Use of portable Raman spectrometers for detection of sulfates: potential application in exobiology

The detection of mineral phases under in situ conditions has become a primary but sometimes also challenging task in many fields of geoscience. Raman spectroscopy has been used as a powerful tool for the identification of various minerals and organic compounds. The advantages and the relative simplicity made this method a promising choice in the future planetary exploration missions to Mars. The deposits of aqueous minerals including sulfates have been found on the Martian surface. With the development of miniaturized handheld spectrometers there is a need for evaluation of Raman spectroscopy as a method of identification of sulfate phases in their natural conditions. In the first part of this work a handheld spectrometer equipped with 532 nm excitation laser was tested under laboratory conditions during which the ability to distinguish mineral samples representing sulfates of different chemical composition and different degree of hydration was investigated. In the second part, two handheld Raman spectrometers equipped with 532 and 785 nm excitation lasers were used for the characterization of sulfate phases on sites of their natural occurrence located in the Czech Republic. The quality of the Raman spectra acquired under outdoor conditions by both spectrometers was rather average but sufficient to..

ANALYSIS OF A SLOPE DEFORMATION OF THE D11 MOTORWAY CUT

This diploma thesis consists of a research and a practical part. The research part summarises the problem of slopes movements. The practical part deals with the determination of the slope deformation causes, at the 76th km of the D11 motorway. Causes determination was based on laboratory tests of soil samples taken from the disrupted motorway cut, made at PřF UK soil mechanics lab. Tests of grain size composition were done, plasticity of the L 26 sample was determined and critical strength of the reconstituted L26 and L27 samples was found out in the Translational apparatus box. Soils were categorized due to the according standards and the acquired data were evaluated. In the BricsCAD software, a well arranged locality situation and the slope deformation crosscut underlayed with the geophysical ERT cut were illustrated. In the GEO5 software, slope stability models were created using the Spencer Method of Slices. The slip surface and the groundwater level during the disruption were determined. The practical part also covers a proposal of a remediation appropriate for this deformation and it's modelling in GEO5. For the remediation, the slope stability level is determined. The work is based on the specialized literature, articles, research reports and standards. Powered by TCPDF (www.tcpdf.org

Additional file 5: Figure S3. of Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

Hierarchical clustering of the (A) phylogenetic and (B) functional profiles of the samples. Profiles (rows) are colored by the cluster assignment (k = 15), and samples (columns) are colored by the twin variable. The medoid profile per cluster (written in black) was chosen as a representative and shown on Fig. 2. (PDF 3597 kb

Additional file 8: Figure S5. of Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

Scatter plots of data collected for the Human Microbiome Project [22] for (A) blood pressure vs. M. smithii abundance and (B) BMI vs. E. sireum. In our data, both these associations have a threshold-like behavior, however this is not observed in the HMP data [21]. (PDF 3520 kb

Genes Expressed with Dorsal or Ventral Domains

<div><p>These genes were chosen as candidate targets of Bmp activation or repression. All embryos are oriented as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040291#pbio-0040291-g002" target="_blank">Figure 2</a> with anterior to the top and left of each panel and dorsal in the top right of each panel, unless otherwise specified. The telotroch or ciliated band is marked by white arrowheads. Expression of <i>dlx</i> at (A) day 2 of development, just after gastrulation and (B) at day 3 of development.</p> <p>(C) <i>Tbx 2/3</i> expression just after gastrulation, and (D) at day 3 of development.</p> <p>(E) Expression of <i>hex</i> at day 3 of development (F) Expression of <i>nk2.3/2.5</i> at day 4.</p> <p>(G) Expression of olig on day 2, just after gastrulation, and (H) at day 3.</p> <p>(I) <i>poxN</i> expression at day 4 of development.</p> <p>(J) <i>Pitx</i> expression at day 2 of development, dorsal midline toward the viewer, a glancing optical section through the dorsal-most ectoderm.</p> <p>(K) <i>Pitx</i> expression at day 4 of development. Note the two domains of expression.</p> <p>(L) <i>Netrin</i> expression, a transverse section of a post-gastrula embryo at the level of the ciliated band. Note the broad ventral expression of <i>netrin</i>, and (M) the more narrow domain at day 3 of development.</p> <p>(N) Expression of <i>lim3</i> at day 3 of development.</p> <p>(O) Expression of <i>mnx</i> at day 2 of development, and (P) at day 4. Note the ventral endodermal expression.</p> <p>(Q) Expression of <i>mox</i> (also called <i>gax</i>) at day 3 of development, and (R) a close up of the ventral domain at day 3, ventral midline toward the viewer, displaying the metasome and part of the mesosome.</p> <p>(S) Expression of <i>sim</i> at day 2 of development, and (T) at day 5.</p></div

The Anatomy of S. kowalevskii to Illustrate Differentiations along the Dorsoventral Axis

<div><p>The ventral side, assigned because of the mouth location, is down in this schematic figure. Anterior is to the left. Note the three parts of the body: the prosome (proboscis) at the anterior end, the narrow mesosome (collar) in the middle, and the elongated metasome to the posterior (only half the length is shown). Ectodermal derivatives are colored blue, mesodermal red, and endodermal yellow. Prominent structures of the dorsoventral axis include the dorsal and ventral axon tracts, the dorsal and ventral blood vessels, the dorsal stomochord with the heart/kidney complex, the dorsal gill slits, the ventral mouth, and the ventral tail (only in the juvenile, not shown).</p> <p>Redrawn with modification from Benito and Pardos [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040291#pbio-0040291-b105" target="_blank">105</a>].</p></div

Ventralization of the S. kowalevskii Embryo following Injection of the Egg with Anti-<i>bmp</i> siRNAs

<div><p>Eggs were injected immediately following fertilization with <i>bmp</i> siRNA and development was allowed to continue.</p> <p>(A) Low magnification micrograph of a group of embryos at the beginning of day 3 of development from injected eggs, showing the consistency of the phenotype. The dorsoventral orientation cannot be determined since the embryos are cylindrically symmetric. Note the deep indentation between the prosome and mesosome, and the short posterior end beyond the telotroch (ciliated band).</p> <p>(B) Optical section of an embryo at the same stage of development from an injected egg.</p> <p>(C) In the siRNA treated embryo, the expression of <i>dlx</i> continues in scattered cells in the anterior ectoderm of the prosome but disappears from the dorsal midline.</p> <p>(D) Expression of <i>pitx</i> at day 4 of development in a siRNA treated embryo, showing expanded expression throughout the majority of the metasome anterior to the telotroch, whereas the prosome dorsal spot is absent. The prosome has detached from the mesosome at this stage, as the mouth indentation encircles the embryo. The same developmental stage is shown in panel E and F.</p> <p>(E) Expression of <i>admp</i> expands strongly throughout the ectoderm of the detached prosome.</p> <p>(F) Low magnification micrograph of day 4 embryos showing expansion of expression of <i>netrin</i> from a ventral midline stripe to the entire ectoderm including that of the detached prosome. White arrowhead shows the position of the telotroch.</p></div

Dorsalization of the S. kowalevskii Embryo by Application of Exogenous Bmp4 Protein

<div><p>Exogenous Bmp4 protein was applied to the late blastula embryo (14 h post fertilization), and development was allowed to continue. All embryos are shown at a similar developmental stage, day 3 of development.</p> <p>(A) Side view of a control embryo cultured without Bmp4. The mouth is indicated by a black arrowhead on the ventral side. The normally developing endoderm shows a dorsal, anterior projection of the gut called the stomochord, indicated with a white arrowhead. One of the mesocoels is clearly visible on the dorsal midline, indicated by a yellow arrowhead. The endoderm is divided into two sections, the pharyngeal region in the anterior, divided from the posterior gut region by a posterior constriction shown by blue arrows. The first gills slit is indicated by a green arrowhead, just anterior to the gut division.</p> <p>(B) Embryos treated with 250ng/ml of Bmp 4, fixed at the same time as the control in panel A. The dorsoventral orientation is not possible to determine since they are cylindrically symmetric. Black arrowheads indicate thick condensations of mesenchyme around the anterior gut.</p> <p>(C) Embryos fixed at a similar development stage following a treatment with 500 ng/ml Bmp4 displaying a consistent phenotype between samples. Note the flattened anterior end and the thick connection of prosome and mesosome.</p> <p>(D) Expression of <i>bmp2/4</i> following treatment with Bmp4 protein showing activation of endogenous expression throughout the ectoderm.</p> <p>(E) Stereomicrographs of uncleared embryos showing the expression of <i>chordin</i> in control embryos, with broad ventral expression, and (F) embryos following treatment with Bmp4 protein at 100 ng/ml.</p> <p>(G) Stereomicrographs of uncleared embryos showing the expression of <i>elv</i> in control embryos, with broad expression, but stronger at the midlines, and (H) embryos following treatment with Bmp4 protein at 100 ng/ml. Note the persistence of <i>elv</i> expression; it is not repressed by Bmp4.</p> <p>(I) Ubiquitous ectodermal expression of <i>dlx</i> following treatment with 100 ng/ml of Bmp4.</p> <p>(J) Expression of <i>tbx2/3</i> expands throughout the ectoderm following treatment of the embryo with Bmp4 protein (250 ng/ml). White arrowheads indicate the position of the telotroch/ciliated band.</p> <p>(K) Expression of <i>pitx</i> expands from a spot to a ring around the base of the prosome in both the ectoderm and underlying mesenchyme, after Bmp4 protein treatment.</p> <p>(L) Control expression of <i>hex</i> at day 4 of development, and (M) following treatment with Bmp4 at 100ng/ml.</p> <p>(N) <i>Pax1/9</i> expression expands from a dorsolateral spot to a circumferential ring in the endoderm following Bmp4 treatment at 100 ng/ml.</p> <p>(O) Like <i>pax1/9,</i> the <i>nk2–3/2–5</i> domain expands from a short dorsal stripe to a ring in the endoderm, after Bmp4 treatment.</p> <p>(P) Expression of <i>admp</i> in the most anterior endoderm following treatment with 500 ng/ml of Bmp4. This is a residual spot (thus showing that the staining procedure has worked), whereas the entire ventral domains of ectoderm and endoderm have disappeared.</p></div

Summary of Inferred Evolutionary Changes of the Dorsoventral Axis in Deuterostome Evolution, with Emphasis on Hemichordates and Chordates

<p>Mesoderm is shown in red, endoderm in yellow and ectoderm in blue (neural) and grey (epidermis). An ancestral secreted Bmp axis was involved in dorsoventral patterning of the three germ layers in the bilaterian ancestor. This ancestor we propose was characterized by a diffuse organization of its nervous system, shown by blue dots. A Bmp gradient was involved in dorsoventral patterning of all three germ layers. In the basal deuterostome and hemichordates the role of the Bmp gradient is conserved in general dorsoventral patterning. During chordate (and protostome) evolution, the existing Bmp/Chordin axis was co-opted for an additional developmental role in nervous system centralization.</p

Early Midline Signaling of Bmp and Chordin

<div><p>All embryos are cleared (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040291#s4" target="_blank">Materials and Methods</a>) otherwise specified. All embryos have a similar orientation: anterior in the top left and dorsal in the top right of each panel, unless otherwise specified.</p> <p>(A) Expression of <i>bmp2/4</i> at late gastrula stage and (B) at day 3 of development.</p> <p>(C) Hatched juvenile oriented with dorsal toward the viewer. White arrowhead indicates the position of the collar where the <i>bmp2/4</i> expression domain follows the submerged ectodermal track of the dorsal cord.</p> <p>(D) Section of a juvenile of a similar stage to (C). Dorsal is at the top of the panel. Note the submerged <i>bmp</i> domain, stained purple.</p> <p>(E) Dorsal view of <i>bmp5/8</i> expression at day 3 of development with dorsal toward the viewer, and (F) in a hatching juvenile at day 5 of development. White arrowhead indicates the submerged domain in the collar (mesosome) similar to that of <i>bmp2/4</i> in panel D.</p> <p>(G) Expression of <i>bmp5/8</i> in the far posterior of a late juvenile at day 13 of development. White arrow indicates the position of the anus, before which the <i>bmp5/8</i> domain stops. Posterior to the anus is the post anal tail.</p> <p>(H) Expression of <i>tolloid</i>/<i>xolloid</i> at day 3 of development.</p> <p>(I) Expression of <i>bambi</i> at the late gastrula stage. (J) Expression of <i>crossveinless</i> at the late gastrula stage and (K) at day 3 of development, with the dorsal midline oriented toward the viewer.</p> <p>(L) <i>Tsg</i> expression at day two of development.</p> <p>(M–P) <i>Chordin</i> expression from early to late developmental stages.</p> <p>(M) Expression at mid gastrula.</p> <p>(N) Sagittal section an embryo at day 2 of development just anterior to the telotroch; ventral is at the bottom of the panel.</p> <p>(O) Day 3 of development, a surface view of the lateral ectoderm, (P) and day 4 of development, in sagittal section.</p> <p>(Q) <i>Admp</i> and <i>bmp2/4</i> double in situ hybridization at day 2 of development; brown is <i>admp</i> and blue is <i>bmp2/4</i>, and (R) a cross section of the same stage just anterior to the telotroch.</p> <p>(S) <i>Admp</i> expression at day 5 of development, and (T) surface view of an uncleared embryo, ventral midline toward the viewer.</p></div