In Vitro Analysis of Immersed Human Tissues by Raman Microspectroscopy

Raman microspectroscopy is a powerful tool for the analysis of tissue sections, providing a molecular map of the investigated samples. Nevertheless, data pre-processing and, particularly, the removal of the broad background to the spectra remain problematic. Indeed, the physical origin of the background has not been satisfactorily determined. Using 785 nm as source in a confocal geometry, it is demonstrated for the example of the protein kappa-elastin that the background and resulting quality of the recorded spectrum are dependent on the morphology of the sample. Whereas a fine powder yields a dominant broad background, compressed pellets and solution-cast thin films produce, respectively, improved quality spectra and significantly reduced spectral background. As the chemical composition of the samples is identical, the background is ascribed to stray light due to diffuse scattering rather than an intrinsic photoluminescence. The recorded spectra from a tissue sample exhibit a large and spatially variable background, resulting in poorly defined spectral features. A significant reduction of the background signal as well as improvement of the spectral quality is achieved by immersion of the sample in water and measurement with an immersion objective. The significant improvement in signal to background is attributed to a reduction of the diffuse scattering due to a change in the effective morphology as a result of an improved index matching at the water/tissue interface compared to the air/tissue interface. Compared to sections measured in air, the background is reduced to that of the water, and pre-processing is reduced to the subtraction of the substrate and water signal and correction for the instrument response, both of which are highly reproducible. Data pre-processing is thus greatly simplified and the results significantly more reliable

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of field soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the community composition from phylum to amplicon sequence variant (ASV) level. Alpha diversity was significantly reduced by BOA or quercetin, but not by gramine. BOA treatment caused a decrease of the relative abundance of 11 ASVs, while only 10 ASVs were increased. Gramine or quercetin treatment resulted in the increase in relative abundance of many more ASVs (33 or 38, respectively), most of them belonging to the Proteobacteria. Isolation and characterization of cultivable bacteria indicated an enrichment in Pseudarthrobacter or Pseudomonas strains under BOA/quercetin or BOA/gramine treatments, respectively. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a predominantly inhibitory effect, with only few genera being able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, BOA or gramine biosynthesis, which have evolved in different barley species, is accompanied with the association of distinct bacterial communities in the soil, presumably after mutual adaptation during evolution

Detectable contributions of colloids to soil P and C content in arid and hyperarid region of the Atacama (Chile)

Atacama Desert is mainly known as the driest place on Earth where life has been developed under arid to hyper arid conditions since Oligocene-Miocene. Therefore, soils of Atacama contain fingerprints of past and present life which might be used as an analog to study the evolution of life under equivalent arid conditions, like Mars. In this study, we quantify the colloidal phosphorus and carbon distribution in the first 10 cm of soil profile along an altitudinal transect. Samples were taken along a transect in the region of Quebrada Aroma spanning from the arid Percordillera of the Andes (2720 m a.s.l.) towards the hyper arid core of the desert (1340 m a.s.l.). Water dispersible colloids (WDC) were separated and measured using the field-flow-field fractionation (FFF) method and subsequently their Corg and P content were characterized and quantified by detectors (DLS, ICP-MS, UV, OCD, fluorescence). Data was compared to total C, P and (available) Olsen-P also measured in the samples. The Olsen-P (available-P) varied within the Aroma transect from ca. 2 to 8 mg P kg-1, but was not related to either altitude or depth in the upper soil (0-10 cm). Colloidal P contents ranged from <0.1 to 4 mg P kg-1 soil, with increasing trend from low to higher elevations. Thereby, suggesting an increasing proportion of the available P potential being present in the WDC fraction. The Colloidal Corg content of the Aroma transect did range from 65 to 90 (for sites 2020 to 1340m) and 110 mg Corg kg-1 soil WDC (2720 m). Colloidal Corg content as a function of the altitude showed a similar trend to the Corg content of the soils: the highest colloidal Corg content was found at 2720 m. The proportion of soil Corg within the colloidal fraction was up to 6% of the bulk soil organic matter (OM) content, as the OM content was intensively enriched in the colloidal fraction. Further quantification of phosphorus and carbon content in WDC in deeper part of soil is required to obtain a more comprehensive view of role of colloidal inputs and dynamics in the Atacama Desert

Neural Correlates of Speech Processing in Prelingually Deafened Children and Adolescents with Cochlear Implants

Prelingually deafened children with cochlear implants stand a good chance of developing satisfactory speech performance. Nevertheless, their eventual language performance is highly variable and not fully explainable by the duration of deafness and hearing experience. In this study, two groups of cochlear implant users (CI groups) with very good basic hearing abilities but non-overlapping speech performance (very good or very bad speech performance) were matched according to hearing age and age at implantation. We assessed whether these CI groups differed with regard to their phoneme discrimination ability and auditory sensory memory capacity, as suggested by earlier studies. These functions were measured behaviorally and with the Mismatch Negativity (MMN). Phoneme discrimination ability was comparable in the CI group of good performers and matched healthy controls, which were both better than the bad performers. Source analyses revealed larger MMN activity (155–225 ms) in good than in bad performers, which was generated in the frontal cortex and positively correlated with measures of working memory. For the bad performers, this was followed by an increased activation of left temporal regions from 225 to 250 ms with a focus on the auditory cortex. These results indicate that the two CI groups developed different auditory speech processing strategies and stress the role of phonological functions of auditory sensory memory and the prefrontal cortex in positively developing speech perception and production

Spin detection with a micromechanical trampoline: towards magnetic resonance microscopy harnessing cavity optomechanics

We explore the prospects and benefits of combining the techniques of cavity optomechanics with efforts to image spins using magnetic resonance force microscopy (MRFM). In particular, we focus on a common mechanical resonator used in cavity optomechanics&mdash;high-stress stoichiometric silicon nitride (Si3N4) membranes. We present experimental work with a 'trampoline' membrane resonator that has a quality factor above 106 and an order of magnitude lower mass than a comparable standard membrane resonators. Such high-stress resonators are on a trajectory to reach 0.1 force sensitivities at MHz frequencies by using techniques such as soft clamping and phononic-crystal control of acoustic radiation in combination with cryogenic cooling. We present a demonstration of force-detected electron spin resonance of an ensemble at room temperature using the trampoline resonators functionalized with a magnetic grain. We discuss prospects for combining such a resonator with an integrated Fabry&ndash;Perot cavity readout at cryogenic temperatures, and provide ideas for future impacts of membrane cavity optomechanical devices on MRFM of nuclear spins. </div

High-Pressure Amorphous Nitrogen

The phase diagram and stability limits of diatomic solid nitrogen have been explored in a wide pressure--temperature range by several optical spectroscopic techniques. A newly characterized narrow-gap semiconducting phase $\eta$ has been found to exist in a range of 80--270 GPa and 10--510 K. The vibrational and optical properties of the $\eta$ phase produced under these conditions indicate that it is largely amorphous and back transforms to a new molecular phase. The band gap of the $\eta$ phase is found to decrease with pressure indicating possible metallization by band overlap above 280 GPa.Comment: 5 pages, 4 figure

Soil methane sink capacity response to a long-term wildfire chronosequence in Northern Sweden

Boreal forests occupy nearly one fifth of the terrestrial land surface and are recognised as globally important regulators of carbon (C) cycling and greenhouse gas emissions. Carbon sequestration processes in these forests include assimilation of CO2 into biomass and subsequently into soil organic matter, and soil microbial oxidation of methane (CH4). In this study we explored how ecosystem retrogression, which drives vegetation change, regulates the important process of soil CH4 oxidation in boreal forests. We measured soil CH4 oxidation processes on a group of 30 forested islands in northern Sweden differing greatly in fire history, and collectively representing a retrogressive chronosequence, spanning 5000 years. Across these islands the build-up of soil organic matter was observed to increase with time since fire disturbance, with a significant correlation between greater humus depth and increased net soil CH4 oxidation rates. We suggest that this increase in net CH4 oxidation rates, in the absence of disturbance, results as deeper humus stores accumulate and provide niches for methanotrophs to thrive. By using this gradient we have discovered important regulatory controls on the stability of soil CH4 oxidation processes that could not have not been explored through shorter-term experiments. Our findings indicate that in the absence of human interventions such as fire suppression, and with increased wildfire frequency, the globally important boreal CH4 sink could be diminished

Impact of plants on the diversity and activity of methylotrophs in soil

Background Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. Results Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. Conclusion In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle

The Abundance of Pink-Pigmented Facultative Methylotrophs in the Root Zone of Plant Species in Invaded Coastal Sage Scrub Habitat

Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C1 compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pathogen resistance and drought stress tolerance. In contrast, little is known about the PPFM abundance and diversity in natural ecosystems, let alone their interactions with non-crop species. Here we surveyed PPFM abundance in the root zone soil of 5 native and 5 invasive plant species along ten invasion gradients in Southern California coastal sage scrub habitat. PPFMs were present in every soil sample and ranged in abundance from 102 to 105 CFU/g dry soil. This abundance varied significantly among plant species. PPFM abundance was 50% higher in the root zones of annual or biennial species (many invasives) than perennial species (all natives). Further, PPFM abundance appears to be influenced by the plant community beyond the root zone; pure stands of either native or invasive species had 50% more PPFMs than mixed species stands. In sum, PPFM abundance in the root zone of coastal sage scrub plants is influenced by both the immediate and surrounding plant communities. The results also suggest that PPFMs are a good target for future work on plant-microorganism feedbacks in natural ecosystems

Discovery and population genomics of structural variation in a songbird genus

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping