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Fig. 2 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 2 Western blot analysis of MSP in P. redivivus. In adult animals, MSP is detected as double band with approximate weight 15 and 16 kDa. a Both male and female samples reveal MSP signal, because the latter include mated females. α-Tubulin was used as a loading control (approximate weight 55 kDa). b Analysis of young males and females. MSP is not detected in females, because most of them are unmated. Abbreviations: m, males; f, females
Fig. 3 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 3 Schematic representation of P. redivivus spermatozoa based on transmission electron microscopy. a Morphology of immature and mature spermatozoa. Immature spermatozoon is an unpolarized cell with nucleus devoid of nuclear envelope, mitochondria, and membranous organelles. Mature spermatozoon in female reproductive system is a bipolar cell with anterior pseudopodium and posterior main cell body containing chromatin, mitochondria, and membranous organelles that attached to cell membrane and open to the exterior via pores. Reproduced from Zograf (2014) with the permission from copyright holder (Russian Journal of Nematology). b Chain of conjugated mature spermatozoa in female reproductive system. Abbreviations: N, nucleus; mt, mitochondria; mo, membranous organelles; ch, nuclear chromatin; ps, pseudopodium; mcb, mail cell body
Fig. 1 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 1 Phylogeny of nematodes and MSP-based sperm motility. Phylogenetic relationships within phylum Nematoda derived primarily from SSU rDNA sequence data are given according to De Ley and Blaxter (2002). Suborders of the order Rhabditida, in which representatives highly homologous MSPs are found at DNA, RNA, or protein levels, are marked by underlining. Taxa whose species used in this study are marked with asterisks. Orders Trefusi- ida, Isolaimida, Dioctophyma- tida, Muspiceida, Marimermith- ida, and Desmoscolecida are not shown in this tree
Fig. 8 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 8 Putative MSPs those are most similar to peptide antigen. a P. redivivus MSPs aligned with peptide antigen. Protein sequences (Pan_g61.t1, Pan_g6018.t1, Pan_g6424.t1, Pan_g9068.t1, Pan_ g19433.t1, and Pan_g21178.t1) were found by Blast using peptide
Fig. 4 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 4 Immunolocalization of MSP in P. redivivus sperm. a Immature spermatozoa extracted from male. MSP localizes in granules. In some cells, MSP has strongest signals in the periphery (arrowheads) (scale bar 10 µm). b Chain of mature spermatozoa extracted from female.
FIGURE 4 in First occurrence of Gracilaria chilensis, and distribution of Gracilariopsis lemaneiformis (Gracilariaceae, Gracilariales) in Peru on the basis of rbcL sequence analysis
FIGURE 4. Phylogenetic tree based on rbcL sequences inferred from a maximum-likelihood analysis as implemented by RAxML. Taxa highlighted in red were newly sequenced for this study. GenBank numbers are listed after each taxon. Bootstrap proportions (>50%) for ML (1000 replicates, Left) and Bayesian Posterior Probability (Right) are shown at the nodes. Full support denoted as *.
FIGURE 3 in First occurrence of Gracilaria chilensis, and distribution of Gracilariopsis lemaneiformis (Gracilariaceae, Gracilariales) in Peru on the basis of rbcL sequence analysis
FIGURE 3. Habit of a female gametophyte of Gracilariopsis lemaneiformis from San Andres, Ica, Peru (IMARPE 05-000325).
FIGURE 2 in First occurrence of Gracilaria chilensis, and distribution of Gracilariopsis lemaneiformis (Gracilariaceae, Gracilariales) in Peru on the basis of rbcL sequence analysis
FIGURE 2. Habit of non-reproductive specimens of Gracilaria chilensis from Morro Sama, Peru. Fig. 2A. IMARPE 05-000326-1. Fig. 2B. IMARPE 05-000326-2.
FIGURE 1 in First occurrence of Gracilaria chilensis, and distribution of Gracilariopsis lemaneiformis (Gracilariaceae, Gracilariales) in Peru on the basis of rbcL sequence analysis
FIGURE 1. Distribution map of terete Gracilariaceae from Peru. Occurrence of Gracilariopsis lemaneiformis along the northern and central coast: Paita (Piura), Eten (Lambayeque), Ancon and Chorrillos (Lima), and San Andres (Ica). Also, Gracilaria chilensis from the southern coast (Sama, Tacna).
Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.
Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
Background: Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. Results: Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. Conclusion: MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
FIGURE 6 in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 6. Palaeogeographic scenario (Scenario B). (1) The Tyrrhenian basin in the Tortonian time (modified from OrszagSperber et al., 1993) with a land bridge connecting Sardinia with the peninsula. (2) Separation of the CalabroPeloritan massif (CPm) from Sardinia (modified from Duermeijer et al., 1998). Arrows hypothesize dispersal routes. See the text for comments.
FIGURE 5 in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 5. Palaeogeographic scenario (Scenario A). The Italian Peninsula in the Pliocene (modified from Pinna, 1989). Black triangles: sampling sites of Salamandrina populations included in the PER clade. Black stars: sampling sites of Salamandrina populations included in the TER clade. See text for details and confront to the Fig. 1.
FIGURE 4 in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 4. Haplotype network of Salamandrina terdigitata, reconstructed using parsimony probability as implemented in TCS. Each circle in the network corresponds to one observed haplotype. Size of circles is proportional to the number of individuals (in parentheses) carrying a given haplotype. The three letters codes of the populations are indicated; numbered codes in italic mean different individuals when more than one haplotype was found in a population.
FIGURE 3 in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 3. Maximum likelihood tree for Salamandrina terdigitata samples plus outgroup, based on combined 12S, 16S and cytb. HKY85+ model (ln = 2864.386; shape parameter = 0.1203) was assumed. Numbers in boxes (from top to bottom) are bootstrap support values for ML (100 replicates), MP (1000 replicates) and NJ (1000 replicates) and posterior probability percentages in the Bayesian analysis (2 million generators). Specimens are identified by code of sampling locality (as in Tab.1) and by a progressive number.
FIGURE 1. A in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 1. A female specimen of Salamandrina terdigitata from Lepini Mountains (Latium, Central Italy).
Data from: Whole genome sequencing and rare variant analysis in essential tremor families
Essential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative single nucleotide variant (SNV) or indel due to incomplete coverage of the entire coding region of the genome, in addition to accurate detection of larger structural variants (SVs) and copy number variants (CNVs). Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n=40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare SNV and indel classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test. A separate analysis of rare SV and CNVs segregating within ET families was also performed. Prioritization of candidate genes identified within families was performed using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). Functional studies of CACNA1G and SLIT3 suggest a role for these genes in ET disease pathogenesis.
Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae
<p>Two datasets are provided to support the journal article (https://doi.org/10.1643/i2020112) by T. C. Grande and M. V. H. Wilson naming the new Bermuda fish species <em>Polymixia hollisterae</em>. The first dataset is for 2-D multivariate morphometric comparisons of selected specimens and species of the fish genus <em>Polymixia</em>. The file is in TPS format, as a plain text file, for use in the application MorphoJ. The data are for 27 specimens with pixel coordinates for 34 landmarks digitized in ImageJ and used to generate Fig. 13 in the referenced publication. The second dataset, published here courtesy of Dr. R. Eytan, is a mitochondrial DNA barcode sequence in fasta format for the second paratype specimen, a small juvenile of the new species. The specimen is only the third one known of the new species and the only one not from Bermuda. It was collected in the north-central Gulf of Mexico and is now deposited in the Harvard University MCZ fish collection as catalog number MCZ 174218. The fasta file can be used as input to the barcode identification function at boldsystems.org, although its original identification in BOLD was incorrect.</p>
Comparative Analysis of Complete Chloroplast Genomes and Multiple DNA Sequences Reveals Interspecific Relationships of C. bretschneideri and Related Species in China
<p><strong> ITS, and <em>LEAFY</em> intron 1 sequencing of 36 Crataegus accessions.</strong></p>
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
<p>The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.