Bayesian Inference Analysis of Unmodelled Gravitational-Wave Transients

We report the results of an in-depth analysis of the parameter estimation capabilities of BayesWave, an algorithm for the reconstruction of gravitational-wave signals without reference to a specific signal model. Using binary black hole signals, we compare BayesWave's performance to the theoretical best achievable performance in three key areas: sky localisation accuracy, signal/noise discrimination, and waveform reconstruction accuracy. BayesWave is most effective for signals that have very compact time-frequency representations. For binaries, where the signal time-frequency volume decreases with mass, we find that BayesWave's performance reaches or approaches theoretical optimal limits for system masses above approximately 50 M_sun. For such systems BayesWave is able to localise the source on the sky as well as templated Bayesian analyses that rely on a precise signal model, and it is better than timing-only triangulation in all cases. We also show that the discrimination of signals against glitches and noise closely follow analytical predictions, and that only a small fraction of signals are discarded as glitches at a false alarm rate of 1/100 y. Finally, the match between BayesWave- reconstructed signals and injected signals is broadly consistent with first-principles estimates of the maximum possible accuracy, peaking at about 0.95 for high mass systems and decreasing for lower-mass systems. These results demonstrate the potential of unmodelled signal reconstruction techniques for gravitational-wave astronomy.Comment: 10 pages, 7 figure

Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

© 2012 Matyášek et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Fertilization and early embryology: The chromosomal complements of multipronuclear human zygotes resulting from intracytoplasmic sperm injection

Implementation of intracytoplasmic sperm injection (ICSI) in human in-vitro fertilization (IVF) has highlighted the need for information about the risk of nuclear spindle damage caused by this procedure. For this purpose we studied the final products of oocyte meiosis at the first cleavage division of multipronuclear zygotes arising after ICSI, and compared the results with abnormally fertilized oocytes after conventional in-vitro insemination. Of 37 successfully analysed tripronuclear zygotes, 18 had three individual metaphases. Abnormal complements of 11 zygotes in this group indicated that non-disjunction occurred predominantly at the second meiotic division of the oocytes. Nine of the 37 tripronuclear zygotes exhibited two individual metaphases. Seven were abnormal and there were some indications that non-disjunction took place during oocyte meiosis. Of the 37 tripronuclear zygotes, 10 had a single metaphase and three showed an aneuploid number of chromosomes. The overall rate of aneuploidy among tripronuclear microinjected zygotes was 56.7%. In addition, seven zygotes with more than three pronuclei arising after ICSI displayed severely depleted chromosome complements. The incidence of non-disjunction in oocytes fertilized by conventional in-vitro insemination was significantly lower (20.0%, P < 0.01), since only four zygotes had an aneuploid number of chromosomes. Our findings suggest that ICSI might interfere with regular chromosome segregation at the second meiotic division of the oocyte

Andrology: Effects of nitric oxide on human spermatozoa: evidence that nitric oxide decreases sperm motility and induces sperm toxicity

Endogenous nitric oxide (NO) is an important functional mediator in several physiological systems, including the reproductive system. However, when generated in excessive amounts for long periods, mainly during immunological reactions, NO is cytotoxic and cytostatic for invading microbes, as well as for the cells generating it and the tissues present around it. Since infertility associated with urogenital tract infection in males and females is also accompanied by reduced sperm motility and viability, it is possible that reduced fertility in these patients is due to NO-induced sperm toxicity. We therefore evaluated the direct effects of NO, chemically derived from S-nitroso-N-acetylpenicillamine (SNAP, 0.012-0.6 mM) and sodium nitroprusside (SNP, 0.25-2.5 mM), on the motility and viability of human spermatozoa. Furthermore, we tested whether inhibition of NO synthesis prevents sperm motility and viability by incubating washed total cells present in the semen (spermatozoa, round cells) with N-nitro-L-arginine-methyl-ester (L-NAME), a NO synthesis inhibitor. Treatment of purified spermatozoa with SNAP or SNP decreased forward progressive sperm motility and straight line velocity, and also increased the percentage of immotile spermatozoa in a concentration-dependent manner. Furthermore, the percentage of immotile spermatozoa positively correlated with the percentage of dead spermatozoa. In contrast to freshly prepared SNAP, SNAP preincubated for 48 h had no effect on the motility and viability of the spermatozoa. Furthermore, as compared to untreated controls, a significantly higher percentage of forward progressive sperm motility as well as viability (P < 0.05) was maintained in washed semen incubated with L-NAME (0.15 mM). Seminal plasma concentrations of nitrite-nitrate (stabile metabolites of NO/106 spermatozoa correlated positively (P < 0.05) with the percentage of immotile spermatozoa. Our results suggest that NO can cause sperm toxicity as well as inhibit sperm motility. In conclusion, excessive NO synthesis in response to infection and inflammation could be an important factor contributing to functional change of the spermatozoa, leading to their dysfunction and to infertilit

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes

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 > 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.)

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

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

Isomelezitose overproduction by alginate-entrapped recombinant E. coli cells and In vitro evaluation of its potential prebiotic effect

In this work, the trisaccharide isomelezitose was overproduced from sucrose using a biocatalyst based on immobilized Escherichia coli cells harbouring the α-glucosidase from the yeast Metschnikowia reukaufii, the best native producer of this sugar described to date. The overall process for isomelezitose production and purification was performed in three simple steps: (i) oligosaccharides synthesis by alginate-entrapped E. coli; (ii) elimination of monosaccharides (glucose and fructose) using alginate-entrapped Komagataella phaffii cells; and (iii) semi-preparative high performance liquid chromatography under isocratic conditions. As result, approximately 2.15 g of isomelezitose (purity exceeding 95%) was obtained from 15 g of sucrose. The potential prebiotic effect of this sugar on probiotic bacteria (Lactobacillus casei, Lactobacillus rhamnosus and Enterococcus faecium) was analysed using in vitro assays for the first time. The growth of all probiotic bacteria cultures supplemented with isomelezitose was significantly improved and was similar to that of cultures supplemented with a commercial mixture of fructo-oligosaccharides. In addition, when isomelezitose was added to the bacteria cultures, the production of organic acids (mainly butyrate) was significantly promoted. Therefore, these results confirm that isomelezitose is a potential novel prebiotic that could be included in healthier foodstuffs designed for human gastrointestinal balance maintenanc

The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities".JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131).IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributionsPeer reviewe