Estimation of Mycobacterium avium subsp. paratuberculosis load in raw bulk tank milk in Emilia-Romagna Region (Italy) by qPCR

Consumption of milk and dairy products is considered one of the main routes of human exposure to Mycobacterium avium subsp. paratuberculosis (MAP). Quantitative data on MAP load in raw cows’ milk are essential starting point for exposure assessment. Our study provides this information on a regional scale, estimating the load of MAP in bulk tank milk (BTM) produced in Emilia-Romagna region (Italy). The survey was carried out on 2934 BTM samples (88.6% of the farms herein present) using two different target sequences for qPCR (f57 and IS900). Data about the performances of both qPCRs are also reported, highlighting the superior sensitivity of IS900-qPCR. Seven hundred and eighty-nine samples tested MAP-positive (apparent prevalence 26.9%) by IS900 qPCR. However, only 90 of these samples were quantifiable by qPCR. The quantifiable samples contained a median load of 32.4 MAP cells mL−1 (and maximum load of 1424 MAP cells mL−1). This study has shown that a small proportion (3.1%) of BTM samples from Emilia-Romagna region contained MAP in excess of the limit of detection (1.5 × 101 MAP cells mL−1), indicating low potential exposure for consumers if the milk subsequently undergoes pasteurization or if it is destined to typical hard cheese production.

Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data.

Pathogens in Milk: Enterobacter Species. Reference Module in Food Sciences.

Enterobacter species commonly occur in the environment and are recognized as opportunistic human pathogens in clinical settings. However, with the exception of Enterobacter sakazakii (Cronobacter), Enterobacter species are not normally considered foodborne pathogens. Cronobacter are particularly associated with illness in infants, particularly within the first 3 months after birth. Therefore, although Cronobacter are found in a wide range of fresh and dried food materials, it is their contamination of the infant formula production chain that is the major cause for concern. Cronobacter are noted for their ability to survive during desiccation and their persistence in dried infant food for at least 2 years.

Nicotinamide Riboside Is a Major NAD+ Precursor Vitamin in Cow Milk

Background: Nicotinamide riboside (NR) is a recently discovered NAD+ precursor vitamin with a unique biosynthetic pathway. Although the presence of NR in cow milk has been known for more than a decade, the concentration of NR with respect to the other NAD+ precursors was unknown.

Objective: We aimed to determine NAD+ precursor vitamin concentration in raw samples of milk from individual cows and from commercially available cow milk.

Methods: LC tandem mass spectrometry and isotope dilution technologies were used to quantify NAD+ precursor vitamin concentration and to measure NR stability in raw and commercial milk. Nuclear magnetic resonance (NMR) spectroscopy was used to test for NR binding to substances in milk.

Results: Cow milk typically contained ∼12 μmol NAD+ precursor vitamins/L, of which 60% was present as nicotinamide and 40% was present as NR. Nicotinic acid and other NAD+ metabolites were below the limits of detection. Milk from samples testing positive for Staphylococcus aureus contained lower concentrations of NR (Spearman ρ = −0.58, P = 0.014), and NR was degraded by S. aureus. Conventional milk contained more NR than milk sold as organic. Nonetheless, NR was stable in organic milk and exhibited an NMR spectrum consistent with association with a protein fraction in skim milk.

Conclusions: NR is a major NAD+ precursor vitamin in cow milk. Control of S. aureus may be important to preserve the NAD+ precursor vitamin concentration of milk.

Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits

The morphology of a sample of four bulls and 43 cows, presumed to be descendants of the extinct cattle breed ‘Algarvia’ (AG), was used to assign their relationship with animals from other Portuguese autochthonous breeds – Arouquesa (AR), Barrosa˜ (BA), Cachena (CA), Marinhoa (MA), Maronesa (MO), Minhota (MN), Mirandesa (MI), (only bulls), Alentejana (AL), Garvonesa (GA), Mertolenga (ME) and Preta (PR). Standard numerical taxonomic methods were applied to a set of 183 (cows) and 170 (bulls) traits, to derive average pairwise taxonomic distances among the sample of 257 cows and 76 bulls. Distance coefficients (morphological index of distance) ranged from 0.22 to 2.62 (cows) and from 0.49 to 2.13 (bulls). Unweighted pair group method using arithmetic averages (UPGMA)-based phenograms and a principal coordinate analysis showed that bulls were highly clustered and cows showed a tendency to cluster according to their geographical and breed origin. The AG population grouped together with GA, AL, ME and MN breeds in the Red Convex group. The average taxonomic distance among breeds was 1.02, the highest being 1.39 (ME versus BA) and the lowest being 0.64 (MA versus AR). The approach allowed for the identification of a phenotypically differentiated set of animals, comprising 19 cows and four bulls representative of the AG breed, and which can be targeted in further studies aiming at the recovery of this extinct breed.

Polymorphisms at the five exons of gowth hormone gene in the Algarvia Goat. Possible association with milk traits

The present preliminary study attempts to establish associations between milk production traits and genetic polymorphisms at the GH gene in the Algarvia goat. The DNA of 108 goats of the indigenous Portuguese Algarvia breed was evaluated.

The Activity of Breast Milk and Monoclonal HIV-specific Antibodies in Mother-to-Child Transmission

Mother-to-child transmission of HIV is a unique setting that allows us to explore both the correlates of protective immunity and the characteristics of transmitted variants. This thesis first describes the levels and functional capacity of breast milk HIV-specific antibodies in 19 women with high plasma viral loads. Neutralizing antibodies (Nabs) were detected in breast milk supernatant (BMS) of 4 of 19 women examined, were of low potency and were not associated with infant infection. The low NAb activity in BMS was reflected in binding antibody levels with HIV envelope specific IgG titers being 2.2 log10 lower in BMS versus plasma. In contrast, non- neutralizing antibodies (nNAbs) capable of antibody dependent cell-mediated cytotoxicity (ADCC) were detected in the BMS from all 19 women. BMS ADCC activity was associated with envelope-specific IgG titers (p = 0.014) and was inversely associated with infant infection risk (p = 0.039). Our data indicate that BMS has limited HIV neutralizing activity, however, BMS ADCC activity is a correlate of transmission that may impact infant infection risk. In the second part of this thesis the neutralization sensitivity of 111 variants of diverse subtypes obtained from mothers and infants was determined against 7 HIVspecific broadly neutralizing monoclonal antibodies (mAbs) (NIH45-46w, VRC01, PGT128, PGT121, PG9 PGT145 and b12). Maternal and infant variants did not differ in their neutralization sensitivity to these mAbs and neither did variants from transmitting versus those from non-transmitting women. However, subtype A viruses were iii significantly more sensitive to neutralization by NIH45-46w and VRC01 (p= 0.0001 in both cases) and PGT145 (p=0.03) compared to non-subtype A viruses. Together, NIH45- 46w and PGT128 neutralization profiles resulted in 100% coverage of the variants tested. These data suggest that the epitopes targeted by these mAbs are present and accessible in both circulating and transmitted variants and that a combination of antibodies would provide maximum coverage against diverse subtypes commonly found in HIV endemic regions. Overall, this data suggest that an antibody based HIV vaccine capable of eliciting antibodies of multiple specificities that can mediate ADCC and/or neutralizing activity can provide protection and conquer the genetic diversity displayed by HIV.

Relationship of milk intake and physical activity to abdominal obesity among adolescents

Background: Diet and physical activity (PA) are recognized as important factors to prevent abdominal obesity (AO), which is strongly associated with chronic diseases. Some studies have reported an inverse association between milk consumption and AO. Objective: This study examined the association between milk intake, PA and AO in adolescents. Methods: A cross-sectional study was conducted with 1209 adolescents, aged 15–18 from the Azorean Archipelago, Portugal in 2008. AO was defined by a waist circumference at or above the 90th percentile. Adolescent food intake was measured using a semi-quantitative food frequency questionnaire, and milk intake was categorized as ‘low milk intake’ (<2 servings per day) or ‘high milk intake’ ( 2 servings per day). PA was assessed via a self-report questionnaire, and participants were divided into active (>10 points) and low-active groups ( 10 points) on the basis of their reported PA. They were then divided into four smaller groups, according to milk intake and PA: (i) low milk intake/low active; (ii) low milk intake/active; (iii) high milk intake/low active and (iv) high milk intake/active. The association between milk intake, PA and AO was evaluated using logistic regression analysis, and the results were adjusted for demographic, body mass index, pubertal stage and dietary confounders. Results: In this study, the majority of adolescents consumed semi-skimmed or skimmed milk (92.3%). The group of adolescents with high level of milk intake and active had a lower proportion of AO than did other groups (low milk intake/low active: 34.2%; low milk intake/active: 26.9%; high milk intake/low active: 25.7%; high milk intake/active: 21.9%, P = 0.008). After adjusting for confounders, low-active and active adolescents with high levels of milk intake were less likely to have AO, compared with low-active adolescents with low milk intake (high milk intake/low active, odds ratio [OR] = 0.412, 95% confidence intervals [CI]: 0.201– 0.845; high milk intake/active adolescents, OR = 0.445, 95% CI: 0.235–0.845).Conclusion: High milk intake seems to have a protective effect on AO, regardless of PA level

Molecular tools in the diagnostic and epidemiology of infections caused by members of Mycobacterium avium Complex

Mycobacterium avium Complex (MAC) comprises microorganisms that affect a wide range of animals including humans. The most relevant are Mycobacterium avium subspecies hominissuis (Mah) with a high impact on public health affecting mainly immunocompromised individuals and Mycobacterium avium subspecies paratuberculosis (Map) causing paratuberculosis in animals with a high economic impact worldwide. In this work, we characterized 28 human and 67 porcine Mah isolates and evaluated the relationship among them by Multiple-Locus Variable number tandem repeat Analysis (MLVA). We concluded that Mah population presented a high genetic diversity and no correlations were inferred based on geographical origin, host or biological sample. For the first time in Portugal Map strains, from asymptomatic bovine faecal samples were isolated highlighting the need of more reliable and rapid diagnostic methods for Map direct detection. Therefore, we developed an IS900 nested real time PCR with high sensitivity and specificity associated with optimized DNA extraction methodologies for faecal and milk samples. We detected 83% of 155 faecal samples from goats, cattle and sheep, and 26% of 98 milk samples from cattle, positive for Map IS900 nested real time PCR. A novel SNPs (single nucleotide polymorphisms) assay to Map characterization based on a Whole Genome Sequencing analysis was developed to elucidate the genetic relationship between strains. Based on sequential detection of 14 SNPs and on a decision tree we were able to differentiate 14 phylogenetic groups with a higher discriminatory power compared to other typing methods. A pigmented Map strain was isolated and characterized evidencing for the first time to our knowledge the existence of pigmented Type C strains. With this work, we intended to improve the ante mortem direct molecular detection of Map, to conscientiously aware for the existence of Map animal infections widespread in Portugal and to contribute to the improvement of Map and Mah epidemiological studies.

Land of the rising soy an internationalization plan for nutre to the Japanese Soy milk market

The present work project studies the next step in the internationalization process of Shoyce, the soy milk products brand of Nutre. In order to select the best target market in the Asia-Pacific for Nutre to export, a sequential screening process was developed using two complementary approaches: preliminary country screening and country ranking, followed by an in-depth analysis of the country ranking first. The analysis revealed Japan as the most attractive country for Shoyce’s international expansion. Potential entry modes in the Japanese soy milk market were then evaluated, whereby direct exporting via a local distributor was found to be the most appropriate.

Guernsey Milk Can

In 1969, Sir William Arnold, Bailiff of Guernsey - the birthplace of Sir Isaac Brock - was invited by Dr. Gibson to come to Canada and visit Brock University on the 200th anniversary of Sir Isaac Brock's birth. Following his visit in October of that year, the Bailiff presented Brock University with this miniature silver milk can. This milk can is of the traditional Guernsey style.

Construction of bovine adenovirus type 3 E1 and E3, substitution plasmids and the sequencing analysis of DNA pol and pTP /

The relative ease to concentrate and purify adenoviruses, their well characterized mid-sized genome, and the ability to delete non-essential regions from their genome to accommodate foreign gene, made adenoviruses a suitable candidate for the construction of vectors. The use of adenoviral vectors in gene therapy, vaccination, and as a general vector system for expressing foreign genes have been documented for some time. In this study, the objective was to rescue a BAV3 E1 or E3 recombinant vector carrying the kanamycin resistant gene, a dominant selectable marker with useful applications in studying vectored gene expression in mammalian cells. To accomplish the objective of this study, more information about BAV3 DNA sequences was required in order to make the manipulation of the virus genome accessible. Therefore, sequencing of the BAV3 genome from 1 1 .7% to 30.8% was carried out. Analysis of the determined sequences revealed the primary structure of important viral gene products coded by E2 including BAV3 DNA pol and precursor to terminal protein. Comparative analysis of these proteins with their counterparts from human and non human adenoviruses revealed important insights as to the evolutionary lineage of BAV3. In order to insert the kanamycin resistance gene in either E1 or E3, it was necessary to delete BAV3 sequences to accommodate the foreign gene so as not to exceed the limit of the packaging capacity of the virus. To construct a recombinant BAV3 in which a foreign gene was inserted in the deleted E1 region, an E1 shuttle vector was constructed. This involved the deletion from the viral sequences a region between 1.3% to 9% and inserting the kanamycin resistance gene to replace the deletion. The E1 shuttle vector contained the left (0%- 53.9%) segment of the genome and was expected to generate BAV3 recombinants that can be grown and propagated in cells that can complement the missing E1 functions. To construct a similar shuttle vector for E3 deletion, DNA sequences extending from 78.9% to 82.5% (1281 bp) were deleted from within the E3 region that had been cloned into a plasmid vector. The deleted region corresponds to those that have been shown to be non-essential for viral replication in cell culture. The resulting plasmid was used to construct another recombinant plasmid with BAV3 DNA sequences extending from 37.1% to 100% and with a deletion of E3 sequences that were replaced by kanamycin resistance gene. This shuttle plasmid was used in cotransfections with digested viral DNA in an attempt to rescue a recombinant BAV3 carrying the kanamycin resistance gene to replace the deleted E3. In spite of repeated attempts of transfection, El or E3 recombinant BAV3 were not isolated. It seems that other approaches should be applied to make a final conclusion on BAV3 infectivity.