1,834 research outputs found
Mega-sized pericentromeric blocks of simple telomeric repeats and their variants reveal patterns of chromosome evolution in ancient Cycadales genomes
Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000-fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non-telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase-sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant-specific probes revealed canonical Arabidopsis-type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads.This project was supported by the Czech Academy of Science, Czech Science Foundation (22-16826S), Czech National Infrastructure for Biological data (ELIXIR CZ, LM2018131), NERC and China Scholarship Council (CSC). JP benefited from a RamĂłn y Cajal grant Ref: RYC-2017-2274 funded by MCIN/AEI/INTRODUCTION
RESULTS
Identification and quantification of telomeric repeats in high-throughput reads
In silico identification of telomeric repeat variants
Southern blot hybridization analysis of telomeric variants
Identification of cycad centromeres by immunostaining of chromatin
FISH analysis of telomeric variants
Evolution of chromosome numbers and genome sizes across cycads
DISCUSSION
Variable abundance of telomeric repeats in plant genomes
Origin of telomeric repeat variants in cycad genomes
Epigenetic modification of telomeric repeats
Chromosome evolution in cycads
CONCLUSION
EXPERIMENTAL PROCEDURES
Plant material
DNA isolation and Illumina sequencing
Estimation of telomeric repeats abundance and diversity from high-throughput sequencing data
Ancestral chromosome and genome size reconstruction
Southern blot hybridization and DNA methylation analysis
DNA probe preparation for FISH and southern blotting
FISH
Immunohistochemical staining of chromosomes
ACKNOWLEDGEMENTS
Author CONTRIBUTION
Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by >Â 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)
An Absolute Flux Density Measurement of the Supernova Remnant Casseopia A at 32 GHz
We report 32 GHz absolute flux density measurements of the supernova remnant
Cas A, with an accuracy of 2.5%. The measurements were made with the 1.5-meter
telescope at the Owens Valley Radio Observatory. The antenna gain had been
measured by NIST in May 1990 to be .
Our observations of Cas A in May 1998 yield . We also report absolute flux density measurements of 3C48, 3C147, 3C286,
Jupiter, Saturn and Mars.Comment: 30 pages, 4 figures; accepted for publication by AJ. Revised
systematic error budget, corrected typos, and added reference
Preparing potential teachers for the transition from employment to teacher training: an evaluative case study of a Maths Enhancement Course
In response to a UK government drive to improve maths teaching in schools, the South West London Maths Enhancement Course (MEC) has been set up though collaboration between three Higher Education institutions (HEIs) to provide an efficient route for non maths graduates in employment to upgrade their subject knowledge and give a smooth transition into teacher training (PGCE).
An evaluation of the scheme, measured against Teacher Development Agency (TDA) objectives and success criteria agreed by university staff, involved thematic analysis of focus group discussions and interviews with students and staff during both the MEC and PGCE courses. This has revealed a high level of satisfaction and success related to a number of underlying issues, particularly around student recruitment, curriculum design, peer support and staff collaboration. The model offers an example of practice transferable to a range of programmes aimed at supporting students in the transition between levels and institutions
Early respiratory viral infections in infants with cystic fibrosis
This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Background
Viral infections contribute to morbidity in cystic fibrosis (CF), but the impact of respiratory viruses on the development of airway disease is poorly understood.
Methods
Infants with CF identified by newborn screening were enrolled prior to 4âŻmonths of age to participate in a prospective observational study at 4 centers. Clinical data were collected at clinic visits and weekly phone calls. Multiplex PCR assays were performed on nasopharyngeal swabs to detect respiratory viruses during routine visits and when symptomatic. Participants underwent bronchoscopy with bronchoalveolar lavage (BAL) and a subset underwent pulmonary function testing. We present findings through 8.5âŻmonths of life.
Results
Seventy infants were enrolled, mean age 3.1âŻÂ±âŻ0.8âŻmonths. Rhinovirus was the most prevalent virus (66%), followed by parainfluenza (19%), and coronavirus (16%). Participants had a median of 1.5 viral positive swabs (range 0â10). Past viral infection was associated with elevated neutrophil concentrations and bacterial isolates in BAL fluid, including recovery of classic CF bacterial pathogens. When antibiotics were prescribed for respiratory-related indications, viruses were identified in 52% of those instances.
Conclusions
Early viral infections were associated with greater neutrophilic inflammation and bacterial pathogens. Early viral infections appear to contribute to initiation of lower airway inflammation in infants with CF. Antibiotics were commonly prescribed in the setting of a viral infection. Future investigations examining longitudinal relationships between viral infections, airway microbiome, and antibiotic use will allow us to elucidate the interplay between these factors in young children with CF
Genomic repeat abundances contain phylogenetic signal
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution
HI Narrow Self-Absorption in Dark Clouds: Correlations with Molecular Gas and Implications for Cloud Evolution and Star Formation
We present the results of a comparative study of HI narrow self-absorption
(HINSA), OH, 13CO, and C18O in five dark clouds. The HINSA follows the
distribution of the emission of the carbon monoxide isotopologues, and has a
characteristic size close to that of 13CO. This confirms that the HINSA is
produced by cold HI which is well mixed with molecular gas in well-shielded
regions. The ratio of the atomic hydrogen density to total proton density for
these sources is 5 to 27 x 10^{-4}. Using cloud temperatures and the density of
HI, we set an upper limit to the cosmic ray ionization rate of 10^{-16} s^{-1}.
Comparison of observed and modeled fractional HI abundances indicates ages for
these clouds to be 10^{6.5} to 10^{7} yr. The low values of the HI density we
have determined make it certain that the time scale for evolution from an
atomic to an almost entirely molecular phase, must be a minimum of several
million years. This clearly sets a lower limit to the overall time scale for
star formation and the lifetime of molecular clouds
Second and third season QUaD CMB temperature and polarization power spectra
We report results from the second and third seasons of observation with the
QUaD experiment. Angular power spectra of the Cosmic Microwave Background are
derived for both temperature and polarization at both 100 GHz and 150 GHz, and
as cross frequency spectra. All spectra are subjected to an extensive set of
jackknife tests to probe for possible systematic contamination. For the
implemented data cuts and processing technique such contamination is
undetectable. We analyze the difference map formed between the 100 and 150 GHz
bands and find no evidence of foreground contamination in polarization. The
spectra are then combined to form a single set of results which are shown to be
consistent with the prevailing LCDM model. The sensitivity of the polarization
results is considerably better than that of any previous experiment -- for the
first time multiple acoustic peaks are detected in the E-mode power spectrum at
high significance.Comment: 24 pages, 23 figures, updated to reflect published versio
Search for flavor-changing neutral currents and lepton-family-number violation in two-body D0 decays
Results of a search for the three neutral charm decays, D0 -> mu e, D0 -> mu
mu, and D0 -> e e, are presented. This study was based on data collected in
Experiment 789 at the Fermi National Accelerator Laboratory using 800 GeV/c
proton-Au and proton-Be interactions. No evidence is found for any of the
decays. Upper limits on the branching ratios, at the 90% confidence level, are
obtained.Comment: 28 pages, 18 figures. Submitted to Physical Review
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