Creosote bush (Larrea tridentata), Juniper (Juniperus osteosperma), alfalfa based rabbit chow, cactus (Opuntia spp.)
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ABSTRACT:
PROVIDER: PRJNA766427 | ENA |
REPOSITORIES: ENA
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Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences. Gene expression was compared across 3 groups of woodrats: Neotoma lepida (n=4), N. bryanti Palm Springs (n=4), and N. bryanti Caspers Wilderness (n=4). Animals were fed a rabbit chow diet, called control; intake was monitored over 10 days, after which RNA was extracted from hepatic tissue. One-color arrays were performed.
2013-07-30 | E-GEOD-43941 | biostudies-arrayexpress
Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences.
2013-07-30 | GSE43941 | GEO
Project description:Neotoma lepida Transcriptome or Gene expression
| PRJNA188250 | ENA
Project description:Neotoma lepida fecal inventories Targeted Locus (Loci)
| PRJNA211923 | ENA
Project description:Microbiome analysis of Neotoma lepida following fecal transplants
| PRJNA744220 | ENA
Project description:Neotoma lepida isolate:417 Genome sequencing and assembly
| PRJNA319537 | ENA
Project description:CONTEXTCactus cladodes [Opuntia humifusa (Raf.) Raf. (Cactaceae)] is one of the cactus genera, which has long been used as a folk medicine for skin disorders.OBJECTIVEThis study investigated the skincare potential of cactus cladodes extract (OHE), including its ability to regulate ultraviolet B (UVB)-induced hyaluronic acid (HA) production.MATERIALS AND METHODSGene expression levels of hyaluronic acid synthases (HASs) and hyaluronidase (HYAL) were measured in UVB-irradiated HaCaT cells with OHE treatment (10, 25, 50, 100??g/mL) by real-time polymerase chain reaction (PCR). The HA content was analyzed in hairless mice (SKH-1, male, 6 weeks old) treated with OHE for 10 weeks by using enzyme-linked immunosorbent assay (ELISA). Haematoxylin and eosin (H&E) and immunohistological staining were performed to examine epidermal thickness and levels of CD44 and hyaluronic acid-binding protein (HABP).RESULTSHA synthases (HAS,1 HAS2, HAS3) mRNA levels were increased by 1.9-, 2.2- and 1.6-fold, respectively, with OHE treatment (100??g/mL), while UVB-induced increase of hyaluronidase mRNA significantly decreased by 35%. HA content in animal was decreased from 42.9 to 27.1?ng/mL by OHE treatment. HAS mRNA levels were decreased by 39%, but HYAL mRNA was increased by 50% in OHE group. CD44 and HABP levels, which were greatly increased by UVB-irradiation, were reduced by 64 and 60%, respectively. Epidermal thickness, transepidermal water loss (TEWL), and erythema formation was also decreased by 45 (45.7 to 24.2??m), 48 (48.8 to 25?g/h/m2) and 33%, respectively.CONCLUSIONOHE protects skin from UVB-induced skin degeneration in HaCaT cells and hairless mice.
| S-EPMC6130649 | biostudies-literature