A mathematical framework for clonal data analysis

This dissertation reports on the development of the mathematical and statistical framework that was necessary for the analysis of data from a novel single-cell assay designed to address questions in fundamental biology. Many biological systems function by generating new cells from activated ancestors through cellular division. To investigate such systems, a high throughput experimental protocol was recently developed that marks initial cells so that their cellular offspring, the number of rounds of division from their ancestor, and their phenotype can be determined. The clonal data that result from this technique, however, are characterised by familial associations that impede their analysis using classical quantitative tools, necessitating the development of a new mathematical framework where suitable statistics are formulated that take these complex dependencies into account. The design, development and implementation of that framework, as well as inferences made from its use, are the subject of the present thesis

Effects of pen floor and class of live weight on behavioural and clinical parameters of beef cattle

The study compared behaviour and clinical parameters of beef cattle housed on two different types of floor (fully slatted vs. deep litter) considering animals belonging to 2 live weight classes (less vs. more than 350 kg). The assessment of behavioural and clinical parameters was carried out in 20 intensive farms, all rearing imported bulls. Floor type had no effect on cattle behaviour except for the duration of the lying down sequence, which lasted more for bulls kept on slats. Slatted floor increased also the likelihood of occurrence of hair and skin lesions and lameness. On the other hand, bulls cleanliness was more likely to be impaired on bedded floor. Regarding the class of live weight, behavioural observation showed lighter animals performing more antagonistic interactions, while horning resulted more frequent in heavier bulls. Avoidance distance test indicated that bulls >350 kg were more fearful of humans. About health status, light animals were more affected by respiratory disease and hairless patches, likely because they are more sensitive to the stressful situations imposed by their transfer and adaptation to the new housing environment of the fattening unit. The risk of skin lesions and dirtiness increased instead in heavier bulls

An insight into the dairy chain of a Protected Designation of Origin cheese: The case study of Asiago cheese.

The Protected Designation of Origin (PDO) label of the European Union safeguards and guarantees top-quality traditional agri-food products that must be manufactured in a specific region according to traditional production methods. Production specifications of PDO cheeses are often focused on the cheese-making process and lack information on the dairy farming system that is upstream of the chain. This case study aimed to analyze and cluster the dairy farms that supply milk to the chain of Asiago, an internationally known PDO cheese of northeastern Italy. A large survey involving all of the cheese factories of the Asiago PDO chain was made in 2017. Each cheese factory submitted a questionnaire to its supplying dairy farmers concerning (1) farm facilities and herd management and (2) feeding program of lactating cows. Results from 517 farms were processed; there were 67 ± 27% (mean ± standard deviation) respondents per cheese factory. Four clusters of dairy farms were identified by hierarchical clustering analysis. Cluster 1 (8% of the surveyed farms) and cluster 2 (22%) are small in size and low in yield, representing the traditional milk production system; farms are mainly located on mountains or hills and have autochthonous dual-purpose breeds mostly housed in tiestall barns. By rearing cattle of endangered breeds and feeding cows primarily with forages produced on-farm together with the use of pasture, these clusters, and especially cluster 1, have shown to provide essential ecosystem services for landscape and biodiversity preservation in the alpine areas. Clusters 3 and 4 (34 and 36% of the surveyed farms, respectively) gather medium-scale farms mainly located in the lowland that operate according to modern management and housing systems and rear high-producing dairy cows. These cows are mainly fed total mixed rations based on corn silage, but the dietary forage:concentrate ratio is kept relatively high, as farmers are more interested in producing high-quality milk for cheese-making than pushing for yield. Regardless of the cluster allocation, a considerable cow longevity, which is a recognized "iceberg indicator" of cattle well-being, was highlighted. This study showed that different farming systems may lay behind a single PDO cheese. The knowledge of their characteristics is important to reinforce the PDO production specifications as well as to distinguish and protect niche products that come from specific groups of farms that provide essential ecosystem services

Effect of the number of daily distributions of solid feed on veal calves' health status, behaviour, and alterations of rumen and abomasa

The research aimed at evaluating the effect of three versus two daily distributions of solid feed on veal calves' health, behaviour, and rumen and abomasal mucosa alterations with the rationale that three distributions might improve calves' health and welfare. The study was carried out in two veal calf farms that provided different amounts of solid feed (farm A 200 kg DM/calf; farm B 150 kg DM/calf) during the fattening in addition to liquid milk-replacer. It involved 342 calves in farm A and 108 calves in farm B. The change from two to three solid feed distributions/day started for half calves/farm after the third month of fattening when farm A was feeding 800 g and farm B 600 g DM/calf/day. Health status, blood haemoglobin, and behaviour were assessed on farm at different times. Calves' carcass weight was recorded and rumens and abomasa were inspected post mortem. Increasing solid feed distributions did not improve calves' health but it reduced non-nutritive oral behaviours (4.8 versus 3.2 ± 0.4% for two and three distributions/day, respectively) by prolonging the time spent eating solid feed. Carcass weight was similar between treatments. Three daily solid feed distributions did not reduce the prevalence of rumen mucosa hyperkeratinisation and abomasal alterations, worsening the frequency of rumen plaques. As the partition of daily dose of solid feed in three distributions is more time and labour consuming, its benefits addressing only the reduction of non-nutritive oral behaviours seem not sufficient to justify the routinely adoption of this practice by veal producers

Cyton2:A Model of Immune Cell Population Dynamics That Includes Familial Instructional Inheritance

Lymphocytes are the central actors in adaptive immune responses. When challenged with antigen, a small number of B and T cells have a cognate receptor capable of recognising and responding to the insult. These cells proliferate, building an exponentially growing, differentiating clone army to fight off the threat, before ceasing to divide and dying over a period of weeks, leaving in their wake memory cells that are primed to rapidly respond to any repeated infection. Due to the non-linearity of lymphocyte population dynamics, mathematical models are needed to interrogate data from experimental studies. Due to lack of evidence to the contrary and appealing to arguments based on Occam’s Razor, in these models newly born progeny are typically assumed to behave independently of their predecessors. Recent experimental studies, however, challenge that assumption, making clear that there is substantial inheritance of timed fate changes from each cell by its offspring, calling for a revision to the existing mathematical modelling paradigms used for information extraction. By assessing long-term live-cell imaging of stimulated murine B and T cells in vitro, we distilled the key phenomena of these within-family inheritances and used them to develop a new mathematical model, Cyton2, that encapsulates them. We establish the model’s consistency with these newly observed fine-grained features. Two natural concerns for any model that includes familial correlations would be that it is overparameterised or computationally inefficient in data fitting, but neither is the case for Cyton2. We demonstrate Cyton2’s utility by challenging it with high-throughput flow cytometry data, which confirms the robustness of its parameter estimation as well as its ability to extract biological meaning from complex mixed stimulation experiments. Cyton2, therefore, offers an alternate mathematical model, one that is, more aligned to experimental observation, for drawing inferences on lymphocyte population dynamics

A mathematical framework for clonal data analysis

This dissertation reports on the development of the mathematical and statistical framework that was necessary for the analysis of data from a novel single-cell assay designed to address questions in fundamental biology. Many biological systems function by generating new cells from activated ancestors through cellular division. To investigate such systems, a high throughput experimental protocol was recently developed that marks initial cells so that their cellular offspring, the number of rounds of division from their ancestor, and their phenotype can be determined. The clonal data that result from this technique, however, are characterised by familial associations that impede their analysis using classical quantitative tools, necessitating the development of a new mathematical framework where suitable statistics are formulated that take these complex dependencies into account. The design, development and implementation of that framework, as well as inferences made from its use, are the subject of the present thesis

A mathematical framework for clonal data analysis

This dissertation reports on the development of the mathematical and statistical framework that was necessary for the analysis of data from a novel single-cell assay designed to address questions in fundamental biology. Many biological systems function by generating new cells from activated ancestors through cellular division. To investigate such systems, a high throughput experimental protocol was recently developed that marks initial cells so that their cellular offspring, the number of rounds of division from their ancestor, and their phenotype can be determined. The clonal data that result from this technique, however, are characterised by familial associations that impede their analysis using classical quantitative tools, necessitating the development of a new mathematical framework where suitable statistics are formulated that take these complex dependencies into account. The design, development and implementation of that framework, as well as inferences made from its use, are the subject of the present thesis

A mathematical framework for clonal data analysis

This dissertation reports on the development of the mathematical and statistical framework that was necessary for the analysis of data from a novel single-cell assay designed to address questions in fundamental biology. Many biological systems function by generating new cells from activated ancestors through cellular division. To investigate such systems, a high throughput experimental protocol was recently developed that marks initial cells so that their cellular offspring, the number of rounds of division from their ancestor, and their phenotype can be determined. The clonal data that result from this technique, however, are characterised by familial associations that impede their analysis using classical quantitative tools, necessitating the development of a new mathematical framework where suitable statistics are formulated that take these complex dependencies into account. The design, development and implementation of that framework, as well as inferences made from its use, are the subject of the present thesis