The recent technology of single-cell RNA sequencing can be used to investigate molecular, transcriptional, changes in cells as they develop. I reviewed the literature on the technology, and made a large scale quantitative comparison of the different implementations of single cell RNA sequencing to identify their technical limitations. I investigate how to model transcriptional changes during cellular development. The general forms of expression changes with respect to development leads to nonparametric regression models, in the forms of Gaussian Processes. I used Gaussian process models to investigate expression patterns in early embryonic development, and compared the development of mice and humans. When using in vivo systems, ground truth time for each cell cannot be known. Only a snapshot of cells, all being in different stages of development can be obtained. In an experiment measuring the transcriptome of zebrafish blood precursor cells undergoing the development from hematopoietic stem cells to thrombocytes, I used a Gaussian Process Latent Variable model to align the cells according to the developmental trajectory. This way I could investigate which genes were driving the development, and characterise the different patterns of expression. With the latent variable strategy in mind, I designed an experiment to study a rare event of murine embryonic stem cells entering a state similar to very early embryos. The GPLVM can take advantage of the nonlinear expression patterns involved with this process. The results showed multiple activation events of genes as cells progress towards the rare state. An essential feature of cellular biology is that precursor cells can give rise to multiple types of progenitor cells through differentiation. In the immune system, naive T-helper cells differentiate to different sub-types depending on the infection. For an experiment where mice were infected by malaria, the T-helper cells develop into two cell types, Th1 and Tfh. I model this branching development using an Overlapping Mixture of Gaussian Processes, which let me identify both which cells belong to which branch, and learn which genes are involved with the different branches. Researchers have now started performing high-throughput experiments where spatial context of gene expression is recorded. Similar to how I identify temporal expression patterns, spatial expression patterns can be identified nonparametrically. To enable researchers to make use of this technique, I developed a very fast method to perform a statistical test for spatial dependence, and illustrate the result on multiple data sets.

Eukaryotes have developed stringent regulatory mechanisms that control cell division and ensure proper chromosome segregation. Maintaining genome integrity is especially important during meiosis, the specialised cell division programme in the germline that generates haploid gametes. As these cells transmit genetic information to the next generation, the consequences of meiotic errors are not restricted to an organismal level, but can directly impact the fitness of the offspring. Mammals display a high degree of sexual dimorphism in meiosis with regard to the stringency of regulatory mechanisms. This manifests in a relatively high degree of maternally-derived aneuploidies due to weaker checkpoint control in females, whereas more rigorous checkpoints in males frequently perturb fertility. Mouse models of aneuploidy often exhibit complete male sterility and early germ cell arrest, preventing the study of aneuploidy during late and post-meiotic stages in males. In this thesis, we have used the trans-chromosomic mouse model, Tc1, which carries a single copy of human chromosome 21 (HsChr21) and show that, unlike other aneuploid mouse strains, the Tc1 mouse can successfully passage the exogenous human chromosome through male meiosis and generate aneuploid offspring. Our investigations have shown that the presence of the aneuploid human chromosome causes spermatogenic defects due to an arrest at the first meiotic division. Despite this impairment, we found an unexpectedly high number of aneuploid gametes in Tc1 males and the majority of males were able to produce aneuploid offspring, albeit at a lower frequency. Transmission of HsChr21 through the male germline was less efficient compared to female germline transmission, but allowed us to study the impact of male germline-associated chromatin remodelling on the transcriptional deployment of HsChr21 in the offspring. This revealed that, despite fundamentally different developmental dynamics, male- versus female-germline passage result in indistinguishable transcriptional and regulatory phenotypes. An important pathway in the male germline involves the expression of piRNAs, a class of small non-coding RNAs that are commonly found in the germline of animals where they defend cells against transposable elements. Profiling the expression of small RNAs in the Tc1 mouse showed that conserved human piRNA clusters can be successfully transcribed by the mouse piRNA machinery. In addition, we detected Tc1-specific piRNA sequences that were neither present in human nor mouse, mapping to a human-specific repeat element. In line with the previously observed activation of human-specific repeat elements in the Tc1 mouse, this suggests that novel transcripts arising from human repeats can trigger an adaptive piRNA response, thereby demonstrating the plasticity of this pathway to newly invading repeat elements. Transcriptional profiling of spermatogenic cell populations on a single-cell level allowed us to generate an atlas of gene expression over the course of spermatogenesis and dissect meiotic silencing dynamics in the presence of aneuploidy. Transcriptional silencing during meiosis occurs in response to unpaired chromosomes and, in male germ cells, affects the sex chromosomes due to their largely unpaired nature. We found that the presence of HsChr21 has no impact on the silencing of chromosome X, however, the two chromosomes display drastically different silencing patterns with HsChr21 showing a much weaker repression. Taken together, this study revealed a higher than expected tolerance for aneuploidy in the mouse male germline thus allowing the characterisation of meiotic checkpoint mechanisms, the meiotic silencing response to unpaired chromosomes as well as piRNA expression in the presence of an exogenous human chromosome.

Para a melhor extração da fração hemicelulósica do bagaço de cana-de-açúcar e obtenção do hidrolisado contendo uma mistura de açúcares, predominantemente de xilose, foi definido o processo de hidrólise com ácido na concentração de 100 mg H2S04/g m.s. a 140 °C por 20 minutos de reação. O hidrolisado hemicelulósico obtido foi utilizado para avaliação do crescimento celular e consumo de açúcares por 19 cepas de leveduras e 03 de fungos. Candida tropicalis lZ 1824 foi selecionada como promissora para produção de biomassa microbiana (11,0 g.l-1) e consumo de ART (89,8%) e apresentar fator de conversão (YK/S) de 0.50 g.g-1. Foi verificado ainda que a levedura selecionada apresentou melhores rendimentos em biomassa e consumo de ART, quando cultivada em hidrolisado suplementado com P2O5 (2.0 g.l-1) e uréia (2,0 g.l-1) a pH inicial 6,0. Finalmente verificou-se que na vazão específica de aeração de 2,0 v/v/m houve a maior velocidade específica máxima de crescimento (0,108 h-1), quando comparada com cultivos realizados a 1,0 v/v/m. A biomassa microbiana obtida nestas condições apresentou um teor protéico de 31, 3% com composição de aminoácidos comparável ao padrão da FAO. / For a better extraction of the hemicellulosic fraction from the sugar cane bagasse and obtention of hydrolysate containing a mixture of sugars, predominantly xylose, the hydrolysis process was defined, with acid in the concentration of 100 mg H2SO4/g dry matter, at 140 °C for 20 minutes of reaction. The hemicellulosic hydrolysate obtained was utilized for evaluation of cell growth and sugars consumption by 19 yeast stocks and 3 fungi stocks. Candida tropicalis lZ 1824 was selected for being considered as very promissing for production of microbial biomass (11,8 g.l-1) and TRS consumption (89,8%) and also for presenting a conversion factor (YK/S) of 0,50 g.g-1. It was noticed that the selected yeast gave greater biomass yields and TRS consumption when cultivated in hydrolysate supplemented with P2O5 (2,0 g.l-1) and urea (2,0 g.l-1) at initial pH 6,0. At last it was observed that the specific aeration flow of 2,0 v/v/m caused the highest maximum specific growth velocity (0,108 h-1) when compared to the cultivation accomplished of 1,0 v/v/m. The microbial bíomass obtained under these conditions presented a 31,3% protein content with a composition of amino acids comparable to the FAD standard.

The aim of this project was to investigate the transcriptome of human haematopoietic stem cells (HSCs), megakaryocytes and platelets to gain insights into steady state and accelerated thrombopoiesis that occurs in states of haemostatic demand and in thrombosis by applying these findings to the pathological setting of acute coronary thrombosis. To investigate transcriptional heterogeneity within the human HSC population, single cell RNA sequencing was performed in human bone marrow HSCs. Transcriptionally distinct subpopulations were identified including two megakaryocyte biased subsets with potentially differing functional relevance. Both populations expressed megakaryocyte specific transcripts, one of which also co-expressed common myeloid and megakaryocyte-erythroid progenitor transcripts while the other did not. This study represents the first interrogation of the human bone marrow megakaryocyte transcriptome. Cells were collected from healthy human bone marrow and analysed by low input and single cell RNA sequencing. To identify novel drivers of megakaryocyte maturation, the human bone marrow megakaryocyte transcriptome was compared to that of megakaryocytes cultured from human CD34+ cells, a process known to generate immature megakaryocytes. Transcriptional signatures associated with increasing megakaryocyte ploidy were then investigated. Increasing megakaryocyte ploidy level was found to be associated with an upregulation of transcripts involved in translation and protein processing as well as expression of a number of transmembrane receptors which might have functional relevance. Finally, the pathological setting of acute coronary thrombosis was used as a model for accelerated thrombopoiesis. Megakaryocyte and platelet transcriptomes were compared between patients with acute myocardial infarction (AMI) as well as severe coronary disease and a control group. The transcriptional signature relating to disease compared to control in megakaryocytes included upregulation of platelet activation related transcripts in megakaryocytes isolated from patients with AMI and severe coronary artery disease.

Photonic crystals serve as powerful building blocks for the development of lab-on-chip devices. Currently they are used for a wide range of miniaturized optical components such as extremely compact waveguides to refractive-index based optical sensors. Here we propose a new technique for analyzing and characterizing cells through the design of a micro-flow cytometer using photonic crystals. While lab scale flow cytometers have been critical to many developments in cellular biology they are not portable, difficult to use and relatively expensive. By making a miniature sensor capable of replicating the same functionality as the large scale units with photonic crystals, we hope to produce a device that can be easily integrated into a lab-on-chip and inexpensively mass produced for use outside of the lab. Using specialized FDTD software, the proposed technique has been studied, and multiple important flow cytometry functions have been established. As individual cells flow near the crystal surface, transmission of light through the photonic crystal is influenced accordingly. By analyzing the resulting changes in transmission, information such as cell counting and shape characterization have been demonstrated. Furthermore, correlations for simultaneously determining the size and refractive indices of cells has been shown by applying the statistical concepts of central moments.

The investigation of genetic alterations in cancer-relatedgenes is useful for research, prognostic and therapeuticpurposes. However, the genetic heterogeneity that often occursduring tumour progression can make correct analysischallenging. The objective of this work has been to develop,evaluate and apply techniques that are sufficiently sensitiveand specific to detect and analyse genetic alterations in skintumours as well as in normal skin. Initially, a method based on laser-assisted microdissectionin combination with conventional dideoxy sequencing wasdeveloped and evaluated for the analysis of the p53 tumoursuppressor gene in small tissue samples. This method was shownto facilitate the analysis of single somatic cells fromhistologic tissue sections. In two subsequent studies themethod was used to analyse single cells to investigate theeffects of ultraviolet (UV) light on normal skin. Single p53immunoreactive and nonimmunoreactive cells from differentlayers of sunexposed skin, as well as skin protected fromexposure, were analysed for mutations in the p53 gene. Theresults revealed the structure of a clandestine p53 clone andprovided new insight into the possible events involved innormal differentiation by suggesting a role for allele dropout.The mutational effect of physiological doses of ultravioletlight A (UVA) on normal skin was then investigated by analysingthe p53 gene status in single immunoreactive cells at differenttime-points. Strong indications were found that UVA (even atlow doses) is indeed a mutagen and that its role should not bedisregarded in skin carcinogenesis. After slight modifications, the p53 mutation analysisstrategy was thenused to complement an x-chromosomeinactivation assay for investigation of basal cell cancer (BCC)clonality. The conclusion was that although the majority ofBCC’s are of monoclonal origin, an occasional tumour withapparently polyclonal origin exists. Finally, apyrosequencing-based mutation detection method was developedand evaluated for detection of hot-spot mutations in the N-rasgene of malignant melanoma. More than 80 melanoma metastasissamples were analysed by the standard approach of single strandconformation polymorphism analysis (SSCP)/DNA sequencing and bythis pyrosequencing strategy. Pyrosequencing was found to be agood alternative to SSCP/DNA sequencing and showed equivalentreproducibility and sensitivity in addition to being a simpleand rapid technique. <b>Keywords:</b>single cell, DNA sequencing, p53, mutation,UV, BCC, pyrosequencing, malignant melanoma, N-ras

A primary objective of modern biology is to understand the molecular mechanisms which underlie cellular functions and a crucial part of this task is the ability to manipulate and analyze individual cells. As a result of interdisciplinary research, microfluidics may become the forefront of analytical methods used by biologists. This technology can be used to gain unprecedented opportunities for cell handling, lysis and investigation on a single cell basis. This thesis presents the development of a microfluidic device capable of selecting individual cells and performing selective electrical lysis of the plasma membrane, while verifying intactness of the nuclear membrane. The device is fabricated by an improved photolithography method and integrates molten solder as electrodes for lysis by a DC electric field. Quantification of lysis is accomplished by video and image analysis, and measurement of the rate of ion diffusion from the cell.

A primary objective of modern biology is to understand the molecular mechanisms which underlie cellular functions and a crucial part of this task is the ability to manipulate and analyze individual cells. As a result of interdisciplinary research, microfluidics may become the forefront of analytical methods used by biologists. This technology can be used to gain unprecedented opportunities for cell handling, lysis and investigation on a single cell basis. This thesis presents the development of a microfluidic device capable of selecting individual cells and performing selective electrical lysis of the plasma membrane, while verifying intactness of the nuclear membrane. The device is fabricated by an improved photolithography method and integrates molten solder as electrodes for lysis by a DC electric field. Quantification of lysis is accomplished by video and image analysis, and measurement of the rate of ion diffusion from the cell.

A comprehensive understanding of how the body and all its components function is essential when this knowledge is exploited for medical purposes. The achievements in biological and medical research during last decades has provided us with the complete human genome and identified signaling pathways that governs the cellular processes that facilitates the development and maintenance of higher order organisms. This has brought about the realization that diseases such as cancer is a consequence of genomic aberrations that effects these signaling pathways, endowing cancer cells with the capacity to circumvent homeostasis by acquiring features like self-sustained proliferation and insensitivity to apoptosis. The increased understanding of biology and medicine has been made possible by the development of advanced methods to carry out biological and clinical analyses. The demands of a method often differ regarding in what context it will be applied. It may be acceptable for method to be laborious and time consuming if it is used in basic research, but for medical purposes molecular methods need to be fast and straightforward to perform. Innovative technologies should preferentially address the demands of both researchers and clinicians and provide data not possible to obtain by other methods. An example of such a method is the in situ proximity ligation assay (in situ PLA). In this thesis I have used this method to determine the activity status, at the single-cell level, of the transforming growth factor-β (TGF-β) signaling pathway and activating protein-1 (AP-1) family of transcription factors.  Both of these pathways are frequently involved in cancer development and progression. In addition to this research I herein also present further modifications of in situ PLA, and analyses thereof, to increase the utility and resolution of this assay.

<p>The investigation of genetic alterations in cancer-relatedgenes is useful for research, prognostic and therapeuticpurposes. However, the genetic heterogeneity that often occursduring tumour progression can make correct analysischallenging. The objective of this work has been to develop,evaluate and apply techniques that are sufficiently sensitiveand specific to detect and analyse genetic alterations in skintumours as well as in normal skin.</p><p>Initially, a method based on laser-assisted microdissectionin combination with conventional dideoxy sequencing wasdeveloped and evaluated for the analysis of the p53 tumoursuppressor gene in small tissue samples. This method was shownto facilitate the analysis of single somatic cells fromhistologic tissue sections. In two subsequent studies themethod was used to analyse single cells to investigate theeffects of ultraviolet (UV) light on normal skin. Single p53immunoreactive and nonimmunoreactive cells from differentlayers of sunexposed skin, as well as skin protected fromexposure, were analysed for mutations in the p53 gene. Theresults revealed the structure of a clandestine p53 clone andprovided new insight into the possible events involved innormal differentiation by suggesting a role for allele dropout.The mutational effect of physiological doses of ultravioletlight A (UVA) on normal skin was then investigated by analysingthe p53 gene status in single immunoreactive cells at differenttime-points. Strong indications were found that UVA (even atlow doses) is indeed a mutagen and that its role should not bedisregarded in skin carcinogenesis.</p><p>After slight modifications, the p53 mutation analysisstrategy was thenused to complement an x-chromosomeinactivation assay for investigation of basal cell cancer (BCC)clonality. The conclusion was that although the majority ofBCC’s are of monoclonal origin, an occasional tumour withapparently polyclonal origin exists. Finally, apyrosequencing-based mutation detection method was developedand evaluated for detection of hot-spot mutations in the N-rasgene of malignant melanoma. More than 80 melanoma metastasissamples were analysed by the standard approach of single strandconformation polymorphism analysis (SSCP)/DNA sequencing and bythis pyrosequencing strategy. Pyrosequencing was found to be agood alternative to SSCP/DNA sequencing and showed equivalentreproducibility and sensitivity in addition to being a simpleand rapid technique.</p><p><b>Keywords:</b>single cell, DNA sequencing, p53, mutation,UV, BCC, pyrosequencing, malignant melanoma, N-ras</p>