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388 results for “gene loss”
Data from: Species tree estimation and the impact of gene loss following whole-genome duplication
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Severe inbreeding, increased mutation load, and gene loss-of-function in the critically endangered Devil’s Hole pupfish
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Data from: Molecular evolution of anthocyanin pigmentation genes following losses of flower color
Background: Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development. For example, trait losses can result in molecular decay of the pathways underlying the trait. Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr). Results: We recovered intact coding regions for the three genes in all of the lineages that have lost floral pigmentation, suggesting that molecular decay is not associated with these flower color transitions. However, two of the three genes (Chi, F3h) show significantly elevated dN/dS ratios in lineages without floral pigmentation. Maximum likelihood analyses suggest that this increase is due to relaxed constraint on anthocyanin genes in the unpigmented lineages as opposed to positive selection. Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci. Conclusions: The broad conservation of anthocyanin pathway genes across lineages with and without floral anthocyanins is consistent with the growing consensus that losses of pigmentation are largely achieved by changes in gene expression as opposed to structural mutations. Moreover, this conservation maintains the potential for regain of flower color, and indicates that evolutionary losses of floral pigmentation may be readily reversible.
FIGURE 7 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 7. MultiPip analysis showing overall sequence similarity of plastid genomes based on complete plastome alignment using Capparis spinosa var. spinosa as a reference sequence. Levels of sequence similarity are indicated by red (75±100%), green (50±75%), and white (<50%). Arrows indicate gene losses.
FIGURE 6 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 6. Nucleotide diversity and hotspot regions in genus Capparis. The X-axis represents the nucleotide position and Y-axis represents nucleotide diversity (Pi). 6a. Interspecific variation among four taxa of Capparis. 6b. Intraspecific variation among two varieties of Capparis spinosa viz. var. spinosa and var. herbacea.
FIGURE 2 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 2. Plastome maps of Capparis spinosa var. spinosa and Capparis spinosa var. herbacea. Genes shown outside the circles are transcribed clockwise and those inside are transcribed anticlockwise. Genes belonging to different functional groups are in various colours. The dashed area in inner circles indicates the GC content of plastome. ORF – Open reading frame. Asterisks indicate genes containing introns.
FIGURE 5 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 5. Comparison of SSRs in four Capparis taxa viz. C. spinosa var. herbacea, var. spinosa, C. versicolor and C. urophylla. 5a. Types of SSRs; 5b. Size of SSRs; 5c. Number of SSR repeats in LSC, SSC and IRs. Numbers above each bar represents the number of repeats.
FIGURE 4 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 4. Codon usage of four taxa of Capparis viz. Capparis spinosa var. spinosa, var. herbacea, C. versicolor and C. urophylla. Xaxis: Amino acid, Y- axis: codon usage in percentage. * indicates stop codon.
FIGURE 1 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 1. Map depicting distribution and altitudinal ranges of seven varieties of Capparis spinosa. (as per Jacobs 1965, Fici 2014, and POWO 2019).
FIGURE 3 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 3. Comparison of LSC, SSC and IR borders of Capparaceae with members of Cleomaceae (Tarenaya hassleriana) and Brassicaceae (Aethionema arabicum). Numbers in boxes indicate total length of the particular region; numbers below the arrows show base pair shift or overlapping regions. Gene and IR lengths are not to scale.
Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.
Figure 1 in Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations
Figure 1. Sampling sites (number of specimens per location in brackets) with the current Mediterranean monk seal distribution range in green.
Figure 3 in Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations
Figure 3. Mitochondrial genome clades sequenced in our study. A, female monk seal with its pup on Desertas Islands (Madeira); photo credit: Rosa Pires. B, Bayesian phylogeny using the complete mtDNA. Black dots indicate posterior probability values ≥ 0.95. (*) indicates historical specimens. The colours of the bars match the colours used on the network analyses and maps in Figure 2.
Weight Loss in Response to Sibutramine (MERIDIA) is Influenced by the Inherited Genes
ClinicalTrials.gov study NCT00433641. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Obesity-related Genes in Taiwanese Undergoing Weight Loss
ClinicalTrials.gov study NCT01684280. IPD Sharing: Not stated. Countries: 1. Publications: 12.
Influence of Dairy Protein Breakfast on Glycemia, Weight Loss and Clock Genes in T2D
ClinicalTrials.gov study NCT03772067. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Molecular evolution of anthocyanin pigmentation genes following losses of flower color
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Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
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Data from: Climate-driven range shifts explain the distribution of extant gene pools and predict future loss of unique lineages in a marine brown alga
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Alu-Mediated MEN1 Gene Deletion and Loss of Heterozygosity in a Patient with Multiple Endocrine Neoplasia Type 1
<p>Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder caused by mutations of the tumor suppressor gene <i>MEN1</i>. Most of the germline <i>MEN1</i> gene mutations have been small mutations, and the whole gene deletion is rarely observed. In the present study, we revealed <i>Alu </i>retrotransposon-mediated <i>de novo</i> germline deletion of the whole <i>MEN1</i> gene and somatic copy-neutral loss of heterozygosity (LOH) in a patient with MEN1. The patient is a 39-year-old woman who was referred to our department for the management of prolactinoma. She was also diagnosed with primary hyperparathyroidism and suspected of MEN1. Although nucleotide sequencing did not detect any <i>MEN1</i> gene mutations, multiplex ligation-dependent probe amplification (MLPA) revealed a large germline deletion of the <i>MEN1</i> gene. Subsequent quantitative polymerase chain reaction (qPCR)-based copy number mapping showed a monoallelic loss of approximately 18.5-kilobase region containing the whole <i>MEN1</i> gene. Intriguingly, the two breakpoints were flanked by <i>Alu</i> repetitive elements, suggesting the contribution of <i>Alu</i>/<i>Alu</i>-mediated rearrangements to the whole <i>MEN1 </i>gene deletion. Furthermore, copy number mapping using MLPA and qPCR in combination with single nucleotide polymorphism analysis revealed copy-neutral LOH as a somatic event for parathyroid tumorigenesis. In conclusion, copy number mapping revealed a novel combination of <i>Alu</i>/<i>Alu</i>-mediated <i>de novo</i> germline deletion of the <i>MEN1</i> gene and somatic copy-neutral LOH as a cytogenetic basis for the MEN1 pathogenesis. Moreover, subsequent <i>in silico</i> analysis highlighted the possible predisposition of the <i>MEN1 </i>gene to <i>Alu </i>retrotransposon-mediated genomic deletion.</p>
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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.