scholarly journals Plant-associated microbiomes promote nutrient turnover in impoverished substrates of a biodiversity hotspot

2021 ◽  
Author(s):  
Antonio Pedro Camargo ◽  
Rafael Soares Correa de Souza ◽  
Juliana Jose ◽  
Isabel Rodrigues Gerhardt ◽  
Ricardo Augusto Dante ◽  
...  
Keyword(s):  
Sequence Data ◽  
Compositional Analysis ◽  
Taxonomic Structure ◽  
Campos Rupestres ◽  
Nutrient Mobilization ◽  
Strongly Coupled ◽  
Low Concentrations ◽  
Nutrient Turnover ◽  
Stressful Environments ◽  
Phosphorus Turnover

The substrates of the Brazilian campos rupestres have extremely low concentrations of key nutrients, mainly phosphorus, imposing severe restrictions to plant growth. Regardless, this ecosystem harbors enormous biodiversity which raises the question of how nutrients are cycled and acquired by the biosphere. To uncover the nutrient turnover potential of plant-associated microorganisms in the campos rupestres, we investigated the compositions and functions of microbiomes associated with two species of the Velloziaceae family that grow over distinct substrates (soil and rock). Amplicon, metagenomic, and metagenome-assembled genome sequence data showed that the campos rupestres harbor a novel assemblage of plant-associated prokaryotes and fungi. Compositional analysis revealed that the plant-associated soil and rock communities differed in taxonomic structure but shared a core of highly efficient colonizers that were strongly coupled with nutrient mobilization. Investigation of functional and abundance data revealed that the plant hosts actively recruit communities by exuding organic compounds and that the root-associated microbiomes possess a diverse repertoire of phosphorus turnover mechanisms. We also showed that the microbiomes of both plant species encompass novel populations capable of mobilizing nitrogen and that the substrate strongly influences the dynamics of this cycle. Our results show that the interplay between plants and their microbiomes shapes nutrient turnover in the campos rupestres. We highlight that investigation of microbial diversity is fundamental to understand plant fitness in stressful environments.

scholarly journals Deep phylogeographic splits but no taxonomic structure in the disjointly distributed Draba pacheri (Brassicaceae), a subendemic of the Eastern Alps

2021 ◽  
Author(s):  
Erich Kucs ◽  
Peter Schönswetter ◽  
Gerald M. Schneeweiss
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Single Species ◽  
Eastern Alps ◽  
Phylogenetic Position ◽  
Taxonomic Structure ◽  
European Alps ◽  
Aflp Data ◽  
Dna Sequence Data ◽  
Mountain Habitats

AbstractDraba (Brassicaeae), a model group for diversification and evolution in Arctic and mountain habitats, is taxonomically challenging and many of its species are insufficiently investigated. One such species is D. pacheri, an endemic of the eastern European Alps and the western Carpathians (here presumably extinct). Several hypotheses exist with respect to the phylogenetic position and the taxonomy of this species, but none of these has ever been tested using molecular data. In this article we examine (i) DNA sequence data to assess the phylogenetic position of D. pacheri within the genus and (ii) AFLP fingerprint data as well as morphometric data to address whether this species can be divided taxonomically into species or subspecies. DNA sequence data firmly place D. pacheri within the Core Draba Group III, whose internal relationships are, however, insufficiently resolved to precisely identify the closest relative of D. pacheri. AFLP data identify several genetically divergent lineages corresponding to geographically distinct regions. Although these lineages are congruent with hypotheses distinguishing either two species (D. pacheri s. str., D. norica) or one species with several subspecies, the lack of clear morphological separation, both with respect to the entire set of traits and single presumably diagnostic characters such as trichome morphology, renders recognition of a single species D. pacheri, as suggested previously, the best taxonomic solution. The deep and geographically strongly structured splits of D. pacheri likely are the result of isolation in several Pleistocene refugia and warrant that conservation efforts should involve populations from each of the main geographic subgroups.

scholarly journals Surface Imprinted Layer of Cypermethrin upon Au Nanoparticle as a Specific and Selective Coating for the Detection of Template Pesticide Molecules

Coatings ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 751
Author(s):  
Jaya Sitjar ◽  
Ying-Chen Hou ◽  
Jiunn-Der Liao ◽  
Han Lee ◽  
Hong-Zheng Xu ◽  
...  
Keyword(s):  
Photoelectron Spectroscopy ◽  
Compositional Analysis ◽  
Surface Enhanced Raman Spectroscopy ◽  
Au Nanoparticle ◽  
Selective Coating ◽  
Transmission Electron ◽  
Low Concentrations ◽  
Target Analytes ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

The detection of specific pesticides on food products is essential as these substances pose health risks due to their toxicity. The use of surface-enhanced Raman spectroscopy (SERS) takes advantage of the straightforward technique to obtain fingerprint spectra of target analytes. In this study, SERS-active substrates are made using Au nanoparticles (NPs) coated with a layer of polymer and followed by imprinting with a pesticide–Cypermethrin, as a molecularly imprinted polymer (MIP). Cypermethrin was eventually removed and formed as template cavities, then denoted as Au NP/MIP, to capture the analogous molecules. The captured molecules situated in-between the areas of high electromagnetic field formed by plasmonic Au NPs result in an effect of SERS. The formation of Au NP/MIP was, respectively, studied through morphological analysis using transmission electron microscopy (TEM) and compositional analysis using X-ray photoelectron spectroscopy (XPS). Two relatively similar pesticides, Cypermethrin and Permethrin, were used as analytes. The results showed that Au NP/MIP was competent to detect both similar molecules despite the imprint being made only by Cypermethrin. Nevertheless, Au NP/MIP has a limited number of imprinted cavities that result in sensing only low concentrations of a pesticide solution. Au NP/MIP is thus a specific design for detecting analogous molecules similar to its template structure.

scholarly journals Avipoxvirus phylogenetics: identification of a PCR length polymorphism that discriminates between the two major clades

2006 ◽  
Vol 87 (8) ◽  
pp. 2191-2201 ◽  
Author(s):  
Susan Jarmin ◽  
Ruth Manvell ◽  
Richard E. Gough ◽  
Stephen M. Laidlaw ◽  
Michael A. Skinner
Keyword(s):  
Vaccinia Virus ◽  
Core Protein ◽  
Sequence Data ◽  
Fragment Size ◽  
Taxonomic Structure ◽  
Avian Host ◽  
Virus Core ◽  
Phylogenetic Studies ◽  
Tight Correlation ◽  
First Time

Avipoxvirus infections have been observed in an extensive range of wild, captive and domesticated avian hosts, yet little is known about the genome diversity and host-range specificity of the causative agent(s). Genome-sequence data are largely restricted to Fowlpox virus (FWPV) and Canarypox virus (CNPV), which have been sequenced completely, showing considerable divergence between them. It is therefore proving difficult, by empirical approaches, to identify pan-genus, avipoxvirus-specific oligonucleotide probes for PCR and sequencing to support phylogenetic studies. A previous preliminary study used the fpv167 locus, which encodes orthologues of vaccinia virus core protein P4b (A3). PCR per se did not discriminate between viruses, but restriction-enzyme or sequence analysis indicated that the avipoxviruses clustered either with FWPV or with CNPV. Here, further study of the P4b locus demonstrated a third cluster, from psittacine birds. A newly identified locus, flanking fpv140 (orthologue of vaccinia virus H3L), confirms the taxonomic structure. This locus is particularly useful in that viruses from the fowlpox-like and canarypox-like clusters can be discriminated by PCR on the basis of fragment size, whilst sequence comparison allows discrimination for the first time between Pigeonpox virus and Turkeypox virus. Except within the psittacines, virus and avian host taxonomies do not show tight correlation, with viruses from the same species located in very different clades. Nor are all the existing recognized avipoxvirus species, defined primarily by avian host species (such as CNPV and Sparrowpox virus), resolved within the present structure.

Lapidia, a new monotypic genus of Asteraceae (Eupatorieae) from Brazil, and its phylogenetic placement

Phytotaxa ◽  
2017 ◽  
Vol 291 (1) ◽  
pp. 1 ◽  
Author(s):  
NÁDIA ROQUE ◽  
SILVANA C. FERREIRA ◽  
CÁSSIO VAN DEN BERG
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Sequence Data ◽  
Sister Group ◽  
Species Number ◽  
Monotypic Genus ◽  
Campos Rupestres ◽  
Chapada Diamantina ◽  
Phylogenetic Placement ◽  
The Family

Asteraceae is the family with the highest species number in the rocky fields (campos rupestres) of the Chapada Diamantina, Bahia, Brazil. On the basis of several collections from this area, we are proposing a new genus of Asteraceae based on morphology and phylogeny, to accommodate a species newly described here. Lapidia apicifolia is a loosely ramified shrub 2–4 m high, stem tomentose, leaves opposite-decussate, laminae conduplicate, petiolate, receptacle flat, epaleaceous, glabrous, and pappus of bristles fused at base, irregular in length, fringed and purplish. In a phylogenetic analysis using sequence data from ITS and trnL-trnF of selected members of Eupatorieae, Lapidia is indicated as sister group of a highly supported clade with Morithamnus, Bahianthus and Catolesia. This group is composed by loosely branched shrubs, most with leaves that are lax, stems, leaves and involucral bracts that are viscid (Bahianthus and Morithamnus) and, if not, trichomes (tomentose indumentum) are developed (Lapidia), to protect against both solar radiation and loss of water. A description, illustrations, and a discussion about related and sympatric genera are presented.

scholarly journals Expansion of known ssRNA phage genomes: From tens to over a thousand

2020 ◽  
Vol 6 (6) ◽  
pp. eaay5981 ◽  
Author(s):  
J. Callanan ◽  
S. R. Stockdale ◽  
A. Shkoporov ◽  
L. A. Draper ◽  
R. P. Ross ◽  
...  
Keyword(s):  
Markov Models ◽  
Phage Genome ◽  
Sequence Data ◽  
Aquatic Environments ◽  
Taxonomic Structure ◽  
Genome Database ◽  
Dna And Rna ◽  
Bacteriophage Ms2 ◽  
Ecological Importance ◽  
Phage Proteins

The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studies.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

The CM120 Biotwin: a high-contrast objective lens, optimum cryo-vacuum and improved EDX performance

1995 ◽  
Vol 53 ◽  
pp. 584-585
Author(s):  
Uwe Lücken ◽  
Michael Felsmann ◽  
Wim M. Busing ◽  
Frank de Jong
Keyword(s):  
Life Science ◽  
Focal Length ◽  
Objective Lens ◽  
High Contrast ◽  
Contrast Imaging ◽  
X Ray ◽  
Forming Mechanism ◽  
Similar Image ◽  
High Contrast Imaging ◽  
Low Concentrations

A new microscope for the study of life science specimen has been developed. Special attention has been given to the problems of unstained samples, cryo-specimens and x-ray analysis at low concentrations.A new objective lens with a Cs of 6.2 mm and a focal length of 5.9 mm for high-contrast imaging has been developed. The contrast of a TWIN lens (f = 2.8 mm, Cs = 2 mm) and the BioTWTN are compared at the level of mean and SD of slow scan CCD images. Figure 1a shows 500 +/- 150 and Fig. 1b only 500 +/- 40 counts/pixel. The contrast-forming mechanism for amplitude contrast is dependent on the wavelength, the objective aperture and the focal length. For similar image conditions (same voltage, same objective aperture) the BioTWIN shows more than double the contrast of the TWIN lens. For phasecontrast specimens (like thin frozen-hydrated films) the contrast at Scherzer focus is approximately proportional to the √ Cs.

Immunogold labeling of CMP-KDO synthetase produced by recombinant E. Coli cells

1987 ◽  
Vol 45 ◽  
pp. 924-925
Author(s):  
F. A. Durum ◽  
R. G. Goldman ◽  
T. J. Bolling ◽  
M. F. Miller
Keyword(s):  
Inclusion Bodies ◽  
Large Scale ◽  
Recombinant Dna ◽  
Test System ◽  
Cell Protein ◽  
Gram Negative Bacteria ◽  
Cytoplasmic Inclusions ◽  
Isolation And Purification ◽  
E Coli ◽  
Low Concentrations

CMP-KDO synthetase (CKS) is an enzyme which plays a key role in the synthesis of LPS, an outer membrane component unique to gram negative bacteria. CKS activates KDO to CMP-KDO for incorporation into LPS. The enzyme is normally present in low concentrations (0.02% of total cell protein) which makes it difficult to perform large scale isolation and purification. Recently, the gene for CKS from E. coli was cloned and various recombinant DNA constructs overproducing CKS several thousandfold (unpublished data) were derived. Interestingly, no cytoplasmic inclusions of overproduced CKS were observed by EM (Fig. 1) which is in contrast to other reports of large proteinaceous inclusion bodies in various overproducing recombinant strains. The present immunocytochemical study was undertaken to localize CKS in these cells.Immune labeling conditions were first optimized using a previously described cell-free test system. Briefly, this involves soaking small blocks of polymerized bovine serum albumin in purified CKS antigen and subjecting them to various fixation, embedding and immunochemical conditions.

Phase behavior of cationic and anionic surfactants at low concentrations

1992 ◽  
Vol 50 (1) ◽  
pp. 694-695
Author(s):  
E. Naranjo
Keyword(s):  
Phase Behavior ◽  
Structural Characterization ◽  
Dynamic Systems ◽  
Anionic Surfactants ◽  
Intermolecular Forces ◽  
Stable Form ◽  
Surfactant Mixtures ◽  
Low Concentrations ◽  
Cationic And Anionic Surfactants ◽  
General Method

Equilibrium vesicles, those which are the stable form of aggregation and form spontaneously on mixing surfactant with water, have never been demonstrated in single component bilayers and only rarely in lipid or surfactant mixtures. Designing a simple and general method for producing spontaneous and stable vesicles depends on a better understanding of the thermodynamics of aggregation, the interplay of intermolecular forces in surfactants, and an efficient way of doing structural characterization in dynamic systems.

Compositional Analysis of III-V Interface Lattice Images

1980 ◽  
Vol 38 ◽  
pp. 318-319
Author(s):  
A. Olsen ◽  
J.C.H. Spence ◽  
P. Petroff
Keyword(s):  
Crystal Structure ◽  
Image Matching ◽  
Compositional Analysis ◽  
Depth Of Field ◽  
Limit Set ◽  
High Contrast ◽  
Resolution Limit ◽  
Fourier Image ◽  
Lattice Images ◽  
True Structure

Since the point resolution of the JEOL 200CX electron microscope is up = 2.6Å it is not possible to obtain a true structure image of any of the III-V or elemental semiconductors with this machine. Since the information resolution limit set by electronic instability (1) u0 = (2/πλΔ)½ = 1.4Å for Δ = 50Å, it is however possible to obtain, by choice of focus and thickness, clear lattice images both resembling (see figure 2(b)), and not resembling, the true crystal structure (see (2) for an example of a Fourier image which is structurally incorrect). The crucial difficulty in using the information between Up and u0 is the fractional accuracy with which Af and Cs must be determined, and these accuracies Δff/4Δf = (2λu2Δf)-1 and ΔCS/CS = (λ3u4Cs)-1 (for a π/4 phase change, Δff the Fourier image period) are strongly dependent on spatial frequency u. Note that ΔCs(up)/Cs ≈ 10%, independent of CS and λ. Note also that the number n of identical high contrast spurious Fourier images within the depth of field Δz = (αu)-1 (α beam divergence) decreases with increasing high voltage, since n = 2Δz/Δff = θ/α = λu/α (θ the scattering angle). Thus image matching becomes easier in semiconductors at higher voltage because there are fewer high contrast identical images in any focal series.

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