Archilochus colubris
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ABSTRACT:
PROVIDER: PRJNA919979 | ENA |
REPOSITORIES: ENA
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Project description:Archilochus colubris Transcriptome or Gene expression
| PRJNA369257 | ENA
Project description:Archilochus colubris Genome sequencing and assembly
| PRJNA811496 | ENA
Project description:Glucose transporter (GLUT) proteins play a key role in the transport of monosaccharides across cellular membranes, and thus, blood sugar regulation and tissue metabolism. Patterns of GLUT expression, including the insulin-responsive GLUT4, have been well characterized in mammals. However, relatively little is known about patterns of GLUT expression in birds with existing data limited to the granivorous or herbivorous chicken, duck and sparrow. The smallest avian taxa, hummingbirds, exhibit some of the highest fasted and fed blood glucose levels and display an unusual ability to switch rapidly and completely between endogenous fat and exogenous sugar to fuel energetically expensive hovering flight. Despite this, nothing is known about the GLUT transporters that enable observed rapid rates of carbohydrate flux. We examined GLUT (GLUT1, 2, 3, & 4) expression in pectoralis, leg muscle, heart, liver, kidney, intestine and brain from both zebra finches (Taeniopygia guttata) and ruby-throated hummingbirds (Archilochus colubris). mRNA expression of all four transporters was probed using reverse-transcription PCR (RT-PCR). In addition, GLUT1 and 4 protein expression were assayed by western blot and immunostaining. Patterns of RNA and protein expression of GLUT1-3 in both species agree closely with published reports from other birds and mammals. As in other birds, and unlike in mammals, we did not detect GLUT4. A lack of GLUT4 correlates with hyperglycemia and an uncoupling of exercise intensity and relative oxidation of carbohydrates in hummingbirds. The function of GLUTs present in hummingbird muscle tissue (e.g. GLUT1 and 3) remain undescribed. Thus, further work is necessary to determine if high capillary density, and thus surface area across which cellular-mediated transport of sugars into active tissues (e.g. muscle) occurs, rather than taxon-specific differences in GLUT density or kinetics, can account for observed rapid rates of sugar flux into these tissues.
| S-EPMC3796544 | biostudies-literature
Project description:Background:Autumn latitudinal migrations generally exhibit one of two different temporal migration patterns: type 1 where southern populations migrate south before northern populations, or type 2 where northern populations overtake southern populations en route. The ruby-throated hummingbird (Archilochus colubris) is a species with an expansive breeding range, which allows opportunities to examine variation in the timing of migration. Our objective was to determine a relationship between natal origin of ruby-throated hummingbirds and arrival at a Gulf coast stopover site; and if so, what factors, such as differences in body size across the range as well as the cost of migration, might drive such a pattern. To carry out our objectives, we captured hummingbirds at a coastal stopover site during autumn migration, at which time we collected feathers from juveniles for analysis of hydrogen stable isotopes. Using the hydrogen stable isotope gradient of precipitation across North America and published hydrogen isotope values of feathers from populations of breeding ruby-throated hummingbirds, we assigned migrants to probable natal latitudes. Results:Our results confirm that individuals from across the range (30-50° N) stopover along the Gulf of Mexico and there is a positive relationship between arrival day and latitude, suggesting a type 1 migration pattern. We also found no relationship between fuel load (proxy for migration cost) or fat-free body mass (proxy for body size) and natal latitude. Conclusions:Our results, coupled with previous work on the spatial migration patterns of hummingbirds, show a type 1 chain migration pattern. While the mechanisms we tested do not seem to influence the evolution of migratory patterns, other factors such as resource availability may play a prominent role in the evolution of this migration system.
| S-EPMC5761100 | biostudies-literature
Project description:Background:Hummingbirds oxidize ingested nectar sugars directly to fuel foraging but cannot sustain this fuel use during fasting periods, such as during the night or during long-distance migratory flights. Instead, fasting hummingbirds switch to oxidizing stored lipids that are derived from ingested sugars. The hummingbird liver plays a key role in moderating energy homeostasis and this remarkable capacity for fuel switching. Additionally, liver is the principle location of de novo lipogenesis, which can occur at exceptionally high rates, such as during premigratory fattening. Yet understanding how this tissue and whole organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation. Findings:We generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, then clustered isoforms into gene families to generate de novo gene contigs using Cogent. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. Finally, we closely examined homology of critical lipid metabolism genes between our transcriptome data and avian and human genomes. Conclusions:We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the hepatic lipogenic pathways. Our results leverage cutting-edge technology and a novel bioinformatics pipeline to provide a first direct look at the transcriptome of this incredible organism.
| S-EPMC5869288 | biostudies-literature
Project description:Proctophyllodes huitzilopochtlii Atyeo & Braasch 1966 (Acariformes: Astigmata: Proctophyllodidae), a feather mite, was found on feathers collected from five hummingbird species in California. This mite has not been previously documented on feathers from Anna's (Calypte anna [Lesson 1829]) or Black-chinned (Archilochus alexandri [Bourcier & Mulsant 1846]) Hummingbirds. A total of 753 hummingbirds were evaluated for the presence of mites by species (Allen's n = 112; Anna's n = 500; Black-chinned n = 122; Rufous n = 18; Calliope n = 1), sex (males n = 421; females n = 329; 3 unidentified), and age (juvenile n = 199; after-hatch-year n = 549; 5 unidentified). Of these 753 hummingbirds evaluated, mites were present on the rectrices of 40.9% of the birds. Significantly more Anna's Hummingbirds were positive for rectricial mites (59.2%) compared with 8.2% of Black-chinned, 0.9% of Allen's, 5.6% of Rufous Hummingbirds, and 0% for Calliope (p-value < 0.0001). Across all hummingbird species, male hummingbirds (44.9%) had a higher prevalence of rectricial mites compared to female hummingbirds (36.2%; p-value = 0.004), while juvenile hummingbirds (46.2%) had a non-significantly higher prevalence compared to after-hatch-year hummingbirds (39.0%; p-value = 0.089). On average, the percentage of the long axis of the rachis occupied by mites for the outer rectrices (R4 and R5) was 19%, compared to 11% for inner rectrices (R1 and R2), a significant difference (p-value = <0.0001). There was a marginal lack of significance for symmetrical distribution of tail mites with the mean left side percentage of long axis of the rachis occupied by mites being 16% and very close to the mean right side score of 18% (p-value = 0.003). The identification of the feather mite species was based on light microscopic morphometry, and mite distribution on feathers was further evaluated using tabletop scanning electron microscopy (TSEM). The hummingbird-feather mite relationship is not well understood, but the specialized TSEM technique may be especially useful in examining natural positioning and developmental aspects of the mites since it allows in situ feather examination of live mites.
| S-EPMC5812578 | biostudies-literature
Project description:Genome sequencing for investigating genetic features of one female of black-chinned hummingbird. The library and the sequencing were made at the Plateforme de Séquençage Haut Débit I2BC (Gif-sur-Yvette 91198 France.
| PRJEB27670 | ENA
Project description:modENCODE_submission_5986 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population; EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody NURF-1 SDQ3525 (target is NURF-1)
2013-08-28 | E-GEOD-50296 | biostudies-arrayexpress