A search for polycyclic aromatic hydrocarbons over the Martian South Polar Residual Cap

We present our research on compositional mapping of the Martian South Polar Residual Cap (SPRC), especially the detection of organic signatures within the dust content of the ice, based on hyperspectral data analysis. The SPRC is the main region of interest for this investigation, because of the unique CO 2 ice sublimation features that cover the surface. These flat floored, circular depressions are highly dynamic, and we infer frequently expose dust particle s previously trapped within the ice during the wintertime. Here we identify suitable regions for potential dust exposure on the SPRC, and utilise data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) on board NASA's Mars Reconnaissance Orbiter (MRO) satellite to examine infrared spectra of dark regions assumed to be composed mainly of dust particles to establish their mineral composition, to eliminate the effects of ices on sub-pixel dusty features, and to look for signatures indicative of Polycyclic Aromatic Hydrocarbons (PAHs). Spectral mapping has identified compositional differences between depression rims and the majority of the SPRC and CRISM spectra have been corrected to minimise the influence of CO 2 ice. Whilst no conclusive evidence for PAHs has been found within the detectability limits of the CRISM instrument, depression rims are shown to have higher water content than regions of featureless ice, and there are possible indications of magnesium carbonate within the dark, dusty regions

The Detectability Limit of Organic Molecules Within Mars South Polar Laboratory Analogs

A series of laboratory experiments was carried out in order to generate a diagnostic spectrum for Polycyclic Aromatic Hydrocarbons (PAHs) of astrobiological interest in the context of the Martian South Polar Residual Cap (SPRC), to establish PAH spectral features more easily detectable in CO2 ice (mixed with small amounts of H2O ice) than the previously reported absorption feature at 3.29 µm in order to constrain their detectability limit. There is currently no existing literature on PAH detection within SPRC features, making this work novel and impactful given the recent discovery of a possible subglacial lake beneath the Martian South Pole. Although they have been detected in Martian meteorites, PAHs have not been detected yet on Mars, possibly due to the deleterious effects of ultraviolet radiation on the surface of the planet. SPRC features may provide protection to fragile molecules, and this work seeks to provide laboratory data to improve interpretation of orbital remote sensing spectroscopic imaging data. We also ascertain the effect of CO2 ice sublimation on organic spectra, as well as provide PAH reference spectra in mixtures relevant to Mars. A detectability limit of ∼0.04% has been recorded for observing PAHs in CO2 ice using laboratory instrument parameters emulating those of the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM), with new spectral slope features revealed between 0.7 and 1.1 µm, and absorption features at 1.14 and, most sensitively, at 1.685 µm. Mars regolith analogue mixed with a concentration of 1.5% PAHs resulted in no discernible organic spectral features. These detectability limits measured in the laboratory are discussed and extrapolated to the effective conditions on the Mars South Polar Cap in terms of dust and water ice abundance and CO2 ice grain size for both the main perennial cap and the H2O ice-dust sublimation lag deposit

Subsurface Reflectors Detected by SHARAD Reveal Stratigraphy and Buried Channels over Central Elysium Planitia, Mars

The Central Elysium Planitia (CEP) is one of the youngest geological units on Mars and displays evidence of volcanic and fluvial activities on the surface. The origin of the CEP material has long been debated with a range of hypotheses from purely fluvial to solely volcanic origins. This study presents a comprehensive investigation of SHARAD (SHAllow RADar) data to reveal subsurface radar reflectors over the CEP region. Distribution of the detected radar reflectors show possible connections between the CEP and outflow channels, such as Athabasca Valles and Marte Vallis. Analysis of the radar reflectors in the CEP region show six subsurface layers implying multiple depositional and erosional episodes. Two of the layers are found to correspond to two exposed layers of one terraced crater. By measuring the depth accurately of these exposed layers in the derived HiRISE (High Resolution Imaging Scientific Experiment) and CTX (Context Camera) DTMs (Digital Terrain Models) and inverting the dielectric constant combining the layers in radargrams, an interpretation that the filling material contains water ice is favoured

The antimicrobial polymer PHMB enters cells and selectively condenses bacterial chromosomes

To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance

Optimizing substitution matrix choice and gap parameters for sequence alignment

<p>Abstract</p> <p>Background</p> <p>While substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or approximately optimal gap penalties. It is also not well understood which substitution matrices are the most effective when alignment accuracy is the goal rather than homolog recognition. Here a new parameter optimization procedure, POP, is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments.</p> <p>Results</p> <p>POP is compared to a recent method due to Kim and Kececioglu and found to achieve from 0.2% to 1.3% higher accuracies on pair-wise benchmarks extracted from BALIBASE. The VTML matrix series is shown to be the most accurate on several global pair-wise alignment benchmarks, with VTML200 giving best or close to the best performance in all tests. BLOSUM matrices are found to be slightly inferior, even with the marginal improvements in the bug-fixed RBLOSUM series. The PAM series is significantly worse, giving accuracies typically 2% less than VTML. Integer rounding is found to cause slight degradations in accuracy. No evidence is found that selecting a matrix based on sequence divergence improves accuracy, suggesting that the use of this heuristic in CLUSTALW may be ineffective. Using VTML200 is found to improve the accuracy of CLUSTALW by 8% on BALIBASE and 5% on PREFAB.</p> <p>Conclusion</p> <p>The hypothesis that more accurate alignments of distantly related sequences may be achieved using low-identity matrices is shown to be false for commonly used matrix types. Source code and test data is freely available from the author's web site at <url>http://www.drive5.com/pop</url>.</p

Microalgae production in fresh market wastewater and its utilization as a protein substitute in formulated fish feed for oreochromis spp.

Rapid growing of human population has led to increasing demand of aquaculture production. Oreochromis niloticus or known as tilapia is one of the most globally cultured freshwater fish due to its great adaptation towards extreme environment. Besides, farming of tilapia not only involves small scales farming for local consumption but also larger scales for international market which contributes to a foreign currency earning. Extensive use of fishmeal as feed for fish and for other animals indirectly caused an increasing depletion of the natural resource and may consequently cause economic and environmental unstable. Microalgae biomass seems to be a promising feedstock in aquaculture industry. It can be used for many purposes such as live food for fish larvae and dried microalgae to substitute protein material in fish feed. The microalgae replacement in fish feed formulation as protein alternative seem potentially beneficial for long term aqua-business sustainability. The present chapter discussed the potential of microalgae as an alternative nutrition in fish feed formulations, specifically Tilapia

Considering the Case for Biodiversity Cycles: Reexamining the Evidence for Periodicity in the Fossil Record

Medvedev and Melott (2007) have suggested that periodicity in fossil biodiversity may be induced by cosmic rays which vary as the Solar System oscillates normal to the galactic disk. We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by Rohde & Mueller (2005), as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by RM may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.Comment: Minor modifications to reflect final published versio

A role for core planar polarity proteins in cell contact-mediated orientation of planar cell division across the mammalian embryonic skin

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2017. Supplementary information accompanies this paper at doi:10.1038/s41598-017-01971-2.The question of how cell division orientation is determined is fundamentally important for understanding tissue and organ shape in both healthy or disease conditions. Here we provide evidence for cell contact-dependent orientation of planar cell division in the mammalian embryonic skin. We propose a model where the core planar polarity proteins Celsr1 and Frizzled-6 (Fz6) communicate the long axis orientation of interphase basal cells to neighbouring basal mitoses so that they align their horizontal division plane along the same axis. The underlying mechanism requires a direct, cell surface, planar polarised cue, which we posit depends upon variant post-translational forms of Celsr1 protein coupled to Fz6. Our hypothesis has parallels with contact-mediated division orientation in early C. elegans embryos suggesting functional conservation between the adhesion-GPCRs Celsr1 and Latrophilin-1. We propose that linking planar cell division plane with interphase neighbour long axis geometry reinforces axial bias in skin spreading around the mouse embryo body.Peer reviewe

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens

<p>Abstract</p> <p>Background</p> <p>The Enteropathogen Resource Integration Center (ERIC; <url>http://www.ericbrc.org</url>) has a goal of providing bioinformatics support for the scientific community researching enteropathogenic bacteria such as <it>Escherichia coli </it>and <it>Salmonella </it>spp. Rapid and accurate identification of experimental conclusions from the scientific literature is critical to support research in this field. Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process.</p> <p>Description</p> <p>We have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity. Evaluations on blind datasets show an F-measure average of greater than 90% for entities (genes, operons, etc.) and over 70% for relations (gene/gene product to role, etc). This IE capability, combined with text indexing and relational database technologies, constitute the core of our recently deployed text mining application.</p> <p>Conclusion</p> <p>Our Text Mining application is available online on the ERIC website <url>http://www.ericbrc.org/portal/eric/articles</url>. The information retrieval interface displays a list of recently published enteropathogen literature abstracts, and also provides a search interface to execute custom queries by keyword, date range, etc. Upon selection, processed abstracts and the entities and relations extracted from them are retrieved from a relational database and marked up to highlight the entities and relations. The abstract also provides links from extracted genes and gene products to the ERIC Annotations database, thus providing access to comprehensive genomic annotations and adding value to both the text-mining and annotations systems.</p

MACSIMS : multiple alignment of complete sequences information management system

BACKGROUND: In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. RESULTS: MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. CONCLUSION: MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at