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160 results for “Molecular detection”
Molecular composition of dissolved organic matter in NTL-LTER lakes detected by Fourier-transform ion cyclotron resonance mass spectrometry
The composition of dissolved organic matter (DOM) varies widely in the environment due to distinct sources of the material and subsequent processing. DOM composition drives its reactivity in terms of many processes including photochemical reactions, microbial metabolism, and carbon cycling within water bodies. This study uses ultra-high resolution mass spectrometry via a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) to evaluate DOM composition at the molecular level to determine differences in DOM composition among the NTL-LTER lakes. Whole water samples were collected from the surface of each lake near the shore on August 18th and 19th in 2016 in. Ultraviolet-visible spectra were recorded as light absorbance can also give information about DOM composition. Additionally, concentrations of anions, cations, and pH were measured waters because these can all alter DOM reactivity in the environment. Both water chemistry and DOM composition vary widely among the lakes with the bogs displaying the most terrestrial-like signature in DOM and the oligotrophic lakes show more microbial-like or environmentally processed DOM.
Fig. 1 in Evidence for intercontinental parasite exchange through molecular detection and characterization of haematozoa in northern pintails (Anas acuta) sampled throughout the North Pacific Basin
Fig. 1. Approximate locations in North America and East Asia at which northern pintail tissue samples were collected during 2011–2012 to test for haemosporidian infection. Regions (i.e. Alaska, California, and Japan) and sub-regions (Koyukuk-Nowitna NWR, Yukon-Kuskokwim Delta NWR, Izembek NWR, Sacramento Valley, San Joaquin Valley) for sampling locations are indicated (NWR = National Wildlife Refuge). The number of tissue samples per location is indicated in parentheses. Sample tissue was whole blood unless indicated by an asterisk (signifying wing muscle tissue).
Fig. 2 in First molecular detection of Francisella tularensis in turtle (Testudo graeca) and ticks (Hyalomma aegyptium) in Northwest of Iran
Fig. 2. The evolutionary lineage was determined using the Maximum Likelihood method and the Tamura-Nei model. The displayed tree represents the one with the most favorable log likelihood (429.22). Additionally, the branches are accompanied by the percentage denoting how frequently the related taxa formed clusters in the trees. The initial trees for exploratory purposes were automatically created using the Neighbor-Join and BioNJ algorithms. This was accomplished by utilizing a matrix of pairwise distances, which were calculated employing the Tamura-Nei model. From these initial trees, the one with the most favorable log likelihood value was selected. This analysis was conducted on a collection of 31 nucleotide sequences. The encompassed codon positions consisted of 1st+2nd+3rd +Noncoding. The final dataset consisted of a total of 306 positions. The evolutionary analyses were performed utilizing MEGA11.
Fig. 3 in First molecular detection of Francisella tularensis in turtle (Testudo graeca) and ticks (Hyalomma aegyptium) in Northwest of Iran
Fig. 3. The lineage's evolutionary narrative was deduced through the application of the Neighbor-Joining technique. The most advantageous tree configuration is depicted. Adjacent to the branches, the percentages reflect how often the related taxa aggregated within the bootstrap test, comprising 1000 replicates. Evolutionary distances were calculated using the Maximum Composite Likelihood method, expressed as the count of base substitutions per site. In this study, a collective of 32 nucleotide sequences were taken into account. The codon positions covered 1st+2nd+3rd + Noncoding. Ambiguous positions were excluded for each sequence pair, following the pairwise deletion technique. In the culminating dataset, a collective count of 542 positions was encompassed. The evolutionary analyses were executed using MEGA11.
Fig. 3 in Detection and molecular characterization of the mosquito-borne filarial nematode Setaria tundra in Danish roe deer (Capreolus capreolus)
Fig. 3. Neighbor-Joining phylogenetic relationship of four isolates of Setaria tundra from distant localities in Denmark. The analysis was based on cox1 gene sequences (578 bp). Percentage bootstrap support from 1000 replicate samples is indicated at the right of the supported node. Accession numbers for sequences obtained from GenBank are given in parentheses, followed by origin of isolate, only applicable to S. tundra. The scale bar indicates distance.
Fig. 1 in Detection and molecular characterization of the mosquito-borne filarial nematode Setaria tundra in Danish roe deer (Capreolus capreolus)
Fig. 1. Geographical origin (black dots) of Setaria tundra recovered from six infected roe deer. A: October 2010, B: May 2011, C: December 2012, D: May 2013 (two cases), and E: March 2014.
Fig. 2 in Detection and molecular characterization of the mosquito-borne filarial nematode Setaria tundra in Danish roe deer (Capreolus capreolus)
Fig. 2. Morphology of adult worms of Setaria tundra (A‾C) and microfilaria (D and E) recovered from roe deer in Denmark. A: Cephalic region showing the bifid projections (bp) carried on top of a peribuccal crown (pc) and one of the four cephalic papillae (cp). B: Posterior end of male worm with papillae weakly visible (arrowheads). C: Posterior end of female worm showing a knob at the tip of the tail (arrow head), that possesses longitudinal grooves and pores, a papilla (pa), and a collar composed of a row of bosses (co). D: Microfilaria collected from a female worm. The length of the microfilaria including the sheath (white arrow heads) was approximately 316 Mm, whereas the microfilaria was approximately 287 Mm, with a blunt anterior end and a tapering posterior end. E: Setaria tundra coiled under the liver capsule (case 3). Scale bars indicated for all but figure E.
Solvent sites detection from molecular dynamics in mixed solvents
<p>In this zip file, you will find 3 molecular dynamics (MDs) that were run using the AMBER molecular dynamics package (https://ambermd.org/), and the necessary scripts to obtain the solvent sites.</p> <p>The MDs correspond to the kinase and rubredoxin domains of protein kinase G from Mycobacterium tuberculosis. </p> <p> </p> <p> </p>
Figure 1 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 1. The aggregated Argas persicus ticks at different stages around a thatched birdhouse in Lorestan province.
Figure 3 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 3. The phylogenetic tree inferred from flaB amino acids sequence data of B. anserina (clade I) and other Borrelia taxa (clade II, KX171816 and JF693808) constructed using Neighbor-Joining (NJ) method with bootstrap test (1,000 replicates). The main clade in right side of tree separated with colored rectangular shape. Taxa are as species name following GenBank accession number, taxon of the present study indicated as bold. Nodes indicated with bootstrap value. Branch lengths are proportional to evolutionary changes, the units of the number of amino acid substitutions per site. The analysis involved 12 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 166 positions in the final dataset. The more diverged Pakistani strain of B. anserina (JF693808) located outside the main B. anserina (clade I). The members of clade II and B. hermsii are as outgroup.
Figure 2 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 2. The stereomicroscopic view of dissected salivary glands (A); ovary and uterus (B) of female Argas tick in normal saline.
Figure 4 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 4. The phylogenetic tree inferred from flaB nucleotide sequence data of B. anserina (clade I) and other Borrelia taxa (clade II and KX171816) constructed using Neighbor-Joining (NJ) method with bootstrap test (1000 replicates). The main clade in right side of tree separated with colored rectangular shape. Taxa are as species name following GenBank accession number, taxon of the present study indicated as bold. Nodes indicated with bootstrap value. Branch lengths are proportional to evolutionary changes, the units of the number of base substitutions per site the units of the number of amino acid substitutions per site. The analysis involved 12 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 500 positions in the final dataset. The more diverged Pakistani strain of B. anserina (JF693808) located inside the main B. anserina (clade I). The members of clade II and B. hermsii are as outgroup.
Fig. 3 in Molecular detection of Wolbachia endosymbiont in reptiles and their ectoparasites
Fig. 3 Phylogenetic relationship of Wolbachia detected in this study (in bold) and other available from GenBank belonging to different supergroups based on a partial sequence of the 16S rRNA gene. Evolutionary analysis was conducted on 1000 bootstrap replications using Maximum Likelihood method and Kimura 2-parameter model with discrete Gamma distribution (+ G) to model evolutionary rate differences among sites selected by best-fit model. GenBank accession number and host species are indicated
Fig. 1 in Molecular detection of Angiostrongylus vasorum in gastropods in Surrey, UK
Fig. 1 Neighbour joining tree based on cytochrome oxidase I (COI) sequences representing all clades of the Agriolimacidae family. Values next to branches indicate percentage bootstrap support. The asterisk (*) indicates the Agriolimacidae specimen collected in this study
Fig. 3 in Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California
Fig. 3. Phylogenetic assignment of hematozoa mitochondrial DNA cytochrome b sequences originating from northern pintails collected from the Central Valley of California (asterisks). Reference sequences for Leucocytozoon (white circles), Haemoproteus (grey circles), and Plasmodium (black circles) parasites were obtained from the National Center for Biotechnology Information. Bootstrap support values for differentiation of broad taxonomic groups are indicated. Values reported for Haemoproteus and Plasmodium show support for phylogenetic differentiation from the mixed subclade formed by reference sequences a and b.
Fig. 4. Minimum spanning network for hematozoa mitochondrial DNA cytochrome b in Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California
Fig. 4. Minimum spanning network for hematozoa mitochondrial DNA cytochrome b haplotypes detected in Central Valley northern pintails. Circles are drawn proportional to the frequency at which haplotypes were observed. Shading represents the sample collection from which haplotypes originated: white (2006– 2007 wing muscle), grey (2011–2012 wing muscle), and black (2011–2012 blood). A single mutation separates nodes unless explicitly indicated by number. Lines separating nodes are drawn to scale unless indicated by a break. Parasite taxa have been abbreviated in haplotype names (Leu = Leucocytozoon, Hae = Haemoproteus and Pla = Plasmodium).
Fig. 1 in Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California
Fig. 1. Locations in the Central Valley of California from which northern pintail tissue samples were collected. Samples (n in 2006–2007, n in 2011–2012) were collected in the Sacramento Valley sub-region at: (A) Sacramento National Wildlife Refuge (NWR; 44,92), (B) Delevan NWR (35,7), (C) Colusa NWR (0,2), (D) Sutter NWR (0,1), (E) Little Dry Creek State Wildlife Area (SWA; 0,5), (F) Howard Slough SWA (0,1), (G) Yolo SWA (0,8) and (H) a private duck hunting club (0,1). Samples were collected in the San Joaquin Valley sub-region at: (I) San Luis NWR (7,0), (J) Kesterson NWR (4,0), (K) Los Banos SWA (14,0), (L) Volta SWA (10,0), (M) a private duck hunting club (2,0), and (N) Mendota SWA (30,40).
Fig. 2 in Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California
Fig. 2. Estimated prevalence of Leucocytozoon (white bars), Haemoproteus (grey bars), and Plasmodium (black bars) parasites in northern pintails sampled in the Central Valley of California in 2006–2007 and 2011–2012 using occupancy modeling. Error bars represent 95% confidence intervals around point estimates.
Figure 2. a in Evidence of Ehrlichia chaffeensis in Argentina through molecular detection in marsh deer (Blastocerus dichotomus)
Figure 2. a_Summary of the E. chaffeensis molecular amplification of the 16SrRNA and the VLPT genes in marsh deer and tick samples at different time points. b_ Alignment of a fragment of the 16SrRNA nucleotide sequences from reference Anaplasma and Ehrlichia strains and those amplified from deer (C2, C7, D11 and C12) and a tick (tick1_C7) in the present study. The red line marks the hypervariable V1 region.
Fig. 1 in Evidence of Ehrlichia chaffeensis in Argentina through molecular detection in marsh deer (Blastocerus dichotomus)
Fig. 1. Map of the two marsh deer populations (Paraná River Delta and Ibera Wetlands) located along the alluvial plain of the Paraná River (Argentina).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.