Current advances in genomics and breeding of leaf chicory (Cichorium intybus L.)

This review gives an overview of agricultural topics on a non-model species, in other words, leaf chicory. Often classified as a minor crop, \u201cRadicchio\u201d, the Italian name of leaf chicory, is assuming a very important role at both a local and national level, as it characterizes a high proportion of the agricultural income of suited areas. Botanical classification along the genus Cichorium is reported and a detailed description of the most important cultivated biotypes typical of northern Italy is presented. A special consideration is reserved to breeding aspects, from molecular marker-assisted selection to the implementation of the first genome draft and leaf transcriptomes. Sexual barriers, for example, self-incompatibility or male-sterility, are described in great detail with the aim to be utilized for breeding purposes. The main aspects of seed production are also critically presented. In conclusion, the present work is a sort of handbook to better understand this orphan crop and it is mainly directed to breeders and seed producers dealing with leaf chicory

DNA barcoding as a molecular tool to track down mislabeling and food piracy

DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the total DNA of a cell, both chloroplast and mitochondrial barcodes chosen for identifying plant and animal species, respectively, have shown sufficient nucleotide diversity to assess the taxonomic identity of the vast majority of organisms used in agriculture. Consequently, cpDNA and mtDNA barcoding protocols are being used more and more in the food industry and food supply chains for food labeling, not only to support food safety but also to uncover food piracy in freshly commercialized and technologically processed products. Since the extranuclear genomes are present in many copies within each cell, this technology is being more easily exploited to recover information even in degraded samples or transformed materials deriving from crop varieties and livestock species. The strong standardization that characterizes protocols used worldwide for DNA barcoding makes this technology particularly suitable for routine analyses required by agencies to safeguard food safety and quality. Here we conduct a critical review of the potentials of DNA barcoding for food labeling along with the main findings in the area of food piracy, with particular reference to agrifood and livestock foodstuffs

The gravitational wave contribution to CMB anisotropies and the amplitude of mass fluctuations from COBE results

A stochastic background of primordial gravitational waves may substantially contribute, via the Sachs--Wolfe effect, to the large--scale Cosmic Microwave Background (CMB) anisotropies recently detected by COBE. This implies a {\it bias} in any resulting determination of the primordial amplitude of density fluctuations. We consider the constraints imposed on $n<1$ (``tilted") power--law fluctuation spectra, taking into account the contribution from both scalar and tensor waves, as predicted by power--law inflation. The gravitational--wave contribution to CMB anisotropies generally reduces the required {\it rms} level of mass fluctuation, thereby increasing the linear {\it bias parameter}, even in models where the spectral index is close to the Harrison--Zel'dovich value $n=1$. This ``gravitational--wave bias" helps to reconcile the predictions of CDM models with observations on pairwise galaxy velocity dispersion on small scales.Comment: 11 pages. Two figures available upon reques

cpDNA barcoding by combined End-Point and Real-Time PCR analyses to identify and quantify the main contaminants of oregano (Origanum vulgare L.) in commercial batches

Oregano (Origanum vulgare L.) is a flowering plant that belongs to the mint family (Lamiaceae). It is used as a culinary herb and is often commercialized as a fine powder or a mixture of small fragments of dried leaves, which makes morphological recognition difficult. Like other commercial preparations of drugs and spices, the contamination of oregano mixtures with vegetable matter of lower quality, or the use of generic misleading names, are frequent and stress the need to develop a molecular traceability system to easily, quickly, and cheaply unveil these scams. The DNA-based analytical approach known as cpDNA barcoding is particularly suited for fraud identification in crop plant species (fresh products and food derivatives), and it represents a promising traceability tool as an alternative or complement to traditional detection methods. In the present study, we used a combined approach based on both qualitative and quantitative cpDNA barcoding with end-point and real-time polymerase chain reaction (PCR) analyses to assess the type and degree of contamination in commercial batches of common oregano. In a preliminary qualitative screening, we amplified, cloned, and sequenced a number of universal trnH-psbA- and trnL-barcoded regions, to identify the main contaminants in the samples under investigation. On the basis of these findings, we then developed and validated a species-specific and sequence-targeted method of testing for the quantitative assessment of contaminants, using trnL gene intron assays. Surprisingly, the results obtained in our case study indicated an almost total absence of O. vulgare in the commercial batches analyzed, but a high presence of group I contaminants (Satureja pilosa Velen.), and a moderate presence of group II contaminants (Cistus lanidifer L./Cistus albidus)

The bias field of dark matter haloes

This paper presents a stochastic approach to the clustering evolution of dark matter haloes in the Universe. Haloes, identified by a Press-Schechter-type algorithm in Lagrangian space, are described in terms of `counting fields', acting as non-linear operators on the underlying Gaussian density fluctuations. By ensemble averaging these counting fields, the standard Press-Schechter mass function as well as analytic expressions for the halo correlation function and corresponding bias factors of linear theory are obtained, thereby extending the recent results by Mo and White. The non-linear evolution of our halo population is then followed by solving the continuity equation, under the sole hypothesis that haloes move by the action of gravity. This leads to an exact and general formula for the bias field of dark matter haloes, defined as the local ratio between their number density contrast and the mass density fluctuation. Besides being a function of position and `observation' redshift, this random field depends upon the mass and formation epoch of the objects and is both non-linear and non-local. The latter features are expected to leave a detectable imprint on the spatial clustering of galaxies, as described, for instance, by statistics like bispectrum and skewness. Our algorithm may have several interesting applications, among which the possibility of generating mock halo catalogues from low-resolution N-body simulations.Comment: 23 pages, LaTeX (included psfig.tex), 4 figures. Few comments and references have been added, and minor typos and errors corrected. This version matches the refereed one, in press in MNRA

Physical constraints on the halo mass function

We analyse the effect of two relevant physical constraints on the mass multiplicity function of dark matter halos in a Press--Schechter type algorithm. Considering the random--walk of linear Gaussian density fluctuations as a function of the smoothing scale, we simultaneously i) account for mass semi--positivity and ii) avoid the cloud--in--cloud problem. It is shown that the former constraint implies a severe cutoff of low--mass objects, balanced by an increase on larger mass scales. The analysis is performed both for scale--free power--spectra and for the standard cold dark matter model. Our approach shows that the well--known ``infrared" divergence of the standard Press--Schechter mass function is caused by unphysical, negative mass events which inevitably occur in a Gaussian distribution of density fluctuations.Comment: Revised version (accepted for publication in MNRAS) including a new comparison with numerical results, a new appendix and new references. uuencoded gzip'ed tar archive containing many LaTex files (the main file is mass.tex). 16 pages with 6 figures (all included

The Clustering of Lyman-break Galaxies

We calculate the statistical clustering of Lyman-break galaxies predicted in a selection of currently-fashionable structure formation scenarios. These models are all based on the cold dark matter model, but vary in the amount of dark matter, the initial perturbation spectrum, the background cosmology and in the presence or absence of a cosmological constant term. If Lyman-break galaxies form as a result of hierarchical merging, the amplitude of clustering depends quite sensitively on the minimum halo mass that can host such a galaxy. Interpretation of the recent observations by Giavalisco et al. (1998) would therefore be considerably clarified by a direct determination of the relevant halo properties. For a typical halo mass around $10^{11} h^{-1} M_\odot$ the observations do not discriminate strongly between cosmological models, but if the appropriate mass is larger, say $10^{12} ~h^{-1} M_\odot$ (which seems likely on theoretical grounds), then the data strongly favour models with a low matter-density.Comment: 6 pages, Latex using MN style, 2 figures enclosed. Version accepted for publication in MNRA

The Three--Point Correlation Function of the Cosmic Microwave Background in Inflationary Models

We analyze the temperature three--point correlation function and the skewness of the Cosmic Microwave Background (CMB), providing general relations in terms of multipole coefficients. We then focus on applications to large angular scale anisotropies, such as those measured by the {\em COBE} DMR, calculating the contribution to these quantities from primordial, inflation generated, scalar perturbations, via the Sachs--Wolfe effect. Using the techniques of stochastic inflation we are able to provide a {\it universal} expression for the ensemble averaged three--point function and for the corresponding skewness, which accounts for all primordial second--order effects. These general expressions would moreover apply to any situation where the bispectrum of the primordial gravitational potential has a {\em hierarchical} form. Our results are then specialized to a number of relevant models: power--law inflation driven by an exponential potential, chaotic inflation with a quartic and quadratic potential and a particular case of hybrid inflation. In all these cases non--Gaussian effects are small: as an example, the {\em mean} skewness is much smaller than the cosmic {\em rms} skewness implied by a Gaussian temperature fluctuation field.Comment: 18 pages; LaTeX; 4 PostScript figures included at the end of the file; SISSA REF.193/93/A and DFPD 93/A/8

Contribution to the Three--Point Function of the Cosmic Microwave Background from the Rees--Sciama Effect

We compute the contribution to the three--point temperature correlation function of the Cosmic Microwave Background coming from the non--linear evolution of Gaussian initial perturbations, as described by the Rees--Sciama (or integrated Sachs--Wolfe) effect. By expressing the collapsed three--point function in terms of multipole amplitudes, we are able to calculate its expectation value for any power spectrum and for any experimental setting on large angular scales. We also give an analytical expression for the {\it rms} collapsed three--point function arising from the cosmic variance of a Gaussian fluctuation field. In the case of {\it COBE} DMR, we find that the predicted signal is about three orders of magnitude below that expected from the cosmic variance.Comment: uuencoded compressed postscript, 10 pages text, 2 pages figure

The correlation function of X-ray galaxy clusters in the RASS1 Bright Sample

We analyse the spatial clustering properties of the RASS1 Bright Sample, an X-ray flux-limited catalogue of galaxy clusters selected from the southern part of the $ROSAT$ All-Sky Survey. The two-point correlation function $\xi(r)$ of the whole sample is well fitted (in an Einstein-de Sitter model) by the power-law $\xi=(r/r_0)^{-\gamma}$, with $r_0= 21.5^{+3.4}_{-4.4} h^{-1}$ Mpc and $\gamma=2.11^{+0.53}_{-0.56}$ (95.4 per cent confidence level with one fitting parameter). We use the RASS1 Bright Sample as a first application of a theoretical model which aims at predicting the clustering properties of X-ray clusters in flux-limited surveys for different cosmological scenarios. The model uses the theoretical and empirical relations between mass, temperature and X-ray cluster luminosity, and fully accounts for the redshift evolution of the underlying dark matter clustering and cluster bias factor. The comparison between observational results and theoretical predictions shows that the Einstein-de Sitter models display too low a correlation length, while models with a matter density parameter $\Omega_{\rm 0m}=0.3$ (with or without a cosmological constant) are successful in reproducing the observed clustering. The dependence of the correlation length $r_0$ on the X-ray limiting flux and luminosity of the sample is generally consistent with the predictions of all our models. Quantitative agreement is however only reached for $\Omega_{\rm 0m} = 0.3$ models. The model presented here can be reliably applied to future deeper X-ray cluster surveys: the study of their clustering properties will provide a useful complementary tool to the traditional cluster abundance analyses to constrain the cosmological parameters.Comment: 11 pages, Latex using MN style, 4 figures enclosed. Version accepted for publication in MNRA