Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites.

BACKGROUND: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth's ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen. METHODS: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort. RESULTS: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites. CONCLUSIONS: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders. Video abstract.

Healthcare Professional in the Loop (HPIL): Classification of Standard and Oral Cancer-Causing Anomalous Regions of Oral Cavity Using Textural Analysis Technique in Autofluorescence Imaging.

Oral mucosal lesions (OML) and oral potentially malignant disorders (OPMDs) have been identified as having the potential to transform into oral squamous cell carcinoma (OSCC). This research focuses on the human-in-the-loop-system named Healthcare Professionals in the Loop (HPIL) to support diagnosis through an advanced machine learning procedure. HPIL is a novel system approach based on the textural pattern of OML and OPMDs (anomalous regions) to differentiate them from standard regions of the oral cavity by using autofluorescence imaging. An innovative method based on pre-processing, e.g., the Deriche-Canny edge detector and circular Hough transform (CHT); a post-processing textural analysis approach using the gray-level co-occurrence matrix (GLCM); and a feature selection algorithm (linear discriminant analysis (LDA)), followed by k-nearest neighbor (KNN) to classify OPMDs and the standard region, is proposed in this paper. The accuracy, sensitivity, and specificity in differentiating between standard and anomalous regions of the oral cavity are 83%, 85%, and 84%, respectively. The performance evaluation was plotted through the receiver operating characteristics of periodontist diagnosis with the HPIL system and without the system. This method of classifying OML and OPMD areas may help the dental specialist to identify anomalous regions for performing their biopsies more efficiently to predict the histological diagnosis of epithelial dysplasia.

Impact of Simulated Martian Conditions on (Facultatively) Anaerobic Bacterial Strains from Different Mars Analogue Sites.

Five bacterial (facultatively) anaerobic strains, namely Buttiauxella sp. MASE-IM-9, Clostridium sp. MASE-IM-4, Halanaerobium sp. MASE-BB-1, Trichococcus sp. MASE-IM-5, and Yersinia intermedia MASE-LG-1 isolated from different extreme natural environments were subjected to Mars relevant environmental stress factors in the laboratory under controlled conditions. These stress factors encompassed low water activity, oxidizing compounds, and ionizing radiation. Stress tests were performed under permanently anoxic conditions. The survival rate after addition of sodium perchlorate (Na-perchlorate) was found to be species-specific. The inter-comparison of the five microorganisms revealed that Clostridium sp. MASE-IM-4 was the most sensitive strain (D10-value (15 min, NaClO4) = 0.6 M). The most tolerant microorganism was Trichococcus sp. MASE-IM-5 with a calculated D10-value (15 min, NaClO4) of 1.9 M. Cultivation in the presence of Na-perchlorate in Martian relevant concentrations up to 1 wt% led to the observation of chains of cells in all strains. Exposure to Na-perchlorate led to a lowering of the survival rate after desiccation. Consecutive exposure to desiccating conditions and ionizing radiation led to additive effects. Moreover, in a desiccated state, an enhanced radiation tolerance could be observed for the strains Clostridium sp. MASE-IM-4 and Trichococcus sp. MASE-IM-5. These data show that anaerobic microorganisms from Mars analogue environments can resist a variety of Martian-simulated stresses either individually or in combination. However, responses were species-specific and some Mars-simulated extremes killed certain organisms. Thus, although Martian stresses would be expected to act differentially on microorganisms, none of the expected extremes tested here and found on Mars prevent the growth of anaerobic microorganisms.

Microbial Markers Profile in Anaerobic Mars Analogue Environments Using the LDChip (Life Detector Chip) Antibody Microarray Core of the SOLID (Signs of Life Detector) Platform.

One of the main objectives for astrobiology is to unravel and explore the habitability of environments beyond Earth, paying special attention to Mars. If the combined environmental stress factors on Mars are compatible with life or if they were less harsh in the past, to investigate the traces of past or present life is critical to understand its potential habitability. Essential for this research is the characterization of Mars analogue environments on Earth through the development of techniques for biomarker detection in them. Biosensing techniques based on fluorescence sandwich microarray immunoassays (FSMI) have shown to be a powerful tool to detect biosignatures and depict the microbial profiles of different environments. In this study, we described the microbial biomarker profile of five anoxic Mars analogues sites using the Life Detector Chip (LDChip), an antibody microarray for multiple microbial marker detection. Furthermore, we contributed to new targets by developing a new 26-polyclonal antibodies microarray using crude extracts from anaerobic sampling sites, halophilic microorganisms, and anaerobic isolates obtained in the framework of the European Mars Analogues for Space Exploration (MASE) project. The new subset of antibodies was characterized and implemented into a microarray platform (MASE-Chip) for microbial marker searching in salty and anaerobic environments.

Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know?

To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.

Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic Organism Yersinia intermedia MASE-LG-1 to NaCl and MgSO4 at Identical Water Activity.

Growth in sodium chloride (NaCl) is known to induce stress in non-halophilic microorganisms leading to effects on the microbial metabolism and cell structure. Microorganisms have evolved a number of adaptations, both structural and metabolic, to counteract osmotic stress. These strategies are well-understood for organisms in NaCl-rich brines such as the accumulation of certain organic solutes (known as either compatible solutes or osmolytes). Less well studied are responses to ionic environments such as sulfate-rich brines which are prevalent on Earth but can also be found on Mars. In this paper, we investigated the global metabolic response of the anaerobic bacterium Yersinia intermedia MASE-LG-1 to osmotic salt stress induced by either magnesium sulfate (MgSO4) or NaCl at the same water activity (0.975). Using a non-targeted mass spectrometry approach, the intensity of hundreds of metabolites was measured. The compatible solutes L-asparagine and sucrose were found to be increased in both MgSO4 and NaCl compared to the control sample, suggesting a similar osmotic response to different ionic environments. We were able to demonstrate that Yersinia intermedia MASE-LG-1 accumulated a range of other compatible solutes. However, we also found the global metabolic responses, especially with regard to amino acid metabolism and carbohydrate metabolism, to be salt-specific, thus, suggesting ion-specific regulation of specific metabolic pathways.

Lack of correlation of desiccation and radiation tolerance in microorganisms from diverse extreme environments tested under anoxic conditions.

Four facultative anaerobic and two obligate anaerobic bacteria were isolated from extreme environments (deep subsurface halite mine, sulfidic anoxic spring, mineral-rich river) in the frame MASE (Mars Analogues for Space Exploration) project. The isolates were investigated under anoxic conditions for their survivability after desiccation up to 6 months and their tolerance to ionizing radiation up to 3000 Gy. The results indicated that tolerances to both stresses are strain-specific features. Yersinia intermedia MASE-LG-1 showed a high desiccation tolerance but its radiation tolerance was very low. The most radiation-tolerant strains were Buttiauxella sp. MASE-IM-9 and Halanaerobium sp. MASE-BB-1. In both cases, cultivable cells were detectable after an exposure to 3 kGy of ionizing radiation, but cells only survived desiccation for 90 and 30 days, respectively. Although a correlation between desiccation and ionizing radiation resistance has been hypothesized for some aerobic microorganisms, our data showed that there was no correlation between tolerance to desiccation and ionizing radiation, suggesting that the physiological basis of both forms of tolerances is not necessarily linked. In addition, these results indicated that facultative and obligate anaerobic organisms living in extreme environments possess varied species-specific tolerances to extremes.

Una mirada al pensamiento crítico en el proceso docente educativo de la educación superior / A look at critical thinking in the educational process of higher education

El desarrollo del pensamiento crítico en la educación superior adquiere particular importancia en la formación de los futuros profesionales, pues permite que los egresados se doten de competencias y capacidades que les favorezcan el análisis crítico de los problemas que se les presenten en su quehacer profesional y puedan brindar soluciones prácticas y efectivas. El presente artículo tiene como objetivo realizar una revisión bibliográfica actualizada acerca del tema desde la perspectiva del proceso enseñanza aprendizaje en la educación superior por su pertinencia en este nivel y su significación para la futura labor. Se ofrecen alternativas que les permitan a los docentes desarrollarlo en sus estudiantes.

The development of critical thinking in higher education takes on particular importance in the training of future professionals, since it allows graduates to equip themselves with competences and abilities that favor the critical analysis of the problems presented to them in their professional work and can provide practical and effective solutions. This article aims to carry out an updated bibliographic review about critical thinking from the perspective of the teaching learning process in higher education because of its relevance at this level and its significance for the future professional. Alternatives are offered that allow teachers to develop it in their students.

The responses of an anaerobic microorganism, Yersinia intermedia MASE-LG-1 to individual and combined simulated Martian stresses.

The limits of life of aerobic microorganisms are well understood, but the responses of anaerobic microorganisms to individual and combined extreme stressors are less well known. Motivated by an interest in understanding the survivability of anaerobic microorganisms under Martian conditions, we investigated the responses of a new isolate, Yersinia intermedia MASE-LG-1 to individual and combined stresses associated with the Martian surface. This organism belongs to an adaptable and persistent genus of anaerobic microorganisms found in many environments worldwide. The effects of desiccation, low pressure, ionizing radiation, varying temperature, osmotic pressure, and oxidizing chemical compounds were investigated. The strain showed a high tolerance to desiccation, with a decline of survivability by four orders of magnitude during a storage time of 85 days. Exposure to X-rays resulted in dose-dependent inactivation for exposure up to 600 Gy while applied doses above 750 Gy led to complete inactivation. The effects of the combination of desiccation and irradiation were additive and the survivability was influenced by the order in which they were imposed. Ionizing irradiation and subsequent desiccation was more deleterious than vice versa. By contrast, the presence of perchlorates was not found to significantly affect the survival of the Yersinia strain after ionizing radiation. These data show that the organism has the capacity to survive and grow in physical and chemical stresses, imposed individually or in combination that are associated with Martian environment. Eventually it lost its viability showing that many of the most adaptable anaerobic organisms on Earth would be killed on Mars today.

AstRoMap European Astrobiology Roadmap.

The European AstRoMap project (supported by the European Commission Seventh Framework Programme) surveyed the state of the art of astrobiology in Europe and beyond and produced the first European roadmap for astrobiology research. In the context of this roadmap, astrobiology is understood as the study of the origin, evolution, and distribution of life in the context of cosmic evolution; this includes habitability in the Solar System and beyond. The AstRoMap Roadmap identifies five research topics, specifies several key scientific objectives for each topic, and suggests ways to achieve all the objectives. The five AstRoMap Research Topics are • Research Topic 1: Origin and Evolution of Planetary Systems • Research Topic 2: Origins of Organic Compounds in Space • Research Topic 3: Rock-Water-Carbon Interactions, Organic Synthesis on Earth, and Steps to Life • Research Topic 4: Life and Habitability • Research Topic 5: Biosignatures as Facilitating Life Detection It is strongly recommended that steps be taken towards the definition and implementation of a European Astrobiology Platform (or Institute) to streamline and optimize the scientific return by using a coordinated infrastructure and funding system.

Multinuclear MR and multilevel data processing: an insight into morphologic assessment of in vivo knee articular cartilage.

RATIONALE AND OBJECTIVES: Quantitative assessment of knee articular cartilage (AC) morphology using magnetic resonance (MR) imaging requires an accurate segmentation and 3D reconstruction. However, automatic AC segmentation and 3D reconstruction from hydrogen-based MR images alone is challenging because of inhomogeneous intensities, shape irregularity, and low contrast existing in the cartilage region. Thus, the objective of this research was to provide an insight into morphologic assessment of AC using multilevel data processing of multinuclear ((23)Na and (1)H) MR knee images. MATERIALS AND METHODS: A dual-tuned ((23)Na and (1)H) radio-frequency coil with 1.5-T MR scanner is used to scan four human subjects using two separate MR pulse sequences for the respective sodium and proton imaging of the knee. Postprocessing is performed using customized routines written in MATLAB. MR data were fused to improve contrast of the cartilage region that is further used for automatic segmentation. Marching cubes algorithm is applied on the segmented AC slices for 3D volume rendering and volume is then calculated using the divergence theorem. RESULTS: Fusion of multinuclear MR images results in an improved contrast (factor >3) in the cartilage region. Sensitivity (80.21%) and specificity (99.64%) analysis performed by comparing manually segmented AC shows a good performance of the automated AC segmentation. The average cartilage volume (23.19 ± 1.38 cm(3); coefficient of variation [COV] -0.059) measured from 3D AC models of four data sets shows a marked improvement over average cartilage volume (23.24 cm(3); COV -0.19) reported earlier. CONCLUSIONS: This study confirms the use of multinuclear MR data for cartilage morphology (volume) assessment that can be used in clinical settings.

r-principal subspace for driver cognitive state classification.

Using EEG signals, a novel technique for driver cognitive state assessment is presented, analyzed and experimentally verified. The proposed technique depends on the singular value decomposition (SVD) in finding the distributed energy of the EEG data matrix A in the direction of the r-principal subspace. This distribution is unique and sensitive to the changes in the cognitive state of the driver due to external stimuli, so it is used as a set of features for classification. The proposed technique is tested with 42 subjects using 128 EEG channels and the results show significant improvements in terms of accuracy, specificity, sensitivity, and false detection in comparison to other recently proposed techniques.

Hyperspectral venous image quality assessment for optimum illumination range selection based on skin tone characteristics.

BACKGROUND: Subcutaneous veins localization is usually performed manually by medical staff to find suitable vein to insert catheter for medication delivery or blood sample function. The rule of thumb is to find large and straight enough vein for the medication to flow inside of the selected blood vessel without any obstruction. The problem of peripheral difficult venous access arises when patient's veins are not visible due to any reason like dark skin tone, presence of hair, high body fat or dehydrated condition, etc. METHODS: To enhance the visibility of veins, near infrared imaging systems is used to assist medical staff in veins localization process. Optimum illumination is crucial to obtain a better image contrast and quality, taking into consideration the limited power and space on portable imaging systems. In this work a hyperspectral image quality assessment is done to get the optimum range of illumination for venous imaging system. A database of hyperspectral images from 80 subjects has been created and subjects were divided in to four different classes on the basis of their skin tone. In this paper the results of hyper spectral image analyses are presented in function of the skin tone of patients. For each patient, four mean images were constructed by taking mean with a spectral span of 50 nm within near infrared range, i.e. 750-950 nm. Statistical quality measures were used to analyse these images. CONCLUSION: It is concluded that the wavelength range of 800 to 850 nm serve as the optimum illumination range to get best near infrared venous image quality for each type of skin tone.

Short term N2O, CH4 and CO2 production from soil sampled at different depths and amended with a fine sized slurry fraction.

Little is known about the interaction of the soil's physicochemical environment and livestock slurry throughout the soil profile. In this study, five soil layers (2-6, 6-10, 10-14, 14-18, 18-22 cm) amended with a<45 microm slurry fraction (FS) or water (control) were incubated for 58 d at 20 degrees C to determine the effect of the slurry position in the soil profile on the production of CO(2), N(2)O, CH(4) and total greenhouse gas (GHG) expressed as CO(2) equivalent. FS application increased the CO(2) production in all soil layers by 3-8 times compared to the controls. The total CO(2) produced during the incubation in the 2-6 cm amended soil layer (>1,600 mg CO(2)-C kg(-1) dry soil) was significantly greater (P<0.05) than in other amended layers (<800 mg CO(2)-C kg(-1) dry soil). No detectable N(2)O production was observed from control treatments, and application of FS induced a slow increase in N(2)O production. N(2)O production occurred earlier and at a higher rate in deeper soil layers. Furthermore, a good correlation (r=0.899, P<0.05) was observed between N(2)O production and soil depth. The higher N(2)O production in the deeper soil layers could have been due to enhanced denitrification promoted by a lower aeration and low soil respiration in the deep soil. At the end of the incubation, >11% of the total applied N was lost as N(2)O from the two deeper soil layers against 2.5-5% in all other soil layers. Methane production was only observed from FS amended treatments within the first 7d (range 0.02-0.41 mg C kg(-1) soil d(-1)). The greatest net production of GHGs, expressed as CO(2) equivalents, was observed from the two deeper soil layers ( approximately 4.5 CO(2) eq kg(-1) soil). N(2)O and CO(2) contributed equally (50%) to the total GHG production in 2-14 cm soil layers, whereas N(2)O contributed reached 80% to the total GHG production in the deeper soil layers. The CH(4) contribution was not significant in any treatment.