A multiple-phenotype imputation procedure as a method for prediction of cheese-making efficiency in Spanish Assaf sheep

Sheep milk is mainly intended to manufacture a wide variety of high-quality cheeses. The ovine cheese industry would benefit from an improvement, through genetic selection, of traits related to the milk coagulation properties (MCPs) and cheese yield-related traits, broadly denoted as “cheese-making traits.” Considering that routine measurements of these traits needed for genetic selection are expensive and time-consuming, this study aimed to evaluate the accuracy of a cheese-making phenotype imputation method based on the information from official milk control records combined with the pH of the milk. For this study, we analyzed records of milk production traits, milk composition traits, and measurements of cheese-making traits available from a total of 1,145 dairy ewes of the Spanish Assaf sheep breed. Cheese-making traits included five related to the MCPs and two cheese yield-related traits. The milk and cheese-making phenotypes were adjusted for significant effects based on a general linear model. The adjusted phenotypes were used to define a multiple-phenotype imputation procedure for the cheese-making traits based on multivariate normality and Markov chain Monte Carlo sampling. Five of the seven cheese-making traits considered in this study achieved a prediction accuracy of 0.60 computed as the correlation between the adjusted phenotypes and the imputed phenotypes. Particularly the logarithm of curd-firming time since rennet addition (logK₂₀) (0.68), which has been previously suggested as a potential candidate trait to improve the cheese ability in this breed, and the logarithm of the ratio between the rennet clotting time and the curd firmness at 60 min (logRCT/A60) (0.65), which has been defined by other studies as an indicator trait of milk coagulation efficiency. This study represents a first step toward the possible use of the phenotype imputation of cheese-making traits to develop a practical methodology for the dairy sheep industry to impute cheese-making traits only based on the analysis of a milk sample without the need of pedigree information. This information could be also used in future planning of specific breeding programs considering the importance of the cheese-making efficiency in dairy sheep and highlights the potential of phenotype imputation to leverage sample size on expensive, hard-to-measure phenotypes.     

Efficacy of formic acid in gel for Varroa control in Apis mellifera L.: importance of the dispenser position inside the hive

The efficacy of formic acid in a gel matrix was evaluated in two groups of honeybee colonies. In Group 1, a dispenser with 120 g of formic acid (70%) in gel was placed on the brood combs and another dispenser with the same dose was located on the hive bottom (total dose, 240 g). Group 2 received two doses of 240 g of formic acid (70%) in gel and each application was applied in two dispensers containing 120 g of the formic acid solution each and they were located over the brood chamber (total dose, 480 g). In Group 2, the period between both applications was 15 days, and the efficacies after the first and both applications were calculated. Significant differences were registered for final efficacy between both groups. When final efficacy of Group 1 was compared with efficacy after first application of Group 2, significant differences were found (P=0.0005). Same doses in different positions within the hive have different final efficacy. The higher efficacy was registered when the dispensers were placed over brood combs and on the hive bottom. It is suggested that efficacy is related to dispenser position within the hive.     

Characterization of Fusarium population associated with wilt of jojoba in Israel

Fusarium wilt, caused by Fusarium oxysporum, is a major disease of jojoba, causing serious economic losses. This study was aimed at characterizing the Fusarium populations associated with jojoba in Israel. Fifty Fusarium isolates used in this study included 23 isolates from the 1990s (“past”) and 27 recently isolated (“recent”). All the isolates were characterized by arbitrarily primed (ap)-PCR and 16 representatives were additionally delineated using multilocus (tef1, rpb1, rpb2) phylogeny and evaluated for their pathogenic potential. Consequently, 88% of the isolates were identified and characterized to the F. oxysporum species complex. The remaining 12% grouped within the F. fujikuroi, F. solani, and F. redolens species complexes. Variations in the infection rate (16.7%–100%), disease symptoms (0.08–1.25, on a scale of 0–3), and fungal colonization index (0.67–2.17, on a scale of 0–4) were observed within the tested isolates, with no significant differences between the past and recent isolates. The representative isolates were assigned to 11 groups based on ap-PCR. Pathogenicity tests showed that isolates from Groups II, IV, and V were the most aggressive, whereas isolates from Groups III, VIII, and IX were the least aggressive. Among the tested isolates, F. oxysporum sensu lato was the most aggressive, followed by F. proliferatum, while F. nygamai was the least aggressive. This study demonstrates the complexity and genetic diversity of Fusarium wilt on jojoba in Israel, indicating possible multiple introductions of infected germplasm into the country.     

A chemometric approach to the comparison of different sample treatments for metals determination by atomic absorption spectroscopy in aceto Balsamico tradizionale di Modena

A comparison of different digestion procedures has been carried out for the analysis of metal concentration in samples of vinegars and Aceto Balsamico Tradizionale of Modena (ABTM) coming from an unique barrel set. In particular, classical wet, dry ashing, and closed vessel microwave digestion procedure have been utilized and compared for each investigated species. In a few cases, direct metal determination on ABTM (without treatment procedure) is proposed as possible alternative to sample manipulation. Flame atomic absorption spectrometry was used for the quantification of iron and zinc, while graphite furnace atomic absorption spectrometry was used for all the other elements (i.e., chromium, manganese, cobalt, nickel, copper, cadmium, and lead). The comparison among the different sample treatments was carried out by the use of statistical and chemometric tools. In particular, principal component analysis and ANOVA approaches were used to discriminate between the diverse analytical methods. Furthermore, for all the dissolving techniques, the analytical metal recovery was always evaluated by the application of the recovery function on the same sample matrix. In general, the recoveries were fairly good, ranging from 90 to 103%, except for Cd and Pb with dry ashing, which showed recovery values close to 55% and 67%, respectively. As regards the metals concentration of the investigated samples, the experimental data reveal for some species the presence of concentration slightly over the legal limit fixed for wine and wine vinegar.     

Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine

In mammalian cells, repair of DNA double-strand breaks (DSBs) by nonhomologous end-joining (NHEJ) is critical for genome stability. Although the end-bridging and ligation steps of NHEJ have been reconstituted in vitro, little is known about the end-processing reactions that occur before ligation. Recently, functionally homologous end-bridging and ligation activities have been identified in prokarya. Consistent with its homology to polymerases and nucleases, we demonstrate that DNA ligase D from Mycobacterium tuberculosis (Mt-Lig) possesses a unique variety of nucleotidyl transferase activities, including gap-filling polymerase, terminal transferase, and primase, and is also a 3' to 5' exonuclease. These enzyme activities allow the Mt-Ku and Mt-Lig proteins to join incompatible DSB ends in vitro, as well as to reconstitute NHEJ in vivo in yeast. These results demonstrate that prokaryotic Ku and ligase form a bona fide NHEJ system that encodes all the recognition, processing, and ligation activities required for DSB repair.     

The V-antigen of Yersinia forms a distinct structure at the tip of injectisome needles

Many pathogenic bacteria use injectisomes to deliver effector proteins into host cells through type III secretion. Injectisomes consist of a basal body embedded in the bacterial membranes and a needle. In Yersinia, translocation of effectors requires the YopB and YopD proteins, which form a pore in the target cell membrane, and the LcrV protein, which assists the assembly of the pore. Here we report that LcrV forms a distinct structure at the tip of the needle, the tip complex. This unique localization of LcrV may explain its crucial role in the translocation process and its efficacy as the main protective antigen against plague.     

Signal-driven computations in speech processing

Learning a language requires both statistical computations to identify words in speech and algebraic-like computations to discover higher level (grammatical) structure. Here we show that these computations can be influenced by subtle cues in the speech signal. After a short familiarization to a continuous speech stream, adult listeners are able to segment it using powerful statistics, but they fail to extract the structural regularities included in the stream even when the familiarization is greatly extended. With the introduction of subliminal segmentation cues, however, these regularities can be rapidly captured.     

Identification of a DNA nonhomologous end-joining complex in bacteria

In eukaryotic cells, double-strand breaks (DSBs) in DNA are generally repaired by the pathway of homologous recombination or by DNA nonhomologous end joining (NHEJ). Both pathways have been highly conserved throughout eukaryotic evolution, but no equivalent NHEJ system has been identified in prokaryotes. The NHEJ pathway requires a DNA end-binding component called Ku. We have identified bacterial Ku homologs and show that these proteins retain the biochemical characteristics of the eukaryotic Ku heterodimer. Furthermore, we show that bacterial Ku specifically recruits DNA ligase to DNA ends and stimulates DNA ligation. Loss of these proteins leads to hypersensitivity to ionizing radiation in Bacillus subtilis. These data provide evidence that many bacteria possess a DNA DSB repair apparatus that shares many features with the NHEJ system of eukarya and suggest that this DNA repair pathway arose before the prokaryotic and eukaryotic lineages diverged.     

Heat treatments and expansin gene expression in strawberry fruit

Heat treatments have been applied in fruit postharvest technology for insect disinfestations, decay control, ripening delay and modification of fruit responses to other stresses. Heat treatment affects several aspects of fruit ripening, such as ethylene production and cell wall degradation probably through changes in gene expression and protein synthesis. In this paper, strawberries (Fragaria × ananassa Duch., cv Camarosa) at 50–75% red stage of ripening were heat-treated at 45 °C during 3 h in an air oven and then stored at 20 °C for 0, 4, 18, 24 and 48 h. Fruit firmness was determined and the expression of a set of expansin genes (FaEXP1, FaEXP2, FaEXP4, FaEXP5 and FaEXP6) was analyzed. The firmness of treated fruit was higher than that of control fruit 24 h after treatment, though the differences disappeared after 48 h at 20 °C. The analysis by northern-blot indicated that heat treatments affected differently the expression of expansin genes. The expression of FaEXP1, FaEXP2 and FaEXP6 was lower in treated fruit during the following 24 h post-treatment. The lower expression of these expansin genes could contribute to delay softening after heat treatment.     

Classification of cereal flours by chemometric analysis of MIR spectra

Different kinds of cereal flours submitted to various technological treatments were classified on the basis of their mid-infrared spectra by pattern recognition techniques. Classification in the wavelet domain was achieved by using the wavelet packet transform for efficient pattern recognition (WPTER) algorithm, which allowed singling out the most discriminant spectral regions. Principal component analysis (PCA) on the selected features showed an effective clustering of the analyzed flours. Satisfactory classification models were obtained both on training and test samples. Furthermore, mixtures of varying composition of the studied flours were distributed in the PCA space according to their composition.