scholarly journals Conserved noncoding elements influence the transposable element landscape in Drosophila

2018 ◽  
Author(s):  
Manee M. Manee ◽  
John Jackson ◽  
Casey M. Bergman
Keyword(s):  
Transposable Element ◽  
Significant Proportion ◽  
Purifying Selection ◽  
Noncoding Dna ◽  
Frequency Spectra ◽  
Noncoding Regions ◽  
Selective Constraints ◽  
Large Numbers ◽  
Random Expectation ◽  
Conserved Noncoding Elements

AbstractHighly conserved noncoding elements (CNEs) comprise a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here we combine comparative and population genomic data in Drosophila melanogaster to show that abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no difference in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence supporting the conclusion that CNEs are indeed functionally constrained and not simply mutational cold spots.

Incomplete Intrapulmonary Lymph Node Retrieval After Routine Pathologic Examination of Resected Lung Cancer

2012 ◽  
Vol 30 (23) ◽  
pp. 2823-2828 ◽  
Author(s):  
Robert A. Ramirez ◽  
Christopher G. Wang ◽  
Laura E. Miller ◽  
Courtney A. Adair ◽  
Allen Berry ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Significant Proportion ◽  
External Control ◽  
Pathologic Examination ◽  
Resected Nsclc ◽  
Lymph Node Retrieval ◽  
Large Numbers ◽  
Pathologic Staging ◽  
Clinically Significant ◽  
Time Required

Purpose Pathologic nodal stage affects prognosis in patients with surgically resected non–small-cell lung cancer (NSCLC). Unlike examination of mediastinal lymph nodes (LNs), which depends on surgical practice, accurate examination of intrapulmonary (N1) nodes depends primarily on pathology practice. We investigated the completeness of N1 LN examination in NSCLC resection specimens and its potential impact on stage. Patients and Methods We performed a case-control study of a special pathologic examination (SPE) protocol using thin gross dissection with retrieval and microscopic examination of all LN-like material on remnant NSCLC resection specimens after routine pathologic examination (RPE). We compared LNs retrieved by the SPE protocol with nodes examined after RPE of the same lung specimens and with those of an external control cohort. Results We retrieved additional LNs in 66 (90%) of 73 patient cases and discovered metastasis in 56 (11%) of 514 retrieved LNs from 27% of all patients. We found unexpected LN metastasis in six (12%) of 50 node-negative patients. Three other patients had undetected satellite metastatic nodules. Pathologic stage was upgraded in eight (11%) of 73 patients. The time required for the SPE protocol decreased significantly with experience, with no change in the number of LNs found. Conclusion Standard pathology practice frequently leaves large numbers of N1 LNs unexamined, a clinically significant proportion of which harbor metastasis. By improving N1 LN examination, SPE can have an impact on prognosis and adjuvant management. We suggest adoption of the SPE to improve pathologic staging of resected NSCLC.

scholarly journals Chloroplast Noncoding DNA Sequences Reveal Genetic Distinction and Diversity between Wild and Cultivated Prunus yedoensis

2017 ◽  
Vol 142 (6) ◽  
pp. 434-443
Author(s):  
Eun Ju Cheong ◽  
Myong-Suk Cho ◽  
Seung-Chul Kim ◽  
Chan-Soo Kim
Keyword(s):  
United States ◽  
Dna Sequences ◽  
The United States ◽  
Jeju Island ◽  
Noncoding Dna ◽  
Noncoding Regions ◽  
Naturally Occurring ◽  
Prunus Yedoensis ◽  
History Of ◽  
Ornamental Trees

Cultivated flowering cherries (Prunus subgenus Cerasus), which are one of the most popular ornamental trees around the world, have been developed through artificial hybridizations among wild flowering cherries. Among the hundreds of cultivars of flowering cherries, Prunus ×yedoensis ‘Somei-yoshino’ is the most common and widespread. However, its origin and genetic relationship to wild P. yedoensis, naturally occurring on Jeju Island, South Korea, have long been debated. We used sequence polymorphisms in eight chloroplast DNA (cpDNA) noncoding regions to distinguish wild and cultivated flowering cherries among 104 individuals (55 accessions). We were able to distinguish two distinct groups, one corresponding to wild P. yedoensis collections from Jeju Island and the other collections of cultivated P. ×yedoensis from Korea, Japan, and the United States. The chlorotype diversity of wild P. yedoensis in Jeju Island and cultivated P. ×yedoensis collections in the United States was quite high, suggesting multiple natural hybrid origins and long history of cultivation from different original sources, respectively.

Molecular variation in plant cell populations evolving in vitro in different physiological contexts

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 549-558 ◽  
Author(s):  
Patrizia Bogani ◽  
Alessandra Simoni ◽  
Pietro Lio' ◽  
Angela Germinario ◽  
Marcello Buiatti
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Rflp Analysis ◽  
Enzymatic Digestion ◽  
Noncoding Dna ◽  
Noncoding Regions ◽  
Total Dna ◽  
Context Specific ◽  
Hormone Control ◽  
Selection Of

Previous work has shown the fixation of context-specific random amplified polymorphic DNA (RAPD) patterns in tomato cell cultures grown for 2 years in different hormonal contexts. In this work, RAPD sequences were characterised and RAPD-derived molecular markers used for a further study of variation between and within auto- and auxo-trophic tomato cultures grown in different hormonal equilibria. Results were then compared with those obtained using microsatellite markers located in noncoding regions of differentiation- and hormone-related genes and with those obtained with the external transcribed spacer (ETS) from tomato rDNA. Hybridisation of RAPDs on a tomato genomic DNA bank, or on total DNA after enzymatic digestion, suggested that the markers were repetitive in nature. Sequence analysis, however, showed that the homology between different fragments was due mainly to the presence of homo-AT nucleotide stretches. Moreover, a series of computational methods, such as an information-theory algorithm coupled with ΔG estimates, suggested that the RAPD fragments isolated in our experiments are noncoding. The amplification of SSR-containing RAPD-derived markers, and of other SSRs located in noncoding regions of tomato functional genes, consistently showed polymorphism between auxo- and auto-trophic somaclones (the latter being either habituated or transgenic for Agrobacterium tumefaciens oncogenes) but not within these same clones. Differences were also found between auxotrophic clones and the differentiated tissue. These findings were confirmed by restriction fragment length polymorphism (RFLP) analysis with the REII repetitive element of the ETS from tomato rDNA, which was isolated during this study. The results obtained suggest a possible role for physiological context in the selection of RAPD patterns during the evolution of tomato cells with different endogenous hormonal equilibria. The results are discussed in terms of a possible role for variation in noncoding regions of hormone-related genes in the adaptation to different physiological contexts.Key words: Lycopersicon esculentum, RAPD, SSR, genetic variation, noncoding DNA, hormone control.

A conservation strategy for dugongs: implications of Australian research

1999 ◽  
Author(s):  
Helene Marsh ◽  
Carole Eros ◽  
Peter Corkeron ◽  
Barbara Breen
Keyword(s):  
Life History ◽  
Anthropogenic Impacts ◽  
Significant Proportion ◽  
Global Scale ◽  
Reproductive Rate ◽  
Conservation Strategy ◽  
Slight Reduction ◽  
Large Numbers ◽  
High Investment ◽  
Optimum Management

The dugong (Dugong dugon) is listed as vulnerable to extinction at a global scale. It has a large range that spans some forty countries and includes tropical and subtropical coastal and island waters from east Africa to Vanuatu. A significant proportion of the world’s dugongs is found in northern Australian waters where most modern dugong research has been conducted. Dugongs are long-lived animals with a low reproductive rate, long generation time, and a high investment in each offspring. Population simulations indicate that even with the most optimistic combinations of life-history parameters (e.g. low natural mortality and no human-induced mortality) a dugong population is unlikely to increase by more than 5% per year. Dugongs are vulnerable to anthropogenic impacts because of their life history and their dependence on seagrasses that are restricted to coastal habitats. Even a slight reduction in adult survivorship as a result of habitat loss, disease, hunting or incidental drowning in nets can cause a chronic decline in a dugong population. The optimum management strategy is to identify areas that consistently support large numbers of dugongs and to set these aside as dugong sanctuaries in which dugong mortality is minimized and their habitat protected.

scholarly journals Genomic Selective Constraints in Murid Noncoding DNA

PLoS Genetics ◽  
2006 ◽  
Vol 2 (11) ◽  
pp. e204 ◽  
Author(s):  
Daniel J. Gaffney ◽  
Peter D. Keightley
Keyword(s):  
Noncoding Dna ◽  
Selective Constraints

scholarly journals Detecting cancer vulnerabilities through gene networks under purifying selection in 4,700 cancer genomes

2017 ◽  
Author(s):  
Anika Gupta ◽  
Heiko Horn ◽  
Parisa Razaz ◽  
April Kim ◽  
Michael Lawrence ◽  
...  
Keyword(s):  
Gene Networks ◽  
Large Scale ◽  
Significant Proportion ◽  
Low Frequency ◽  
Interaction Network ◽  
Purifying Selection ◽  
Sequencing Data ◽  
Gene Sets ◽  
Sequencing Studies ◽  
Significant Enrichment

ABSTRACTLarge-scale cancer sequencing studies have uncovered dozens of mutations critical to cancer initiation and progression. However, a significant proportion of genes linked to tumor propagation remain hidden, often due to noise in sequencing data confounding low frequency alterations. Further, genes in networks under purifying selection (NPS), or those that are mutated in cancers less frequently than would be expected by chance, may play crucial roles in sustaining cancers but have largely been overlooked. We describe here a statistical framework that identifies genes that have a first order protein interaction network significantly depleted for mutations, to elucidate key genetic contributors to cancers. Not reliant on and thus, unbiased by, the gene of interest’s mutation rate, our approach has identified 685 putative genes linked to cancer development. Comparative analysis indicates statistically significant enrichment of NPS genes in previously validated cancer vulnerability gene sets, while further identifying novel cancer-specific candidate gene targets. As more tumor genomes are sequenced, integrating systems level mutation data through this network approach should become increasingly useful in pinpointing gene targets for cancer diagnosis and treatment.

scholarly journals Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Pierre Baduel ◽  
Leandro Quadrana ◽  
Ben Hunter ◽  
Kirsten Bomblies ◽  
Vincent Colot
Keyword(s):  
Transposable Element ◽  
Local Adaptation ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Purifying Selection ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Environmentally Responsive ◽  
Main Driver ◽  
Whole Genome Resequencing

AbstractPolyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa, a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 TE insertions we detect in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near environmentally responsive genes. Notably, we show that the major flowering-time repressor gene FLC is disrupted by a TE insertion specifically in the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy leads to an enhanced accumulation of genic TE insertions, some of which likely contribute to local adaptation.

The evolutionary bootstrap: a new approach to the study of taxonomic diversity

Paleobiology ◽  
1986 ◽  
Vol 12 (3) ◽  
pp. 251-268 ◽  
Author(s):  
Norman L. Gilinsky ◽  
Richard K. Bambach
Keyword(s):  
Null Hypothesis ◽  
Dynamic Properties ◽  
Taxonomic Diversity ◽  
New Approach ◽  
The Real ◽  
Statistical Verification ◽  
Large Numbers ◽  
Random Expectation ◽  
History Of ◽  
End Members

The evolutionary bootstrap is a new approach to the analysis of patterns of taxonomic diversity. In general, the evolutionary bootstrap works by surveying the diversity history of a taxon, learning its dynamic properties, and then generating randomly large numbers of artificial diversity histories based upon what was learned. The distribution of artificial—or bootstrapped—diversity histories approximates the distribution of diversity histories that were possible for taxa with the dynamic properties of the real taxon, and serves as a paleontological null hypothesis for studying statistically the diversity history of the real taxon.Two null hypotheses were established, the additive and the multiplicative. The additive null hypothesis assumes that the amount of diversity change that occurs in a higher taxon during an interval of time is independent of the number of member subtaxa present at the beginning of the interval. The multiplicative null hypothesis, in contrast, assumes that the amount of diversity change that occurs is dependent upon the number of member subtaxa present at the start. Thus the two null hypotheses represent end members of a diversity-independent/diversity-dependent continuum of possibilities.Detailed analyses using the evolutionary bootstrap, in conjunction with the clade statistics of Gould et al. (1977), show that several of the 17 higher taxa studied have diversity histories that are statistically significantly different from the random expectation under one or both null hypotheses. Analyses of multiple taxa in aggregate also reveal several properties of diversity histories that are statistically significantly different from random. Real taxa tend to have higher uniformities and lower maximum diversities than expected under the multiplicative null hypothesis. They have lower uniformities, higher maximum diversities, and longer durations than expected under the additive null hypothesis. And, they have lower centers of gravity than expected under either null hypothesis. Overall, the results provide a possible statistical verification of the process of taxonomic (traditionally, adaptive) radiation and suggest the need to consider deterministic explanations for observed diversity patterns.

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