The Potential Of High-Resolution BAC-FISH In Banana Breeding

Abstract The genetic complexity in the genus Musa has been subject of study in many breeding programs worldwide. Parthenocarpy, female sterility, polyploidy in different cultivars and limited amount of genetic and genomic information make the production of new banana cultivars difficult and time consuming. In addition, it is known that part of the cultivars and related wild species in the genus contain numerous chromosomal rearrangements. In order to produce new cultivars more effectively breeders must better understand the genetic differences of the potential crossing parents for introgression hybridization, but extensive genetic information is lacking. As an alternative to achieve information on genetic collinearity we make use of modern chromosome map technology known as high-resolution fluorescent in situ hybridization (FISH). This article presents the technical aspects and applications of such a technology in Musa species. The technique deals with BAC clone positioning on pachytene chromosomes of Calcutta 4 (Musa acuminata ssp. burmanicoides, A genome group, section Eumusa) and M. velutina (section Rodochlamys). Pollen mother cells digestion with pectolytic enzymes and maceration with acetic acid were optimized for making cell spread preparations appropriate for FISH. As an example of this approach we chose BAC clones that contain markers to known resistance genes and hybridize them for establishing their relative positions on the two species. Technical challenges for adapting existing protocols to the banana cells are presented. We also discuss how this technique can be instrumental for validating collinearity between potential crossing parents and how the method can be helpful in future mapping initiatives, and how this method allows identification of chromosomal rearrangements between related Musa species and cultivar

Anti-Listeria activity of lactic acid bacteria in two traditional Sicilian cheeses

Listeria monocytogenes is a pathogen frequently found in dairy products, and its growth is difficult to control. Bacteriocin-like inhibitory substances (BLIS), produced by lactic acid bacteria (LAB), having proven in vitro anti-Listeria activity, could provide an innovative approach to control L. monocytogenes; however, this application needs to be evaluated in vivo. In this study, twenty LAB strains isolated from different Sicilian dairy environments were tested for control of growth of L. monocytogenes in three different experimental trials. First, raw and UHT milk were inoculated with LAB strains alone, and LAB strains mixed with L. monocytogenes. Second, mini-cheeses containing LAB and/or L. monocytogenes were produced. Third, two traditional Sicilian cheeses inoculated with a multi-strain LAB mixture combined with L. monocytogenes were produced. The addition of BLIS produced by LAB to milk and in mini-cheese production was unable to inhibit the growth of L. monocytogenes. However, an anti-Listeria effect was observed in the Pecorino Siciliano cheeses, where, after 15 days of ripening, the cheeses with added LAB had fewer L. monocytogenes compared to the control cheeses with no added LAB, while in the Vastedda della valle del Bel\uecce cheeses, the multi-strain LAB mixture completely prevented the growth of L. monocytogenes

Transfer, composition and technological characterization of the lactic acid bacterial populations of the wooden vats used to produce traditional stretched cheeses

The biofilms of 12 wooden vats used for the production of the traditional stretched cheeses Caciocavallo Palermitano and PDO Vastedda della valle del Belìce were investigated. Salmonella spp. and Listeria monocytogenes were never detected. Total coliforms were at low numbers with Escherichia coli found only in three vats. Coagulase-positive staphylococci (CPS) were below the enumeration limit, whereas lactic acid bacteria (LAB) dominated the surfaces of all vats. In general, the dominance was showed by coccus LAB. Enterococci were estimated at high numbers, but usually between 1 and 2 Log cycles lower than other LAB. LAB populations were investigated at species and strain level and for their technological properties relevant in cheese production. Eighty-five strains were analysed by a polyphasic genetic approach and allotted into 16 species within the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus and Streptococcus. Enterococcus faecium was found in all wooden vats and the species most frequently isolated were Enterococcus faecalis, Lactococcus lactis, Leuconostoc mesenteroides, Pediococcus acidilactici and Streptococcus thermophilus. The study of the quantitative data on acidification rate, autolysis kinetics, diacetyl production, antibacterial compound generation and proteolysis by cluster and principal component analysis led to the identification of some strains with promising dairy characteristics. Interestingly, a consistent percentage of LAB was bacteriocin-like inhibitory substances (BLIS) producer. Thus, the microbial biofilms of the wooden vats analysed in this study might contribute actively to the stability of the final cheeses

Unveiling the nature of the "Green Pea" galaxies

We review recent results on the oxygen and nitrogen chemical abundances in extremely compact, low-mass starburst galaxies at redshifts between 0.1-0.3 recently named to as "Green Pea" galaxies. These galaxies are genuine metal-poor galaxies ($\sim$ one fifth solar) with N/O ratios unusually high for galaxies of the same metallicity. In combination with their known general properties, i.e., size, stellar mass and star-formation rate, these findings suggest that these objects could be experiencing a short and extreme phase in their evolution. The possible action of both recent and massive inflow of gas, as well as stellar feedback mechanisms are discussed here as main drivers of the starburst activity and their oxygen and nitrogen abundances.Comment: To appear in JENAM Symposium "Dwarf Galaxies: Keys to Galaxy Formation and Evolution", P. Papaderos, G. Hensler, S. Recchi (eds.). Lisbon, September 2010, Springer Verlag, in pres

The Multiwavelength Survey by Yale-Chile (MUSYC): Deep Medium-Band optical imaging and high quality 32-band photometric redshifts in the ECDF-S

We present deep optical 18-medium-band photometry from the Subaru telescope over the ~30' x 30' Extended Chandra Deep Field-South (ECDF-S), as part of the Multiwavelength Survey by Yale-Chile (MUSYC). This field has a wealth of ground- and space-based ancillary data, and contains the GOODS-South field and the Hubble Ultra Deep Field. We combine the Subaru imaging with existing UBVRIzJHK and Spitzer IRAC images to create a uniform catalog. Detecting sources in the MUSYC BVR image we find ~40,000 galaxies with R_AB<25.3, the median 5 sigma limit of the 18 medium bands. Photometric redshifts are determined using the EAZY code and compared to ~2000 spectroscopic redshifts in this field. The medium band filters provide very accurate redshifts for the (bright) subset of galaxies with spectroscopic redshifts, particularly at 0.1 < z 3.5. For 0.1 < z < 1.2, we find a 1 sigma scatter in \Delta z/(1+z) of 0.007, similar to results obtained with a similar filter set in the COSMOS field. As a demonstration of the data quality, we show that the red sequence and blue cloud can be cleanly identified in rest-frame color-magnitude diagrams at 0.1 < z < 1.2. We find that ~20% of the red-sequence-galaxies show evidence of dust-emission at longer rest-frame wavelengths. The reduced images, photometric catalog, and photometric redshifts are provided through the public MUSYC website.Comment: 19 pages, 14 image

Characterisation of the microflora contaminating the wooden vats used for traditional sicilian cheese production

Traditional Sicilian cheese productions are carried out employing traditional wooden vats, called tina. Many studies have highlighted the beneficial role of wooden dairy equipment by contributing to enriching the milk microflora and improving the acidification processes. The present work was undertaken to evaluate the safety of the wooden vats used to coagulate milk. To this purpose, the different microbial populations hosted onto the internal surfaces of the vats used to produce two different stretched cheeses, namely Caciocavallo Palermitano and Vastedda della valle del Bel\uecce DOP, were investigated for the presence of spoilage and pathogenic microorganisms as well as for bacteria with inhibitory effect in vitro against pathogenic microorganisms. A wide biodiversity of protechnological lactic acid bacteria (LAB), in terms of species, was revealed. Several LAB inhibited the growth of Listeria monocytogenes ATCC 7644. The wooden vats analysed resulted safe for three main findings: absence of the main pathogenic species, presence of high levels of LAB, anti-Listeria activity of many LAB

Characterization of AGN and their hosts in the Extended Groth Strip: a multiwavelength analysis

We have employed a reliable technique of classification of Active Galactic Nuclei (AGN) based on the fit of well-sampled spectral energy distributions (SEDs) with a complete set of AGN and starburst galaxy templates. We have compiled ultraviolet, optical, and infrared data for a sample of 116 AGN originally selected for their X-ray and mid-infrared emissions (96 with single detections and 20 with double optical counterparts). This is the most complete compilation of multiwavelength data for such a big sample of AGN in the Extended Groth Strip (EGS). Through these SEDs, we are able to obtain highly reliable photometric redshifts and to distinguish between pure and host-dominated AGN. For the objects with unique detection we find that they can be separated into five main groups, namely: Starburst-dominated AGN (24 % of the sample), Starburst-contaminated AGN (7 %), Type-1 AGN (21 %), Type-2 AGN (24 %), and Normal galaxy hosting AGN (24 %). We find these groups concentrated at different redshifts: Type-2 AGN and Normal galaxy hosting AGN are concentrated at low redshifts, whereas Starburst-dominated AGN and Type-1 AGN show a larger span. Correlations between hard/soft X-ray and ultraviolet, optical and infrared luminosities, respectively, are reported for the first time for such a sample of AGN spanning a wide range of redshifts. For the 20 objects with double detection the percentage of Starburst-dominated AGN increases up to 48%.Comment: 38 pages, 8 figures, 5 tables. Accepted by A

Comoving Space Density and Obscured Fraction of High-Redshift Active Galactic Nuclei in the Subaru/{\it XMM-Newton} Deep Survey

We study the comoving space density of X-ray-selected luminous active galactic nuclei (AGNs) and the obscured AGN fraction at high redshifts ($3 < z < 5$) in the Subaru/{\it XMM-Newton} Deep Survey (SXDS) field. From an X-ray source catalog with high completeness of optical identification thanks to deep optical images, we select a sample of 30 AGNs at $z > 3$ with intrinsic (de-absorbed and rest-frame 2--10 keV) luminosities of $L_{\rm X} = 10^{44-45}$ erg s$^{-1}$ detected in the 0.5--2 keV band, consisting of 20 and 10 objects with spectroscopic and photometric redshifts, respectively. Utilizing the $1/V_{\rm max}$ method, we confirm that the comoving space density of luminous AGNs decreases with redshift above $z > 3$. When combined with the {\it Chandra}-COSMOS result of Civano et al.\ (2011), the density decline of AGNs with $L_{\rm X} = 10^{44-45}$ erg s$^{-1}$ is well represented by a power law of $(1 + z)^{-6.2 \pm 0.9}$. We also determine the fraction of X-ray obscured AGNs with $N_{\rm H} > 10^{22}$ cm$^{-2}$ in the Compton-thin population to be 0.54$^{+0.17}_{-0.19}$, by carefully taking into account observational biases including the effects of photon statistics for each source. This result is consistent with an independent determination of the type-2 AGN fraction based on optical properties, for which the fraction is found to be 0.59$\pm$0.09. Comparing our result with that obtained in the local Universe, we conclude that the obscured fraction of luminous AGNs increases significantly from $z=0$ to $z>3$ by a factor of 2.5$\pm$1.1.Comment: 12 pages, 12 figures, 1 table. Accepted for publication in Ap

AGN Populations in Large Volume X-ray Surveys: Photometric Redshifts and Population Types found in the Stripe 82X Survey

Multi-wavelength surveys covering large sky volumes are necessary to obtain an accurate census of rare objects such as high luminosity and/or high redshift active galactic nuclei (AGN). Stripe 82X is a 31.3 deg$^2$ X-ray survey with $Chandra$ and $XMM$-Newton observations overlapping the legacy Sloan Digital Sky Survey (SDSS) Stripe 82 field, which has a rich investment of multi-wavelength coverage from the ultraviolet to the radio. The wide-area nature of this survey presents new challenges for photometric redshifts for AGN compared to previous work on narrow-deep fields because it probes different populations of objects that need to be identified and represented in the library of templates. Here we present an updated X-ray plus multi-wavelength matched catalog, including $Spitzer$ counterparts, and estimated photometric redshifts for 5961 (96% of a total of 6181) X-ray sources, which have a normalized median absolute deviation, $\sigma_{\rm nmad}$ = 0.06 and an outlier fraction, $\eta$ = 13.7%. The populations found in this survey, and the template libraries used for photometric redshifts, provide important guiding principles for upcoming large-area surveys such as $eROSITA$ and 3$XMM$ (in X-ray) and the Large Synoptic Survey Telescope (LSST; optical).Comment: Accepted for publication by The Astrophysical Journal (33 pages, 20 figures, 13 tables). Final catalog of counterparts and photo-z supplementing the paper available here: http://stripe82x.com/docs/stripe82x-photometric-redshifts-and-multiwavelength-data-catalog

Giant Thermoelectric Effect from Transmission Supernodes

We predict an enormous order-dependent quantum enhancement of thermoelectric effects in the vicinity of a higher-order `supernode' in the transmission spectrum of a nanoscale junction. Single-molecule junctions based on 3,3'-biphenyl and polyphenyl ether (PPE) are investigated in detail. The nonequilibrium thermodynamic efficiency and power output of a thermoelectric heat engine based on a 1,3-benzene junction are calculated using many-body theory, and compared to the predictions of the figure-of-merit ZT.Comment: 5 pages, 6 figure