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2,315 results for “Comparative analysis”
Data from: Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude lizard living in the Qinghai-Tibet Plateau
Background: Organisms living at high altitudes must overcome three major environmental challenges: hypoxia, cold, and intense UV radiation. The molecular mechanisms that enable these challenges to be overcome have mainly been studied in endothermic organisms; relatively little attention has been paid to poikilothermic species. Here, we present deep transcriptome sequencing in two closely related lizards, the high altitude-dwelling Phrynocephalus erythrurus and the lowland-dwelling P. putjatia, to identify candidate genes under positive selection and to explore the convergent evolutionary adaptation of poikilothermic animals to high altitude life. Results: More than 70 million sequence reads were generated for each species via Illumina sequencing. De novo assembly produced 56,845 and 63,140 transcripts for P. erythrurus and P. putjatia, respectively. P. erythrurus had higher Ka/Ks ratios than P. putjatia, implying an accelerated evolutionary rate in the high altitude lizard lineage. 206 gene ontology (GO) categories with accelerated evolutionary rates and 43 candidate positively selected genes were detected along the P. erythrurus lineage. Some of these GO categories have functions associated with responses to hypoxia, energy metabolism and responses to UV damage. We also found that the high-altitude ranid frog R. kukunoris had higher Ka/Ks ratios than the closely related low-altitude frog R. chensinensis, and that the functional categories with accelerated evolutionary rates in R. kukunoris overlapped extensively with those detected along the P. erythrurus lineage. Conclusions: The mechanisms of high altitude adaptation in P. erythrurus were tentatively inferred. By comparing two pairs of low- and high-altitude poikilothermic species, we found that similar functional categories had undergone positive selection in high altitude-dwelling Phrynocephalus and Rana lineages, indicating that similar mechanisms of adaptation to high altitude might have evolved in both genera. Our findings provide important guidance for future functional studies on high altitude adaptation in poikilothermic animals.
Data from: Comparative analysis of principal components can be misleading
Most existing methods for modeling trait evolution are univariate, although researchers are often interested in investigating evolutionary patterns and processes across multiple traits. Principal components analysis (PCA) is commonly used to reduce the dimensionality of multivariate data so that univariate trait models can be fit to individual principal components. The problem with using standard PCA on phylogenetically structured data has been previously pointed out yet it continues to be widely used in the literature. Here we demonstrate precisely how using standard PCA can mislead inferences: The first few principal components of traits evolved under constant-rate multivariate Brownian motion will appear to have evolved via an "early burst" process. A phylogenetic PCA (pPCA) has been proprosed to alleviate these issues. However, when the true model of trait evolution deviates from the model assumed in the calculation of the pPCA axes, we find that the use of pPCA suffers from similar artifacts as standard PCA. We show that data sets with high effective dimensionality are particularly likely to lead to erroneous inferences. Ultimately, all of the problems we report stem from the same underlying issue—by considering only the first few principal components as univariate traits, we are effectively examining a biased sample of a multivariate pattern. These results highlight the need for truly multivariate phylogenetic comparative methods. As these methods are still being developed, we discuss potential alternative strategies for using and interpreting models fit to univariate axes of multivariate data.
Data from: Understanding the genomic basis of adaptive response to variable osmotic niches in freshwater prawns: a comparative intraspecific RNA-Seq analysis of Macrobrachium australiense
Understanding the molecular basis of adaptive response to variable environmental conditions is a central goal of evolutionary biology. Here we sought to identify potential outlier SNPs (single nucleotide polymorphisms) in three wild populations of a freshwater prawn (Macrobrachium australiense) that are exposed to differing osmotic niches by using a comparative transcriptomics approach. De novo assembly of approximately 542 million (75 nt) pair end reads collected from 10 individuals revealed 123,396 longer contigs/transcripts of variable length, that showed 97.38% transcriptome assembly completeness. Differential gene expression (DGE) analysis of major osmoregulatory genes revealed that Calreticulin, Na+/H+ exchanger and V-type (H+) ATPase showed the highest expression levels in the Blunder Creek (low ionic) population, while Crustacean cardiovascular peptide (CCP), Na+/K+-ATPase, Na+/K+/2Cl- Co-transporter (NKCC) and Na+/HCO3 exchanger showed the highest expression levels in the Bulimba Creek (higher ionic) population. In total, 16 gene ontology (GO) term categories were functionally enriched among the three studied populations. We identified 4144 raw and 835 high quality filtered SNPs in the three M. australiense populations, of which 84 SNPs were identified as outliers. Outliers were detected in 4 important osmoregulatory genes that include: Calreticulin, Na+/H+ exchanger, Na+/K+-ATPase and V-type-(H+)-ATPase. All outliers in the osmoregulatory genes were located in non-coding regulatory regions (untranslated regions, UTRs) of the gene. We hypothesize that the outlier SNPs identified here in M. australiense populations exposed naturally to different osmotic conditions influence specific gene expression patterns that allow individuals to respond to local environmental conditions.
Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization
The spatial organization of genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets which include the z-axis information in image stacks. Here we compare the suitability of 2D vs 3D distance measurements in the analysis of various features of spatial genome organization. We find in general good agreement between 2D and 3D analysis with higher convergence of measurements as the interrogated distance increases, especially in flat cells. Overall, 3D distance measurements are more accurate than 2D distances, but are also more susceptible to noise. In particular, z-stacks are prone to error due to imaging properties such as limited resolution along the z-axis and optical aberrations, and we also find significant deviations from unimodal distance distributions caused by low sampling frequency in z. These deviations are ameliorated by significantly higher sampling frequency in the z-direction. We conclude that 2D distances are preferred for comparative analyses between cells, but 3D distances are preferred when comparing to theoretical models in large samples of cells. In general and for practical purposes, 2D distance measurements are preferable for many applications of analysis of spatial genome organization.
Data from: Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation
How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli in stationary phase as a result of being starved for glucose, not on the genetic adaptation of E. coli to utilize alternative nutrients. In our analysis, we have taken advantage of the temporal correlations within and among RNA and protein abundances to identify systematic trends in gene regulation. Specifically, we have developed a general computational strategy for classifying expression-profile time courses into distinct categories in an unbiased manner. We have also developed, from dynamic models of gene expression, a framework to characterize protein degradation patterns based on the observed temporal relationships between mRNA and protein abundances. By comparing and contrasting our transcriptomic and proteomic data, we have identified several broad physiological trends in the E. coli starvation response. Strikingly, mRNAs are widely down-regulated in response to glucose starvation, presumably as a strategy for reducing new protein synthesis. By contrast, protein abundances display more varied responses. The abundances of many proteins involved in energy-intensive processes mirror the corresponding mRNA profiles while proteins involved in nutrient metabolism remain abundant even though their corresponding mRNAs are down-regulated.
Figure 4 in Comparative analysis of the karyotype sensitivities of Apodemus flavicollis and laboratory mice to DNA-damaging agents
Figure 4. Pericentric inversions in bone marrow cell of A. flavicollis after Mitomycin C treatment.
Figure 2 in Comparative analysis of the karyotype sensitivities of Apodemus flavicollis and laboratory mice to DNA-damaging agents
Figure 2. Breaks and fragments in bone marrow cell of A. flavicollis after Mitomycin C treatment.
Figure 8 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 8. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VIII. A, Chubb (2004a); B, Harrison et al. (2004).
Figure 9 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 9. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), IX. A, Pereira & Baker (2006a); B, Slack et al. (2006a).
Fig. 7 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 7. Left lateral view of head of Trichogenes longipinnis (Trichogeninae), LIRP 1059 (75.5 mm SL). Antorbital and core of nasal barbels removed.
Fig. 36 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 36. Illustrations of cranial musculature of Nematogenys inermis by (A) Howes (1983a) (right dorsolateral view of anterior region of head) and (B) Diogo et al. (2006) (right lateral view of head). Both illustrations flipped horizontally to facilitate comparisons with other figures. Drawings not altered, but labels modified in order to clarify different names for portions of adductor mandibulae (see explanation on text). Terminology used in the present study marked with gray background.
Fig. 6 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 6. Ventral view of left half of neurocranial floor and suspensorium of Copionodon pecten (Copionodontinae), LIRP 1012 (49.5 mm SL). Internal suspensorial muscles and upper pharyngeal tooth plate with attached levator internus 4 retained; remaining elements of branchial arches removed. Arrow indicates site of origin of adductor operculi.
Fig. 13 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 13. Ventral view of left half of neurocranial floor of Ituglanis cf. gracilior (Trichomycterinae), MZUSP 86821 (53.2 mm SL). Internal suspensorial muscles and upper pharyngeal tooth plate with attached levator internus 4 retained; remaining elements of branchial arches removed.
Fig. 22 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 22. Left lateral view of head of Haemomaster venezuelae (Stegophilinae), LIRP 7438 (36.9 mm SL).
Fig. 28 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 28. Left lateral view of head of Vandellia sanguinea (Vandelliinae), LIRP 7414 (77.1 mm SL). Ventral most premaxillary claw-like teeth removed.
Fig. 9 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 9. Left lateral view of head of Trichomycterus brasiliensis (Trichomycterinae), LIRP 1968 (76.4 mm SL). Core of nasal barbels removed.
Detection, quantification and classification of ripened tomatoes: a comparative analysis of image processing and machine learning
<p>This is an open dataset.</p>
Detection, quantification and classification of ripened tomatoes: a comparative analysis of image processing and machine learning
<p>In this study, specifically for the detection of ripe/unripe tomatoes with/without defects in the crop field, two distinct methods are described and compared from captured images by a camera mounted on a mobile robot. One is a machine learning approach, known as 'Cascaded Object Detector' (COD) and the other is a composition of traditional customised methods, individually known as 'Colour Transformation': 'Colour Segmentation' and 'Circular Hough Transformation'. The (Viola-Jones) COD generates 'histogram of oriented gradient' (HOG) features to detect tomatoes. For ripeness checking, the RGB mean is calculated with a set of rules. However, for traditional methods, colour thresholding is applied to detect tomatoes either from natural or solid background and RGB colour is adjusted to identify ripened tomatoes. This algorithm is shown to be optimally feasible for any micro-controller based miniature electronic devices in terms of its run time complexity of <i>O</i>(<i>n</i><sup>3</sup>) for a traditional method in best and average cases. Comparisons show that the accuracy of the machine learning method is 95%, better than that of the Colour Segmentation Method using MATLAB.</p>
Genomes and annotation files for comparative circularome analysis
<p>Part of a manuscript on eccDNAs in Magnaporthe oryzae</p>
Figure 2 from: Tanga CM, Manrakhan A, Daneel JH, Mohamed SA, Khamis FM, Ekesi S (2015) Comparative analysis of development and survival of two Natal fruit fly Ceratitis rosa Karsch (Diptera, Tephritidae) populations from Kenya and South Africa. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 467-487. https://doi.org/10.3897/zookeys.540.9906
Figure 2 - Linear and non-linear regressions of temperature related developmental rates of immature stages of two groups of Ceratitis rosa from South Africa
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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.