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1.  TAP-independent self-peptides enhance T cell recognition of immune-escaped tumors 
Tumor cells frequently escape from CD8+ T cell recognition by abrogating MHC-I antigen presentation. Deficiency in processing components, like the transporter associated with antigen processing (TAP), results in strongly decreased surface display of peptide/MHC-I complexes. We previously identified a class of hidden self-antigens known as T cell epitopes associated with impaired peptide processing (TEIPP), which emerge on tumor cells with such processing defects. In the present study, we analyzed thymus selection and peripheral behavior of T cells with specificity for the prototypic TEIPP antigen, the “self” TRH4 peptide/Db complex. TEIPP T cells were efficiently selected in the thymus, egressed with a naive phenotype, and could be exploited for immunotherapy against immune-escaped, TAP-deficient tumor cells expressing low levels of MHC-I (MHC-Ilo). In contrast, overt thymus deletion and functionally impaired TEIPP T cells were observed in mice deficient for TAP1 due to TEIPP antigen presentation on all body cells in these mice. Our results strongly support the concept that TEIPPs derive from ubiquitous, nonmutated self-antigens and constitute a class of immunogenic neoantigens that are unmasked during tumor immune evasion. These data suggest that TEIPP-specific CD8+ T cells are promising candidates in the treatment of tumors that have escaped from conventional immunotherapies.
PMCID: PMC4731191  PMID: 26784543
2.  Enhanced flight performance by genetic manipulation of wing shape in Drosophila 
Nature Communications  2016;7:10851.
Insect wing shapes are remarkably diverse and the combination of shape and kinematics determines both aerial capabilities and power requirements. However, the contribution of any specific morphological feature to performance is not known. Using targeted RNA interference to modify wing shape far beyond the natural variation found within the population of a single species, we show a direct effect on flight performance that can be explained by physical modelling of the novel wing geometry. Our data show that altering the expression of a single gene can significantly enhance aerial agility and that the Drosophila wing shape is not, therefore, optimized for certain flight performance characteristics that are known to be important. Our technique points in a new direction for experiments on the evolution of performance specialities in animals.
Insect wings are under multiple competing selection pressures, but which are important in natural populations is not clear. Using RNAi to modify wing shape, Ray et al. show that aerial agility can be significantly enhanced in Drosophila, suggesting that natural variation does not reflect an optimization solely for flight agility.
PMCID: PMC4773512  PMID: 26926954
3.  Sunitinib in patients with chemotherapy-refractory thymoma and thymic carcinoma: an open-label phase 2 trial 
The Lancet. Oncology  2015;16(2):177-186.
No standard treatments are available for advanced thymic epithelial tumours after failure of platinum-based chemotherapy. We investigated the activity of sunitinib, an orally administered tyrosine kinase inhibitor.
Between May 15, 2012, and Oct 2, 2013, we did an open-label phase 2 trial in patients with histologically confirmed chemotherapy-refractory thymic epithelial tumours. Patients were eligible if they had disease progression after at least one previous regimen of platinum-containing chemotherapy, an Eastern Cooperative Oncology Group performance status of two or lower, measurable disease, and adequate organ function. Patients received 50 mg of sunitinib orally once a day, in 6-week cycles (ie, 4 weeks of treatment followed by 2 weeks without treatment), until tumour progression or unacceptable toxic effects arose. The primary endpoint was investigator-assessed best tumour response at any point, which we analysed separately in thymoma and thymic carcinoma cohorts. Patients who had received at least one cycle of treatment and had their disease reassessed were included in the analyses of response. The trial was registered with, number NCT01621568.
41 patients were enrolled, 25 with thymic carcinoma and 16 with thymoma. One patient with thymic carcinoma was deemed ineligible after enrolment and did not receive protocol treatment. Of patients who received treatment, one individual with thymic carcinoma was not assessable because she died. Median follow-up on trial was 17 months (IQR 14·0–18·4). Of 23 assessable patients with thymic carcinoma, six (26%, 90% CI 12·1–45·3, 95% CI 10·2–48·4) had partial responses, 15 (65%, 95% CI 42·7–83·6) achieved stable disease, and two (9%, 1·1–28·0) had progressive disease. Of 16 patients with thymoma, one (6%, 95% CI 0·2–30·2) had a partial response, 12 (75%, 47·6–92·7) had stable disease, and three (19%, 4·1–45·7) had progressive disease. The most common grade 3 and 4 treatment-related adverse events were lymphocytopenia (eight [20%] of 40 patients), fatigue (eight [20%]), and oral mucositis (eight [20%]). Five (13%) patients had decreases in left-ventricular ejection fraction, of which three (8%) were grade 3 events. Three (8%) patients died during treatment, including one individual who died of cardiac arrest that was possibly treatment-related.
Sunitinib is active in previously treated patients with thymic carcinoma. Further studies are needed to identify potential biomarkers of activity.
National Cancer Institute (Cancer Therapy Evaluation Program).
PMCID: PMC4401497  PMID: 25592632
4.  Quality of Life in Major Depressive Disorder Before/After Multiple Steps of Treatment and One-year Follow-up 
Acta psychiatrica Scandinavica  2014;131(1):51-60.
This study examines the impact of Major Depressive Disorder (MDD) and its treatment on Quality of Life (QOL).
From the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) trial, we analyzed complete data of 2,280 adult MDD outpatients at entry/exit of each level of antidepressant treatments and after 12-months of entry to follow-up. QOL was measured using the Quality of Life Enjoyment and Satisfaction Questionnaire (Q-LES-Q). The proportions of patients scoring ‘within-normal’ QOL (within 10% of Q-LES-Q community-norms) and those with ‘severely-impaired’ QOL (>2SD below Q-LES-Q community-norms) were analyzed.
Before treatment, no more than 3% of MDD patients experienced ‘within-normal’ QOL. Following treatment, statistically significant improvements were detected, however the proportion of patients achieving ‘within-normal’ QOL did not exceed 30%, with>50% of patients experiencing ‘severely-impaired’ QOL. Although remitted-patients had greater improvements compared to non-remitters, 32%-60% continued to experience reduced QOL. 12-month follow-up data revealed that the proportion of patients experiencing ‘within-normal’ QOL show a statistically significant decrease in non-remitters.
Symptom-focused treatments of MDD may leave a misleading impression that patients have recovered when, in fact, they may be experiencing ongoing QOL deficits. These findings point to the need for investigating specific interventions to ameliorate QOL in MDD.
PMCID: PMC4267902  PMID: 24954156
Quality of Life; Major Depression; Antidepressants; Functional Outcomes; Patient-reported outcomes
5.  Altered Connexin 43 and Connexin 45 Protein Expression in the Heart as a Function of Social and Environmental Stress in the Prairie Vole 
Stress (Amsterdam, Netherlands)  2014;18(1):107-114.
Exposure to social and environmental stressors may influence behavior as well as autonomic and cardiovascular regulation, potentially leading to depressive disorders and cardiac dysfunction including elevated sympathetic drive, reduced parasympathetic function, and ventricular arrhythmias. The cellular mechanisms that underlie these interactions are not well understood. One mechanism may involve alterations in the expression of Connexin43 (Cx43) and Connexin45 (Cx45), gap junction proteins in the heart that play an important role in ensuring efficient cell-to-cell coupling and the maintenance of cardiac rhythmicity. The present study investigated the hypothesis that long-term social isolation, combined with mild environmental stressors, would produce both depressive behaviors and altered Cx43 and Cx45 expression in the left ventricle of prairie voles – a socially monogamous rodent model. Adult, female prairie voles were exposed to either social isolation (n=22) or control (paired, n=23) conditions (4 weeks), alone or in combination with chronic mild stress (1 week). Social isolation, versus paired control conditions, produced significantly (P < 0.05) increased depressive behaviors in a 5-min forced swim test, and chronic mild stress exacerbated (P < 0.05) these behaviors. Social isolation (alone) reduced (P < 0.05) total Cx43 expression in the left ventricle; whereas chronic mild stress (but not isolation) increased (P < 0.05) total Cx45 expression and reduced (P < 0.05) the Cx43/Cx45 ratio, measured via Western blot analysis. The present findings provide insight into potential cellular mechanisms underlying altered cardiac rhythmicity associated with social and environmental stress in the prairie vole.
PMCID: PMC4675659  PMID: 25338193
cardiac arrhythmic susceptibility; chronic mild stress; connexins; depression; microtus; social isolation
6.  Affect and Cognition in Attitude Formation toward Familiar and Unfamiliar Attitude Objects 
PLoS ONE  2015;10(10):e0141790.
At large attitudes are built on earlier experience with the attitude object. If earlier experiences are not available, as is the case for unfamiliar attitude objects such as new technologies, no stored evaluations exist. Yet, people are still somehow able to construct attitudes on the spot. Depending on the familiarity of the attitude object, attitudes may find their basis more in affect or cognition. The current paper investigates differences in reliance on affect or cognition in attitude formation toward familiar and unfamiliar realistic attitude objects. In addition, individual differences in reliance on affect (high faith in intuition) or cognition (high need for cognition) are taken into account. In an experimental survey among Dutch consumers (N = 1870), we show that, for unfamiliar realistic attitude objects, people rely more on affect than cognition. For familiar attitude objects where both affective and cognitive evaluations are available, high need for cognition leads to more reliance on cognition, and high faith in intuition leads to more reliance on affect, reflecting the influence of individually preferred thinking style. For people with high need for cognition, cognition has a higher influence on overall attitude for both familiar and unfamiliar realistic attitude objects. On the other hand, affect is important for people with high faith in intuition for both familiar and unfamiliar attitude objects and for people with low faith in intuition for unfamiliar attitude objects; this shows that preferred thinking style is less influential for unfamiliar objects. By comparing attitude formation for familiar and unfamiliar realistic attitude objects, this research contributes to understanding situations in which affect or cognition is the better predictor of overall attitudes.
PMCID: PMC4627771  PMID: 26517876
7.  DNA cytosine methylation and hydroxymethylation at the borders 
Epigenomics  2014;6(6):563-566.
PMCID: PMC4321890  PMID: 25531248
5-hydroxymethylcytosine; 5-methylcytosine; chromatin; enhancers; promoters; RNA splicing
8.  Organ specific optical imaging of mitochondrial redox state in a rodent model of hereditary hemorrhagic tel-angiectasia-1 
Journal of biophotonics  2013;7(10):799-809.
Hereditary Hemorrhagic Telangiectasia-1 (HHT-1) is a vascular disease caused by mutations in the endoglin (Eng)/CD105 gene. The objective of this study was to quantify the oxidative state of a rodent model of HHT-1 using an optical imaging technique. We used a cryofluorescence imaging instrument to quantitatively assess tissue metabolism in this model. Mitochondrial redox ratio (FAD/NADH), FAD RR, was used as a quantitative marker of the metabolic status and was examined in the kidneys, and eyes of wild-type and Eng +/− mice. Kidneys and eyes from wild-type P21, 6W, and 10M old mice showed, respectively, a 9% (±2), 24% (±0.4), 15% (±1), and 23% (±4), 33% (±0.6), and 30% (±2) change in the mean FAD RR compared to Eng +/−mice at the same age. Thus, endoglin haploinsufficiency is associated with less oxidative stress in various organs and mitigation of angiogenesis.
Images of FAD for one representative eye (10 months, Eng+/−). Left: volume rendering of half of the eye (with connected optic nerve) including the lens. Right: volume rendering of the eye excluding the lens.
PMCID: PMC4324470  PMID: 23740865
Optical imaging; NADH; FAD; redox ratio; Endoglin; Hereditary Hemorrhagic Telangiectasia-1; oxygen-induced ischemic retinopathy; oxidative stress
11.  Short- and long-term associations between widowhood and mortality in the United States: longitudinal analyses 
Past research shows that spousal death results in elevated mortality risk for the surviving spouse. However, most prior studies have inadequately controlled for socioeconomic status (SES), and it is unclear whether this ‘widowhood effect’ persists over time.
Health and Retirement Study participants aged 50+ years and married in 1998 (n = 12 316) were followed through 2008 for widowhood status and mortality (2912 deaths). Discrete-time survival analysis was used to compare mortality for the widowed versus the married.
Odds of mortality during the first 3 months post-widowhood were significantly higher than in the continuously married (odds ratio (OR) for men = 1.87, 95% CI: 1.27, 2.75; OR for women = 1.47, 95% CI: 0.96, 2.24) in models adjusted for age, gender, race and baseline SES (education, household wealth and household income), behavioral risk factors and co-morbidities. Twelve months following bereavement, men experienced borderline elevated mortality (OR = 1.16, 95% CI: 1.00, 1.35), whereas women did not (OR = 1.07, 95% CI: 0.90, 1.28), though the gender difference was non-significant.
The ‘widowhood effect’ was not fully explained by adjusting for pre-widowhood SES and particularly elevated within the first few months after widowhood. These associations did not differ by sex.
PMCID: PMC4181424  PMID: 24167198
widowhood; spousal loss; mortality; longitudinal studies; socioeconomic status
12.  Targeted Local Support Vector Machine for Age-Dependent Classification 
We develop methods to accurately predict whether pre-symptomatic individuals are at risk of a disease based on their various marker profiles, which offers an opportunity for early intervention well before definitive clinical diagnosis. For many diseases, existing clinical literature may suggest the risk of disease varies with some markers of biological and etiological importance, for example age. To identify effective prediction rules using nonparametric decision functions, standard statistical learning approaches treat markers with clear biological importance (e.g., age) and other markers without prior knowledge on disease etiology interchangeably as input variables. Therefore, these approaches may be inadequate in singling out and preserving the effects from the biologically important variables, especially in the presence of potential noise markers. Using age as an example of a salient marker to receive special care in the analysis, we propose a local smoothing large margin classifier implemented with support vector machine (SVM) to construct effective age-dependent classification rules. The method adaptively adjusts age effect and separately tunes age and other markers to achieve optimal performance. We derive the asymptotic risk bound of the local smoothing SVM, and perform extensive simulation studies to compare with standard approaches. We apply the proposed method to two studies of premanifest Huntington’s disease (HD) subjects and controls to construct age-sensitive predictive scores for the risk of HD and risk of receiving HD diagnosis during the study period.
PMCID: PMC4183366  PMID: 25284918
Statistical learning; Local smoothing; Reproducing kernel Hilbert space; Risk bound; Huntington’s disease
13.  Acid detergent lignin, lodging resistance index, and expression of the caffeic acid O-methyltransferase gene in brown midrib-12 sudangrass 
Breeding Science  2015;65(4):291-297.
Understanding the relationship between acid detergent lignin (ADL) and lodging resistance index (LRI) is essential for breeding new varieties of brown midrib (bmr) sudangrass (Sorghum sudanense (Piper) Stapf.). In this study, bmr-12 near isogenic lines and their wild-types obtained by back cross breeding were used to compare relevant forage yield and quality traits, and to analyze expression of the caffeic acid O-methyltransferase (COMT) gene using quantitative real time-PCR. The research showed that the mean ADL content of bmr-12 mutants (20.94 g kg−1) was significantly (P < 0.05) lower than measured in N-12 lines (43.45 g kg−1), whereas the LRI of bmr-12 mutants (0.29) was significantly (P < 0.05) higher than in N-12 lines (0.22). There was no significant correlation between the two indexes in bmr-12 materials (r = −0.44, P > 0.05). Sequence comparison of the COMT gene revealed two point mutations present in bmr-12 but not in the wild-type, the second mutation changed amino acid 129 of the protein from Gln (CAG) to a stop codon (UAG). The relative expression level of COMT gene was significantly reduced, which likely led to the decreased ADL content observed in the bmr-12 mutant.
PMCID: PMC4542929  PMID: 26366111
acid detergent lignin; brown midrib; dry matter; lodging resistance index; sudangrass
14.  Genetic variation for maize root architecture in response to drought stress at the seedling stage 
Breeding Science  2015;65(4):298-307.
Although the root system is indispensable for absorption of nutrients and water, it is poorly studied in maize owing to the difficulties of direct measurement of roots. Here, 103 maize lines were used to compare root architectures under well-watered and water-stressed conditions. Significant genetic variation, with medium to high heritability and significant correlations, was observed for root traits. Total root length (TRL) and total root surface area (TSA) had high phenotypical diversity, and TRL was positively correlated with TSA, root volume, and root forks. The first two principal components explained 94.01% and 91.15% of total root variation in well-watered and water-stressed conditions, respectively. Thus, TRL and TSA, major contributors to root variation, can be used as favorable selection criteria at the seedling stage. We found that stiff stalk and non-stiff stalk groups (temperate backgrounds) showed relatively higher mean values for root morphological diversity than the TST group (tropical/subtropical background). Of the tested lines, 7, 42, 45, and 9 were classified as drought sensitive, moderately sensitive, moderately drought tolerant, and highly drought tolerant, respectively. Seven of the 9 extremely drought tolerant lines were from the TST group, suggesting that TST germplasms harbor valuable genetic resources for drought tolerance that could be used in breeding to improve abiotic stress tolerance in maize.
PMCID: PMC4542930  PMID: 26366112
maize; drought tolerance; root system; heterotic groups
15.  Interaction of Polymorphisms in Mitotic Regulator Genes With Cigarette Smoking and Pancreatic Cancer Risk 
Molecular carcinogenesis  2013;52(0 1):E103-E109.
Mitotic regulator genes have been associated with several cancers, however little is known about their possible association with pancreatic cancer. Smoking and family history are the strongest risk factors for this highly fatal disease. The main purpose of this study was to determine if polymorphisms of mitotic regulator genes are associated with pancreatic cancer and whether they modify the association between cigarette smoking and pancreatic cancer risk. A population-based case-control study was conducted in Ontario with 455 pathology-confirmed pancreatic cancer cases and 893 controls. Cigarette smoking history was collected using questionnaires and DNA obtained from blood samples. Genotypes were determined by mass-spectrometry. Odds ratio estimates were obtained using multivariate logistic regression. Interactions between genetic variant and smoking were assessed using stratified analyses and the likelihood ratio statistic (significance P < 0.05). Variants of MCPH1, FYN, APC, PRKCA, NIN, TopBP1, RIPK1, and SNW1 were not independently associated with pancreatic cancer risk. A significant interaction was observed between pack-years and MCPH1-2550-C > T (P = 0.02). Compared to never smokers, individuals with 10–27 pack-years and MCPH1-2550-CC genotype were at increased risk for pancreatic cancer (MVOR = 2.49, 95% confidence interval [95% CI]: 1.55, 4.00) as were those with >27 pack-years and MCPH1-2550-TC genotype (MVOR = 2.42, 95% CI: 1.45, 4.05). A significant interaction was observed between smoking status and TopBP1-3257-A > G (P = 0.04) using a dominant model. Current smokers with the TopBP1-3257 A allele were at increased risk for pancreatic cancer (MVOR = 2.55, 95% CI: 1.77, 3.67). MCPH1-2550-C > T and TopBP1-3257-A > G modify the association between smoking and pancreatic cancer. These findings provide insights into the potential molecular mechanisms behind smoking-associated pancreatic cancer.
PMCID: PMC4533929  PMID: 23908141
pancreatic neoplasms; smoking; polymorphism; single nucleotide; mitosis; case-control studies
16.  Introducing a New Stratospheric Dust-Collecting System with Potential Use for Upper Atmospheric Microbiology Investigations 
Astrobiology  2014;14(8):694-705.
The stratosphere is a known host to terrestrial microbes of most major biological lineages, but it is also host to incoming meteoric dust. Our goal is to (1) introduce DUSTER (Dust in the Upper Stratosphere Tracking Experiment and Retrieval), an active collector for the nondestructive collection of nano- to micrometer particles in the stratosphere between 30 and 40 km altitude, and (2) demonstrate that even a single particle can be collected free of resident atmospheric and laboratory contaminant particles. DUSTER improves the pervasive and persistent contamination problem in the field of aerobiology research. Here, we demonstrate the collector's advances by the identification of a (terrestrial) spore particle found among a population of nanometer-scale inorganic meteoric particles. This was possible because the size, shape, morphology, and chemical composition of each particle can be determined while still on the collector surface. Particles can be removed from DUSTER for specific laboratory analyses. So far, DUSTER has not been fitted for aerobiological purposes; that is, no attempts were made to sterilize the collector other than with isopropyl alcohol. Its design and laboratory protocols, however, allow adjustments to dedicated aerobiological sampling opportunities. Key Words: Aerobiology—Upper stratosphere—Dust collector—Single particles—Sampling. Astrobiology 14, 694–705.
PMCID: PMC4126274  PMID: 25046407
17.  Characterization of Ancient DNA Supports Long-Term Survival of Haloarchaea 
Astrobiology  2014;14(7):553-560.
Bacteria and archaea isolated from crystals of halite 104 to 108 years old suggest long-term survival of halophilic microorganisms, but the results are controversial. Independent verification of the authenticity of reputed living prokaryotes in ancient salt is required because of the high potential for environmental and laboratory contamination. Low success rates of prokaryote cultivation from ancient halite, however, hamper direct replication experiments. In such cases, culture-independent approaches that use the polymerase chain reaction (PCR) and sequencing of 16S ribosomal DNA are a robust alternative. Here, we use amplification, cloning, and sequencing of 16S ribosomal DNA to investigate the authenticity of halophilic archaea cultured from subsurface halite, Death Valley, California, 22,000 to 34,000 years old. We recovered 16S ribosomal DNA sequences that are identical, or nearly so (>99%), to two strains, Natronomonas DV462A and Halorubrum DV427, which were previously isolated from the same halite interval. These results provide the best independent support to date for the long-term survival of halophilic archaea in ancient halite. PCR-based approaches are sensitive to small amounts of DNA and could allow investigation of even older halites, 106 to 108 years old, from which microbial cultures have been reported. Such studies of microbial life in ancient salt are particularly important as we search for microbial signatures in similar deposits on Mars and elsewhere in the Solar System. Key Words: Ancient DNA—Halite—Haloarchaea—Long-term survival. Astrobiology 14, 553–560.
PMCID: PMC4094027  PMID: 24977469
18.  Chance and Necessity in Biochemistry: Implications for the Search for Extraterrestrial Biomarkers in Earth-like Environments 
Astrobiology  2014;14(6):534-540.
In this paper, we examine a restricted subset of the question of possible alien biochemistries. That is, we look into how different life might be if it emerged in environments similar to that required for life on Earth. We advocate a principle of chance and necessity in biochemistry. According to this principle, biochemistry is in some fundamental way the sum of two processes: there is an aspect of biochemistry that is an endowment from prebiotic processes, which represents the necessity, plus an aspect that is invented by the process of evolution, which represents the chance. As a result, we predict that life originating in extraterrestrial Earth-like environments will share biochemical motifs that can be traced back to the prebiotic world but will also have intrinsic biochemical traits that are unlikely to be duplicated elsewhere as they are combinatorially path-dependent. Effective and objective strategies to search for biomarkers, and evidence for a second genesis, on planets with Earth-like environments can be built based on this principle. Key Words: Origin of life—Biomarkers—Exobiology—Extraterrestrial life—Prebiotic chemistry. Astrobiology 14, 534–540.
PMCID: PMC4060776  PMID: 24867145
19.  Self-Assembly of Phosphate Amphiphiles in Mixtures of Prebiotically Plausible Surfactants 
Astrobiology  2014;14(6):462-472.
The spontaneous formation of closed bilayer structures from prebiotically plausible amphiphiles is an essential requirement for the emergence of early cells on prebiotic Earth. The sources of amphiphiles could have been both endo- and exogenous (accretion of meteorite carbonaceous material or interstellar dust particles). Among all prebiotic possible amphiphile candidates, those containing phosphate are the least investigated species because their self-assembly occurs in a seemingly too narrow range of conditions. The self-assembly of simple phosphate amphiphiles should, however, be of great interest, as contemporary membranes predominantly contain phospholipids. In contrast to common expectations, we show that these amphiphiles can be easily synthesized under prebiotically plausible environmental conditions and can efficiently form bilayer structures in the presence of various co-surfactants across a large range of pH values. Vesiculation was even observed in crude reaction mixtures that contained 1-decanol as the amphiphile precursor. The two best co-surfactants promoted vesicle formation over the entire pH range in aqueous solutions. Expanding the pH range where bilayer membranes self-assemble and remain intact is a prerequisite for the emergence of early cell-like compartments and their preservation under fluctuating environmental conditions. These mixed bilayers also retained small charged solutes, such as dyes. These results demonstrate that alkyl phosphate amphiphiles might have played a significant role as early compartment building blocks. Key Words: Vesicles—Alkyl phosphate—Prebiotic synthesis—Amphiphile mixtures. Astrobiology 14, 462–472.
PMCID: PMC4060816  PMID: 24885934
20.  Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs 
Astrobiology  2014;14(6):502-521.
The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521.
PMCID: PMC4060779  PMID: 24886100
21.  Data Management in Astrobiology: Challenges and Opportunities for an Interdisciplinary Community 
Astrobiology  2014;14(6):451-461.
Data management and sharing are growing concerns for scientists and funding organizations throughout the world. Funding organizations are implementing requirements for data management plans, while scientists are establishing new infrastructures for data sharing. One of the difficulties is sharing data among a diverse set of research disciplines. Astrobiology is a unique community of researchers, containing over 110 different disciplines. The current study reports the results of a survey of data management practices among scientists involved in the astrobiology community and the NASA Astrobiology Institute (NAI) in particular. The survey was administered over a 2-month period in the first half of 2013. Fifteen percent of the NAI community responded (n=114), and additional (n=80) responses were collected from members of an astrobiology Listserv. The results of the survey show that the astrobiology community shares many of the same concerns for data sharing as other groups. The benefits of data sharing are acknowledged by many respondents, but barriers to data sharing remain, including lack of acknowledgement, citation, time, and institutional rewards. Overcoming technical, institutional, and social barriers to data sharing will be a challenge into the future. Key Words: Data management—Data sharing—Data preservation. Astrobiology 14, 451–461.
PMCID: PMC4060838  PMID: 24840364
22.  Nonphotosynthetic Pigments as Potential Biosignatures 
Astrobiology  2015;15(5):341-361.
Previous work on possible surface reflectance biosignatures for Earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on Earth, such as the vegetation red edge. Although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. We present an interdisciplinary study of the diversity and detectability of nonphotosynthetic pigments as biosignatures, which includes a description of environments that host nonphotosynthetic biologically pigmented surfaces, and a lab-based experimental analysis of the spectral and broadband color diversity of pigmented organisms on Earth. We test the utility of broadband color to distinguish between Earth-like planets with significant coverage of nonphotosynthetic pigments and those with photosynthetic or nonbiological surfaces, using both 1-D and 3-D spectral models. We demonstrate that, given sufficient surface coverage, nonphotosynthetic pigments could significantly impact the disk-averaged spectrum of a planet. However, we find that due to the possible diversity of organisms and environments, and the confounding effects of the atmosphere and clouds, determination of substantial coverage by biologically produced pigments would be difficult with broadband colors alone and would likely require spectrally resolved data. Key Words: Biosignatures—Exoplanets—Halophiles—Pigmentation—Reflectance spectroscopy—Spectral models. Astrobiology 15, 341–361.
PMCID: PMC4442567  PMID: 25941875
23.  The Production of Methane, Hydrogen, and Organic Compounds in Ultramafic-Hosted Hydrothermal Vents of the Mid-Atlantic Ridge 
Astrobiology  2015;15(5):381-399.
Both hydrogen and methane are consistently discharged in large quantities in hydrothermal fluids issued from ultramafic-hosted hydrothermal fields discovered along the Mid-Atlantic Ridge. Considering the vast number of these fields discovered or inferred, hydrothermal fluxes represent a significant input of H2 and CH4 to the ocean. Although there are lines of evidence of their abiogenic formation from stable C and H isotope results, laboratory experiments, and thermodynamic data, neither their origin nor the reaction pathways generating these gases have been fully constrained yet. Organic compounds detected in the fluids may also be derived from abiotic reactions. Although thermodynamics are favorable and extensive experimental work has been done on Fischer-Tropsch-type reactions, for instance, nothing is clear yet about their origin and formation mechanism from actual data. Since chemolithotrophic microbial communities commonly colonize hydrothermal vents, biogenic and thermogenic processes are likely to contribute to the production of H2, CH4, and other organic compounds. There seems to be a consensus toward a mixed origin (both sources and processes) that is consistent with the ambiguous nature of the isotopic data. But the question that remains is, to what proportions? More systematic experiments as well as integrated geochemical approaches are needed to disentangle hydrothermal geochemistry. This understanding is of prime importance considering the implications of hydrothermal H2, CH4, and organic compounds for the ocean global budget, global cycles, and the origin of life. Key Words: Hydrogen—Methane—Organics—MAR—Abiotic synthesis—Serpentinization—Ultramafic-hosted hydrothermal vents. Astrobiology 15, 381–399.
PMCID: PMC4442600  PMID: 25984920
24.  Impact of a High Magnetic Field on the Orientation of Gravitactic Unicellular Organisms—A Critical Consideration about the Application of Magnetic Fields to Mimic Functional Weightlessness 
Astrobiology  2014;14(3):205-215.
The gravity-dependent behavior of Paramecium biaurelia and Euglena gracilis have previously been studied on ground and in real microgravity. To validate whether high magnetic field exposure indeed provides a ground-based facility to mimic functional weightlessness, as has been suggested earlier, both cell types were observed during exposure in a strong homogeneous magnetic field (up to 30 T) and a strong magnetic field gradient. While swimming, Paramecium cells were aligned along the magnetic field lines; orientation of Euglena was perpendicular, demonstrating that the magnetic field determines the orientation and thus prevents the organisms from the random swimming known to occur in real microgravity. Exposing Astasia longa, a flagellate that is closely related to Euglena but lacks chloroplasts and the photoreceptor, as well as the chloroplast-free mutant E. gracilis 1F, to a high magnetic field revealed no reorientation to the perpendicular direction as in the case of wild-type E. gracilis, indicating the existence of an anisotropic structure (chloroplasts) that determines the direction of passive orientation. Immobilized Euglena and Paramecium cells could not be levitated even in the highest available magnetic field gradient as sedimentation persisted with little impact of the field on the sedimentation velocities. We conclude that magnetic fields are not suited as a microgravity simulation for gravitactic unicellular organisms due to the strong effect of the magnetic field itself, which masks the effects known from experiments in real microgravity. Key Words: Levitation—Microgravity—Gravitaxis—Gravikinesis—Gravity. Astrobiology 14, 205–215.
PMCID: PMC3952527  PMID: 24621307
25.  Sulfate Minerals: A Problem for the Detection of Organic Compounds on Mars? 
Astrobiology  2015;15(3):247-258.
The search for in situ organic matter on Mars involves encounters with minerals and requires an understanding of their influence on lander and rover experiments. Inorganic host materials can be helpful by aiding the preservation of organic compounds or unhelpful by causing the destruction of organic matter during thermal extraction steps. Perchlorates are recognized as confounding minerals for thermal degradation studies. On heating, perchlorates can decompose to produce oxygen, which then oxidizes organic matter. Other common minerals on Mars, such as sulfates, may also produce oxygen upon thermal decay, presenting an additional complication. Different sulfate species decompose within a large range of temperatures. We performed a series of experiments on a sample containing the ferric sulfate jarosite. The sulfate ions within jarosite break down from 500°C. Carbon dioxide detected during heating of the sample was attributed to oxidation of organic matter. A laboratory standard of ferric sulfate hydrate released sulfur dioxide from 550°C, and an oxygen peak was detected in the products. Calcium sulfate did not decompose below 1000°C. Oxygen released from sulfate minerals may have already affected organic compound detection during in situ thermal experiments on Mars missions. A combination of preliminary mineralogical analyses and suitably selected pyrolysis temperatures may increase future success in the search for past or present life on Mars. Key Words: Mars—Life detection—Geochemistry—Organic matter—Jarosite. Astrobiology 15, 247–258.
PMCID: PMC4363818  PMID: 25695727

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