A key stage for all microarray analyses is the extraction of feature-intensities from an image. If this step goes wrong, then subsequent preprocessing and processing stages will stand little chance ...of rectifying the matter. Illumina employ random construction of their BeadArrays, making feature-intensity extraction even more important for the Illumina platform than for other technologies. In this paper we show that using raw Illumina data it is possible to identify, control, and perhaps correct for a range of spatial-related phenomena that affect feature-intensity extraction.
We note that feature intensities can be unnaturally high when in the proximity of a number of phenomena relating either to the images themselves or to the layout of the beads on an array. Additionally we note that beads neighbour beads of the same type more often than one might expect, which may cause concern in some models of hybridization. We highlight issues in the identification of a bead's location, and in particular how this both affects and is affected by its intensity. Finally we show that beads can be wrongly identified in the image on either a local or array-wide scale, with obvious implications for data quality.
The image processing issues identified will often pass unnoticed by an analysis of the standard data returned from an experiment. We detail some simple diagnostics that can be implemented to identify problems of this nature, and outline approaches to correcting for such problems. These approaches require access to the raw data from the arrays, not just the summarized data usually returned, making the acquisition of such raw data highly desirable.
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Six‐lined racerunner (Aspidoscelis sexlineata) is an indicator species of frequently burned Longleaf pine (Pinus palustris) forests. To evaluate how the species responded to forest restoration, we ...conducted a mark‐recapture study in formerly fire‐suppressed Longleaf pine forests exposed to prescribed fire or fire surrogates (i.e. mechanical or herbicide‐facilitated hardwood removal) as well as in fire‐suppressed control sites and reference sites, which represented the historic condition. After initial treatment, all sites were exposed to over a decade of prescribed burning with an average return interval of approximately 2 years. We used population‐level response of A. sexlineata as an indicator of the effectiveness of the different treatments in restoring habitat. Specifically, we compared mean numbers of marked adults and juveniles at treatment sites to that of reference sites. After 4 years, restoration objectives were met at sites treated with burning alone and at sites treated with mechanical removal of hardwoods followed by fire. After over 10 years of prescribed burning, restoration objectives were met at all treatments. We conclude that prescribed burning alone was sufficient to restore fire‐suppressed Longleaf pine sandhills for A. sexlineata populations.
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33.
Invasive ants influence native lizard populations Darracq, Andrea K.; Smith, Lora L.; Oi, David H. ...
Ecosphere (Washington, D.C),
January 2017, 2017-01-00, 20170101, Volume:
8, Issue:
1
Journal Article
Peer reviewed
Open access
The red imported fire ant (Solenopsis invicta; hereafter RIFA) is an invasive predator found on four continents, namely South America, North America, Australia, and Asia. Red imported fire ants are ...implicated in the decline of native invertebrates and vertebrates throughout their invaded range. We used the eastern fence lizard (Sceloporus undulatus) as a model species to understand the influence of RIFAs on native reptiles in the southeastern United States. Our objective was to quantify the effects of RIFAs on fence lizard recruitment and survival. We experimentally stocked populations of fence lizards into eight enclosures with either ambient or reduced numbers of RIFAs from May 2012 to October 2013. Fitting Link‐Barker models, we found that the RIFA treatment affected fence lizard recruitment (f), but not survival (Φ). Recruitment was 1.6 times greater in the enclosures with reduced numbers of RIFAs than in those with ambient numbers. Red imported fire ants likely affect reptiles with analogous life history strategies to those of fence lizards similarly. Consequently, RIFAs may have undesirable consequences for the biodiversity of reptiles in the southeastern United States and on other continents with established RIFA populations.
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A novel halovirus, SH1, with a spherical morphology is described. Isolated from a hypersaline lake, SH1 is divalent, producing clear plaques on
Haloarcula hispanica and a natural
Halorubrum isolate. ...Single-step growth curves gave a latent period of 5–6 h and a burst size of around 200 PFU/cell. The host can differentiate to form tight clusters of thick cell-walled forms, and these were shown to be resistant to infection. Purified virions had no visible tail, were about 70 nm in diameter, and displayed a fragile outer capsid layer, possibly with an underlying membrane component. The structural proteins of the virion were analyzed by SDS–PAGE and several were found to be cross-linked, forming protein complexes. The genome was linear, dsDNA, of approximately 30 kb in length. This morphology and linear genome are features not observed in any other euryarchaeal viruses, but have properties similar to the bacterial virus PRD1.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Two isolates of non-alkaliphilic, extremely halophilic archaea, with very similar characteristics, were recovered from a marine solar saltern crystallizer. Cells were pleomorphic, motile and ...Gram-stain-negative and grew on a limited range of carbon sources, with pyruvate being the best substrate. Optimum growth occurred at 18-20 % (w/v) NaCl, pH 6.0-8.5 and 37-40 degrees C. Both isolates possessed typical archaeal lipids, and their 16S rRNA gene sequences were 99.8 % identical. Phylogenetic tree reconstructions indicated that they were most closely related to the haloalkaliphile Natronomonas pharaonis (97.5 % similarity to the type strain), but the different phenotypic properties and low DNA-DNA hybridization values between Nmn. pharaonis DSM 2160(T) and the two isolates suggested that they represent a novel species within the genus Natronomonas. The name Natronomonas moolapensis sp. nov. is proposed for these isolates, with the type strain being 8.8.11(T) (=JCM 14361(T) =CECT 7526(T) =DSM 18674(T)). An emended description of the genus Natronomonas is also provided.
Cultivation of Walsby’s square haloarchaeon Burns, David G.; Camakaris, Helen M.; Janssen, Peter H. ...
FEMS microbiology letters,
09/2004, Volume:
238, Issue:
2
Journal Article
Peer reviewed
The
square
haloarchaea
of
Walsby (SHOW group) dominate hypersaline microbial communities but have not been cultured since their discovery 25 years ago. We show that natural water dilution cultures ...can be used to isolate members of this group and, once in pure culture, they can be grown in standard halobacterial media. Cells display a square morphology and contain gas vesicles and poly-β-hydroxybutyrate (PHB) granules. The 16S rRNA gene sequence was >99% identical to other SHOW group sequences. They prefer high salinities (23–30%), and can grow with a doubling time of 1–2 days in rich media. The ability to culture SHOW group organisms makes it possible to study, in a comprehensive way, the microbial ecology of salt lakes.
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Two halophilic archaea, strains TBN53T and CSW2.24.4T, were characterized to elucidate their taxonomic status. Strain TBN53T was isolated from the Taibei marine solar saltern near Lianyungang city, ...Jiangsu province, China, whereas strain CSW2.24.4T was isolated from a saltern crystallizer in Victoria, Australia. Cells of the two strains were pleomorphic, stained Gram-negative and produced red-pigmented colonies. Strain TBN53T was able to grow at 25–55 °C (optimum 45 °C), with 1.4–5.1 M NaCl (optimum 2.6–3.9 M NaCl), with 0–1.0 M MgCl2 (optimum 0–0.1 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0), whereas strain CSW2.24.4T was able to grow at 25–45 °C (optimum 37 °C), with 2.6–5.1 M NaCl (optimum 3.4 M NaCl), with 0.01–0.7 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0–7.5). Cells of the two isolates lysed in distilled water. The minimum NaCl concentrations that prevented cell lysis were 8 % (w/v) for strain TBN53T and 12 % (w/v) for strain CSW2.24.4T. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, with two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Trace amounts of other unidentified lipids were also detected. On the basis of 16S rRNA gene sequence analysis, strains TBN53T and CSW2.24.4T showed 94.1 % similarity to each other and were closely related to Halobellus clavatus TNN18T (95.0 and 94.7 % similarity, respectively). Levels of rpoB' gene sequence similarity between strains TBN53T and CSW2.24.4T, and between these strains and Halobellus clavatus TNN18T were 88.5, 88.5 and 88.1 %, respectively. The DNA G+C contents of strains TBN53T and CSW2.24.4T were 69.2 and 67.0 mol%, respectively. The level of DNA–DNA relatedness between strain TBN53T and strain CSW2.24.4T was 25 %, and these two strains showed low levels of DNA–DNA relatedness with Halobellus clavatus TNN18T (30 and 29 % relatedness, respectively). Based on these phenotypic, chemotaxonomic and phylogenetic properties, two novel species of the genus Halobellus are proposed to accommodate these two strains, Halobellus limi sp. nov. (type strain TBN53T = CGMCC 1.10331T = JCM 16811T) and Halobellus salinus sp. nov. (type strain CSW2.24.4T = DSM 18730T = CGMCC 1.10710T = JCM 14359T).
In this paper, we show how the methods of systematic reviewing and meta-analysis can be used in conjunction with structural equation modeling to summarize the results of studies in a way that will ...facilitate the theory development and testing needed to advance prevention science. We begin with a high-level overview of the considerations that researchers need to address when using meta-analytic structural equation modeling (MASEM) and then discuss a research project that brings together theoretically important cognitive constructs related to depression to (a) show how these constructs are related, (b) test the direct and indirect effects of dysfunctional attitudes on depression, and (c) test the effects of study-level moderating variables. Our results suggest that the indirect effect of dysfunctional attitudes (via negative automatic thinking) on depression is two and a half times larger than the direct effect of dysfunctional attitudes on depression. Of the three study-level moderators tested, only sample recruitment method (clinical vs general vs mixed) yielded different patterns of results. The primary difference observed was that the dysfunctional attitudes → automatic thoughts path was less strong for clinical samples than it was for general and mixed samples. These results illustrate how MASEM can be used to compare theoretically derived models and predictions resulting in a richer understanding of both the empirical results and the theories underlying them.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Members of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae) are closely related to each other and show 96.6–98 % 16S rRNA gene sequence similarity. This is higher ...than the accepted threshold value (95 %) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4T, Halosarcina pallida BZ256T and Halosarcina limi RO1-6T are related more to each other than to Halogeometricum borinquense CGMCC 1.6168T. Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB′ and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius, Halobellus, Haloquadratum, Haloferax and Halogranum. The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256T = KCTC 4017T = JCM 14848T) and Halogeometricum limi comb. nov. (type strain, RO1-6T = CGMCC 1.8711T = JCM 16054T).
Esophageal adenocarcinoma (EAC) has a poor outcome, and targeted therapy trials have thus far been disappointing owing to a lack of robust stratification methods. Whole-genome sequencing (WGS) ...analysis of 129 cases demonstrated that this is a heterogeneous cancer dominated by copy number alterations with frequent large-scale rearrangements. Co-amplification of receptor tyrosine kinases (RTKs) and/or downstream mitogenic activation is almost ubiquitous; thus tailored combination RTK inhibitor (RTKi) therapy might be required, as we demonstrate in vitro. However, mutational signatures showed three distinct molecular subtypes with potential therapeutic relevance, which we verified in an independent cohort (n = 87): (i) enrichment for BRCA signature with prevalent defects in the homologous recombination pathway; (ii) dominant T>G mutational pattern associated with a high mutational load and neoantigen burden; and (iii) C>A/T mutational pattern with evidence of an aging imprint. These subtypes could be ascertained using a clinically applicable sequencing strategy (low coverage) as a basis for therapy selection.
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