| 1. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
-
Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes
- 2012
-
Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508. ; 163:6-7, s. 407-412
-
Tidskriftsartikel (refereegranskat)abstract
- Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package – Megraft – that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.
|
|
| 2. |
- Checinska, Aleksandra, et al.
(författare)
-
Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
- 2015
-
Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 3
-
Tidskriftsartikel (refereegranskat)abstract
- Background - The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment. Results - Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide–quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site. Conclusions - The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will facilitate future studies to determine how stable the ISS environment is over time. The present results also demonstrate the value of measuring viable cell diversity and population size at any sampling site. This information can be used to identify sites that can be targeted for more stringent cleaning. Finally, the results will allow comparisons with other built sites and facilitate future improvements on the ISS that will ensure astronaut health.
|
|
| 3. |
- Cockell, Charles S., et al.
(författare)
-
Subsurface scientific exploration of extraterrestrial environments (MINAR 5) : analogue science, technology and education in the Boulby Mine, UK
- 2019
-
Ingår i: International Journal of Astrobiology. - : Cambridges Institutes Press. - 1473-5504 .- 1475-3006. ; 18:2, s. 157-182
-
Tidskriftsartikel (refereegranskat)abstract
- The deep subsurface of other planetary bodies is of special interest for robotic and human exploration. The subsurface provides access to planetary interior processes, thus yielding insights into planetary formation and evolution. On Mars, the subsurface might harbour the most habitable conditions. In the context of human exploration, the subsurface can provide refugia for habitation from extreme surface conditions. We describe the fifth Mine Analogue Research (MINAR 5) programme at 1 km depth in the Boulby Mine, UK in collaboration with Spaceward Bound NASA and the Kalam Centre, India, to test instruments and methods for the robotic and human exploration of deep environments on the Moon and Mars. The geological context in Permian evaporites provides an analogue to evaporitic materials on other planetary bodies such as Mars. A wide range of sample acquisition instruments (NASA drills, Small Planetary Impulse Tool (SPLIT) robotic hammer, universal sampling bags), analytical instruments (Raman spectroscopy, Close-Up Imager, Minion DNA sequencing technology, methane stable isotope analysis, biomolecule and metabolic life detection instruments) and environmental monitoring equipment (passive air particle sampler, particle detectors and environmental monitoring equipment) was deployed in an integrated campaign. Investigations included studying the geochemical signatures of chloride and sulphate evaporitic minerals, testing methods for life detection and planetary protection around human-tended operations, and investigations on the radiation environment of the deep subsurface. The MINAR analogue activity occurs in an active mine, showing how the development of space exploration technology can be used to contribute to addressing immediate Earth-based challenges. During the campaign, in collaboration with European Space Agency (ESA), MINAR was used for astronaut familiarization with future exploration tools and techniques. The campaign was used to develop primary and secondary school and primary to secondary transition curriculum materials on-site during the campaign which was focused on a classroom extra vehicular activity simulation.
|
|
| 4. |
- Hartmann, Martin, 1977, et al.
(författare)
-
V-RevComp: automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets
- 2011
-
Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097. ; 319:2, s. 140-145
-
Tidskriftsartikel (refereegranskat)abstract
- Reverse complementary DNA sequences – sequences that are inadvertently given backwards with all purines and pyrimidines transposed – can affect sequence analysis detrimentally unless taken into account. We present an open-source, high-throughput software tool – V-RevComp (http://www.cmde.science.ubc.ca/mohn/software.html) – to detect and reorient reverse complementary entries of the small-subunit rRNA (16S) gene from sequencing datasets, particularly from environmental sources. The software supports sequence lengths ranging from full-length down to the short reads that are characteristic of next generation sequencing technologies. We evaluated the reliability of V-RevComp by screening all 406 781 16S sequences deposited in release 102 of the curated SILVA database and demonstrated that the tool has a detection accuracy of virtually 100%. We subsequently used V-RevComp to analyze 1 171 646 16S sequences deposited in the International Nucleotide Sequence Databases and found that about 1% of these user-submitted sequences were reverse complementary. In addition, a non-trivial proportion of entries were otherwise anomalous, including reverse complementary chimeras, sequences associated with wrong taxa, non-ribosomal genes, sequences of poor quality or otherwise erroneous sequences without reasonable match to any other entry in the database. Thus, V-RevComp is highly efficient in detecting and reorienting reverse complementary 16S sequences of almost any length and can be used to detect various sequence anomalies.
|
|
| 5. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
-
Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
-
Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
|
|
| 6. |
- Pandey, Siddharth, et al.
(författare)
-
Ladakh: diverse, high-altitude extreme environments for off-earth analogue and astrobiology research
- 2020
-
Ingår i: International Journal of Astrobiology. - : Cambridge University Press. - 1473-5504 .- 1475-3006. ; 19:1, s. 78-98
-
Forskningsöversikt (refereegranskat)abstract
- This paper highlights unique sites in Ladakh, India, investigated during our 2016 multidisciplinary pathfinding expedition to the region. We summarize our scientific findings and the site's potential to support science exploration, testing of new technologies and science protocols within the framework of astrobiology research. Ladakh has several accessible, diverse, pristine and extreme environments at very high altitudes (3000–5700 m above sea level). These sites include glacial passes, sand dunes, hot springs and saline lake shorelines with periglacial features. We report geological observations and environmental characteristics (of astrobiological significance) along with the development of regolith-landform maps for cold high passes. The effects of the diurnal water cycle on salt deliquescence were studied using the ExoMars Mission instrument mockup: HabitAbility: Brines, Irradiance and Temperature (HABIT). It recorded the existence of an interaction between the diurnal water cycle in the atmosphere and salts in the soil (which can serve as habitable liquid water reservoirs). Life detection assays were also tested to establish the best protocols for biomass measurements in brines, periglacial ice-mud and permafrost melt water environments in the Tso-Kar region. This campaign helped confirm the relevance of clays and brines as interest targets of research on Mars for biomarker preservation and life detection.
|
|
