detected in all ooid samplesOoids may provide a novel proxy to examine extremophiles in closed basins and help the search for life on Mars [ABSTRACT FROM AUTHOR]

In a randomized clinical trial (RCT), it is often of interest not only to estimate the effect of various treatments on the outcome, but also to determine whether any patient characteristic has a different relationship with the outcome, depending on treatment. In regression models for the outcome, if there is a non-zero interaction between treatment and a predictor, that predictor is called an "effect modifier". Identification of such effect modifiers is crucial as we move towards precision medicine, that is, optimizing individual treatment assignment based on patient measurements assessed when presenting for treatment. In most settings, there will be several baseline predictor variables that could potentially modify the treatment effects. This article proposes optimal methods of constructing a composite variable (defined as a linear combination of pre-treatment patient characteristics) in order to generate an effect modifier in an RCT setting. Several criteria are considered for generating effect modifiers and their performance is studied via simulations. An example from a RCT is provided for illustration. [ABSTRACT FROM AUTHOR]

Knowledge of paleo-redox conditions in the Earth's history provides a window into events that shaped the evolution of life on our planet. The role of microbial activity in paleo-redox processes remains unexplored due to the inability to discriminate biotic from abiotic redox transformations in the rock record. The ability to deconvolute these two processes would provide a means to identify environmental niches in which microbial activity was prevalent at a specific time in paleo-history and to correlate specific biogeochemical events with the corresponding microbial metabolism. Here, we demonstrate that the isotopic signature associated with microbial reduction of hexavalent uranium (U), i.e., the accumulation of the heavy isotope in the U(IV) phase, is readily distinguishable from that generated by abiotic uranium reduction in laboratory experiments. Thus, isotope signatures preserved in the geologic record through the reductive precipitation of uranium may provide the sought-after tool to probe for biotic processes. Because uranium is a common element in the Earth's crust and a wide variety of metabolic groups of microorganisms catalyze the biological reduction of U(VI), this tool is applicable to a multiplicity of geological epochs and terrestrial environments. The findings of this study indicate that biological activity contributed to the formation of many authigenic U deposits, including sandstone U deposits of various ages, as well as modern, Cretaceous, and Archean black shales. Additionally, engineered bioremediation activities also exhibit a biotic signature, suggesting that, although multiple pathways may be involved in the reduction, direct enzymatic reduction contributes substantially to the immobilization of uranium. [ABSTRACT FROM AUTHOR]

The past decade has seen an explosion of new technologies for assessment of biogenicity and syngeneity of carbonaceous material within sedimentary rocks. Advances have been made in techniques for analysis of in situ organic matter as well as for extracted bulk samples of soluble and insoluble (kerogen) organic fractions. The in situ techniques allow analysis of micrometer-to-sub-micrometer-scale organic residues within their host rocks and include Raman and fluorescence spectroscopy/imagery, confocal laser scanning microscopy, and forms of secondary ion/laser-based mass spectrometry, analytical transmission electron microscopy, and X-ray absorption microscopy/spectroscopy. Analyses can be made for chemical, molecular, and isotopic composition coupled with assessment of spatial relationships to surrounding minerals, veins, and fractures. The bulk analyses include improved methods for minimizing contamination and recognizing syngenetic constituents of soluble organic fractions as well as enhanced spectroscopic and pyrolytic techniques for unlocking syngenetic molecular signatures in kerogen. Together, these technologies provide vital tools for the study of some of the oldest and problematic carbonaceous residues and for advancing our understanding of the earliest stages of biological evolution on Earth and the search for evidence of life beyond Earth. We discuss each of these new technologies, emphasizing their advantages and disadvantages, applications, and likely future directions. [ABSTRACT FROM AUTHOR]

The 3.45-billion-year-old Strelley Pool Formation of Western Australia preserves stromatolites that are considered among the oldest evidence for life on Earth. In places of exceptional preservation, these stromatolites contain laminae rich in organic carbon, interpreted as the fossil remains of ancient microbial mats. To better understand the biogeochemistry of these rocks, we performed microscale in situ sulfur isotope measurements of the preserved organic sulfur, including both Δ33S and &delta34SCDT. This approach allows us to tie physiological inference from isotope ratios directly to fossil biomass, providing a means to understand sulfur metabolism that is complimentary to, and independent from, inorganic proxies (e.g., pyrite). Δ33S values of the kerogen reveal mass-anomalous fractionations expected of the Archean sulfur cycle, whereas &delta34SCDT values show large fractionations at very small spatial scales, including values below -15‰. We interpret these isotopic patterns as recording the process of sulf urization of organic matter by H2S in heterogeneous mat pore-waters influenced by respiratory S metabolism. Positive Δ33S anomalies suggest that dispro-portionation of elemental sulfur would have been a prominent microbial process in these communities. [ABSTRACT FROM AUTHOR]

Raman spectroscopy has proven to be a very effective approach for the detection of microorganisms colonising hostile environments on Earth. The ExoMars rover, due for launch in 2018, will carry a Raman laser spectrometer to analyse samples of the martian subsurface collected by the probe's 2-m drill in a search for similar biosignatures. The martian surface is unprotected from the flux of cosmic rays, an ionising radiation field that will degrade organic molecules and so diminish and distort the detectable Raman signature of potential martian microbial life. This study employs Raman spectroscopy to analyse samples of two model organisms, the cyanobacterium Synechocystis sp. PCC 6803 and the extremely radiation resistant polyextremophile Deinococcus radiodurans, that have been exposed to increasing doses of ionising radiation. The three most prominent peaks in the Raman spectra are from cellular carotenoids: deinoxanthin in D. radiodurans and β-carotene in Synechocystis. The degradative effect of ionising radiation is clearly seen, with significant diminishment of carotenoid spectral peak heights after 15 kGy and complete erasure of Raman biosignatures by 150 kGy of ionising radiation. The Raman signal of carotenoid in D. radiodurans diminishes more rapidly than that of Synechocystis, believed to be due to deinoxanthin acting as a superior scavenger of radiolytically produced reactive oxygen species, and so being destroyed more quickly than the less efficient antioxidant β-carotene. This study highlights the necessity for further experimental work on the manner and rate of degradation of Raman biosignatures by ionising radiation, as this is of prime importance for the successful detection of microbial life in the martian near subsurface. [ABSTRACT FROM AUTHOR]

The ability to rapidly detect changes in bone mineral balance (BMB) would be of great value in the early diagnosis and evaluation of therapies for metabolic bone diseases such as osteoporosis and some cancers. However, measurements of BMB are hampered by difficulties with using biochemical markers to quantify the relative rates of bone resorption and formation and the need to wait months to years for altered BMB to produce changes in bone mineral density large enough to resolve by X-ray densitometry. We show here that, in humans, the natural abundances of Ca isotopes in urine change rapidly in response to changes in BMB. In a bed rest experiment, use of high-precision isotope ratio MS allowed the onset of bone loss to be detected in Ca isotope data after about 1 wk, long before bone mineral density has changed enough to be detectable with densitometry. The physiological basis of the relationship between Ca isotopes and BMB is sufficiently understood to allow quantitative translation of changes in Ca isotope abundances to changes in bone mineral density using a simple model. The rate of change of bone mineral density inferred from Ca isotopes is consistent with the rate observed by densitometry in long-term bed rest studies. Ca isotopic analysis provides a powerful way to monitor bone loss, potentially making it possible to diagnose metabolic bone disease and track the impact of treatments more effectively than is currently possible. [ABSTRACT FROM AUTHOR]

We report silician magnetite from banded iron formation (BIF) in the Dales Gorge Member of the Brockman Iron Formation, Hamersley Group, Western Australia. Magnetite mesobands typically consisting of individual ~100 µm micro laminae are revealed to be composed of silician magnetite overgrowths on magnetite. Silician magnetite overgrowths contain from 1 to 3 wt% SiO2, whereas (low-Si) magnetite domains contain less than 1 wt% SiO2. Silicon solid solution is present in the magnetite crystal lattice as determined by in situ micro-X-ray diffraction and high-resolution transmission electron microscopy. Three textures are distinguished in magnetite mesobands: (1) magnetite sub-microlaminae with silician magnetite overgrowths, (2) recrystallized magnetite fragments with silician magnetite overgrowths, and (3) a complex intergrowth of magnetite and silician magnetite. All three textures are found in magnetite mesobands from the BIF4-5 and BIF12-16 macrobands of the Dales Gorge type-section drill core DDH-47A from Wittenoom, Western Australia. Magnetite domains contain numerous submicrometer- to-micrometer inclusions of quartz, carbonate, stilpnomelane, and apatite, whereas silician magnetite overgrowths are devoid of mineral inclusions. The presence of mineral inclusions in magnetite indicates the BIF oxide precipitate was not chemically pure iron oxyhydroxide/oxide. Magnetite domains display textures formed during soft sediment deformation that are the earliest and best preserved relict sedimentary structures in this BIF. Silician magnetite is the dominant iron oxide in the Dales Gorge BIF and is present in many other sub-greenschist facies BIFs worldwide. We suggest the former presence of organic matter creates reducing conditions necessary to stabilize silician magnetite. Thus, silician magnetite is a potential biosignature in BIFs. [ABSTRACT FROM AUTHOR]

With the discovery of Na-sulphate minerals on Mars and Europa, recent studies using these minerals have focused on their ability to assist in the detection of bio/organic signatures. This study further investigates the ability of thenardite (Na2SO4) to effectively facilitate the ionization and identification of aromatic amino acids (phenylalanine, tyrosine and tryptophan) using a technique called geomatrix-assisted laser desorption/ionization in conjunction with a Fourier transform ion cyclotron resonance mass spectrometry. This technique is based on the ability of a mineral host to facilitate desorption and ionization of bio/organic molecules for detection. Spectra obtained from each aromatic amino acid alone and in combination with thenardite show differences in ionization mechanism and fragmentation patterns. These differences are due to chemical and structural differences between the aromatic side chains of their respective amino acid. Tyrosine and tryptophan when combined with thenardite were observed to undergo cation-attachment ([M+Na]+), due to the high alkali ion affinity of their aromatic side chains. In addition, substitution of the carboxyl group hydrogen by sodium led to formation of [M-H+Na]Na+ peaks. In contrast, phenylalanine mixed with thenardite showed no evidence of Na+ attachment. Understanding how co-deposition of amino acids with thenardite can affect the observed mass spectra is important for future exploration missions that are likely to use laser desorption mass spectrometry to search for bio/organic compounds in extraterrestrial environments. [ABSTRACT FROM AUTHOR]