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

Biogas-to-biomethane upgrading: A comparative review and assessment in a life cycle perspective

The study reviews and compares the most utilised techniques to obtain high quality biomethane by upgrading biogas from anaerobic digestion of the organic fraction of municipal solid waste. Environmental and economic aspects of membrane separation, water scrubbing, chemical absorption with amine solvent, and pressure swing adsorption have been quantified in a life cycle perspective. An attributional environmental Life Cycle Assessment has been implemented with the support of a Material Flow Analysis and in combination with a complementary environmental Life Cycle Costing. The analyses are based on data largely obtained from Italian existing plants but they can be generalised to the whole European Union, as demonstrated by a companion sensitivity analysis. The comparative assessment of the results indicates all the examined options as fully sustainable, also identifying the “win-win” situations. In particular, the membrane separation technique appears to have the best performances, even though in some cases with limited differences. With reference to base case scenarios, this technique shows better results for the respiratory inorganics potential (up to 34%, i.e. up to 328 kgPM2.5eq/y), global warming potential (up to 7%, i.e. up to 344 tCO2eq/y), and non-renewable energy potential (up to 12%, i.e. up to 6400 GJprimary/y) as well as for life cycle costs (up to 3.4%, i.e. about 60 k€/y). The performances of the examined techniques appear anyway dependent on site-specific conditions (such as the injection pressure in the gas grid or the existence/amount of local economic incentives) and commercial strategies for the market of interest

Molecular interactions of carbapenem antibiotics with the multidrug efflux transporter acrb of escherichia coli

The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism

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

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

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

Bresaola made from Cinisara cattle: effect of muscle type and animal category on physicochemical and sensory traits

The physicochemical characteristics and sensory traits of Cinisara bresaola were investigated, to explore a new commercial opportunity for autochthonous dairy cattle farms. Semimembranosus, Semitendinosus and Biceps brachii muscles, from adult cows (AC) and grazing (GB) or housed (HB) young bulls of Cinisara breed, were processed to made bresaola. Differences due to animal category and muscle type were observed. Bresaola from AC was richer in fat and volatile organic compounds. The bresaola from Semitendinosus showed higher colorimetric parameters, fat and, when from grazing animals, Warner-Bratzler shear force than those made from other muscles. In general, all bresaola were well appreciated. The principal component analysis performed using selected physicochemical and sensory traits was able to discriminate bresaola produced from different animal categories, effect of muscle type was relevant only for AC. These results evidenced the possibility to obtain bresaola from the meat of different animal categories, comparable for sensory properties and appreciable by consumers.El presente estudio se propuso investigar las características fisicoquímicas y los rasgos sensoriales de la bresaola de ganado Cinisara, con el propósito de explorar nuevas oportunidades comerciales para las granjas autóctonas de ganado lechero. Con el fin de elaborar la carne bresaola se procesaron los músculos Semimembranosus, Semitendinosus y Biceps brachii de vacas adultas (AC), de toros jóvenes que pastan (GB) y de toros jóvenes confinados (HB) de la raza Cinisara. El estudio constató la existencia de diferencias atribuibles a la categoría de los animales, así como al tipo de músculo empleado. La bresaola de AC resultó ser más rica en grasa y compuestos orgánicos volátiles. La bresaola de Semitendinosus mostró parámetros colorimétricos más intensos, mayor contenido de grasa y, cuando provenía de animales de pastoreo, [mayor] fuerza de cizallamiento de WarnerBratzler que las bresaolas elaboradas con otros músculos. En general, todas las bresaolas fueron bastante apreciadas. El análisis de los componentes principales, realizado utilizando rasgos fisicoquímicos y sensoriales seleccionados, fue capaz de discriminar la bresaola producida a partir de diferentes categorías de animales; el efecto del tipo de músculo sólo fue evidente en el caso de las AC. Estos resultados ponen de manifiesto la posibilidad de obtener varias bresaolas a partir de carne de diferentes categorías de animales, las cuales son comparables por sus propiedades sensoriales. Todas ellas son apreciadas por los consumidores

Efficacy of hemostatic powders as monotherapy or rescue therapy in gastrointestinal bleeding related to neoplastic or non-neoplastic lesions

Background Hemostatic powder (HP) in gastrointestinal bleeding (GIB) is mainly used as rescue therapy after failure of conventional hemostatic procedures (CHP). Aim To define the best field of application and the efficacy of HP as first choice monotherapy or rescue therapy. Methods We compared the efficacy of HP monotherapy, HP rescue therapy, and CHP in the management of active GIB due to neoplastic and non-neoplastic lesions. Results A total of 108 patients, 43 treated with HP as either first choice or rescue therapy and 65 with CHP, were included in the study. The most frequent sources of bleeding were peptic ulcer and malignancy. Immediate hemostasis rates were: HP monotherapy = 100% in peptic ulcer and 100% in malignancy; HP rescue therapy = 93.2% in peptic ulcer and 85.7% in malignancy; CHP = 77.9% in peptic ulcer and 41.7 in malignancy. Definitive hemostasis rates were: HP monotherapy = 50% in peptic ulcer and 45.5% in malignancy; HP rescue therapy = 73.3% in peptic ulcer and 85.7% in malignancy; CHP = 69.1% in peptic ulcer and 33.3% in malignancy. No difference was found in terms of additional intervention between the three groups. Conclusions HP is highly effective as monotherapy and rescue therapy in GIB. GIB related to malignancy may be the best field of application of HP, but confirmatory studies are necessary

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