Improvement of in silico strain engineering methods in Saccharomyces cerevisiae

PhD thesis in Bioengineering

Biotechnological approaches for yield improvement of anticancer alkaloids in the plant Catharanthus roseus

Dissertação de mestrado em Biologia Molecular, Biotecnologia e Bioempreendedorismo em Plantas

Genetic algorithms for the non emergency patients transport service

The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the paper. The authors would like to thank Dr. Elaine DeBock for reviewing the manuscript.

Narrative innovations predict symptom improvement: Studying innovative moments in narrative therapy of depression

Objective:Innovative moments (IMs) are moments in the therapeutic dialog that constitute exceptions toward the client's problems. These narrative markers of meaning transformation are associated with change in different models of therapy and diverse diagnoses. Our goal is to test if IMs precede symptoms change, or, on the contrary, are a mere consequence of symptomatic 15 change. Method: For this purpose, IMs and symptomatology (Outcome Questionnaire-10.2) were assessed at every session in a sample of 10 cases of narrative therapy for depression. Hierarchical linear modeling was conducted to explore whether (i) IMs in a given session predict patients' symptoms in the following session and/or (ii) symptoms in a given session predict IMs in the next session. Results: Results suggested that IMs are better predictors of symptoms than the reverse. Conclusions: These results are discussed considering the contribution of meanings and narrative processes' changes to symptomatic improvement.

PTX3-based genetic testing for risk of aspergillosis after lung transplant

PTX3-based genetic testing for risk of aspergillosis after lung transplant

A genetic perspective on African prehistory

The various genetic systems (mitochondrial DNA, the Y-chromosome and the genome-wide autosomes) indicate that Africa is the most genetically diverse continent in the world and the most likely place of origin for anatomically modern humans. However, where in Africa modern humans arose and how the current genetic makeup within the continent was shaped is still open to debate. Here, we summarize the debate and focus especially on the maternally inherited mitochondrial DNA (mtDNA) and a recently revised chronology for the African mtDNA tree. We discuss the possible origin of modern humans in southern, eastern or Central Africa; the possibility of a migration from southern to eastern Africa more than 100 ka, carrying lineages within mtDNA haplogroup L0; the evidence for a climate-change-mediated population expansion in eastern Africa involving mtDNA haplogroup L3, leading to the “out-of-Africa” migration around 70–60 ka; the re-population of North Africa from the Near East around 40–30 ka suggested by mtDNA haplogroups U6 and M1; the evidence for population expansions and dispersals across the continent at the onset of the Holocene ; and the impact of the Bantu dispersals in Central, eastern and southern Africa within the last few millennia.

Citric acid production by Y. lipolytica W29 from crude glycerol: strain improvement by mutagenesis

[Excerpt] Citric acid, an important and versatile organic acid extensively used in several industries, is originally produced by Aspergillus niger in submerged fermentation from molasses [1]. However, Yarrowia lipolytica have been studied and demonstrate a great potential as citric acid producer from several carbon sources [1–5] including crude glycerol, a low cost byproduct from the biodiesel industry [6]. The simultaneous production of the isomer isocitric acid is the major problem in using this yeast in the citric acid production. (...)

Genetic regulatory mechanisms by means of extended interactive Petri nets

In our work we have chosen to integrate formalism for knowledge representation with formalism for process representation as a way to specify and regulate the overall activity of a multi-cellular agent. The result of this approach is XP,N, another formalism, wherein a distributed system can be modeled as a collection of interrelated sub-nets sharing a common explicit control structure. Each sub-net represents a system of asynchronous concurrent threads modeled by a set of transitions. XP,N combines local state and control with interaction and hierarchy to achieve a high-level abstraction and to model the complex relationships between all the components of a distributed system. Viewed as a tool XP,N provides a carefully devised conflict resolution strategy that intentionally mimics the genetic regulatory mechanism used in an organic cell to select the next genes to process.

Psychological approach to endometriosis: Women's pain experience and quality of life improvement

Endometriosis is a chronic condition affecting 10 to15% of women in childbearing age. Understanding the impact of this disease on women’s well-being is still a challenge, namely to intervene. Pain is the most current and troublesome symptom. Although medical treatments for pain relief are effective, recurrence rate remains significant, calling for a better understanding and development of new approaches for pain management. A group Cognitive Behavioral Therapy (CBT) for management of associated co-morbidities is suggested, paying special attention to Chronic Pelvic Pain (CPP). CBT design can be grounded on information collected from focus groups and a one-group exploratory trial. Evaluation of therapy effectiveness is possible to be performed by comparing group CBT to Usual Care (UC) and Support Group (SG) in a randomized controlled trial. Research in this area could represent an important step in providing a solution to the management of endometriosis and, to the best of our knowledge, the first national psychological approach for its understanding and treatment.

Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.