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El Virus de Inmunodeficiencia Humana Tipo-1 (VIH-1) es el agente etiológico responsable del Síndrome de Inmunodeficiencia Adquirida (SIDA). Esta enfermedad se caracteriza por una pérdida sostenida de linfocitos T CD4+, provocando una alteración global del sistema inmunitario, y dejando al individuo expuesto a infecciones oportunistas y al desarrollo de ciertas neoplasias.Desde la introducción de la zidovudina en el año 1986 hasta la implantación a partir del año 1996 de las Terapias Antirretrovirales de Gran Actividad o TARGA (combinaciones de al menos tres compuestos antirretrovirales) se han aprobado un total de 19 nuevos fármacos para el tratamiento de la infección por el VIH-1. En su conjunto, la quimioterapia contra la infección por el VIH-1 incrementa la esperanza de vida de los individuos infectados. Sin embargo, complicaciones surgidas por el uso de estas terapias (p.e una adherencia subóptima, alteraciones en el perfil fármaco-cinético de algunos pacientes o la falta de potencia de los tratamientos) propician la selección de mutaciones de resistencia frente a los fármacos antirretrovirales. La aparición de estas mutaciones en el genoma del VIH-1 constituye una barrera al éxito duradero de las terapias antirretrovirales.Nuestras investigaciones parten del interés por el estudio de la variación en la eficacia biológica o "fitness" del VIH-1 debido a la adquisición de mutaciones de resistencia. La relación entre el mantenimiento de cepas virales con bajo "fitness" y elevada resistencia con un posible beneficio clínico constituye uno de los ejes centrales en los estudios aplicados de "fitness" viral. A lo largo de este trabajo resumiré el conocimiento acumulado en los últimos años en el estudio del VIH-1: su estructura básica y aspectos más relacionados con esta tesis, como son los fenómenos de resistencia a antirretrovirales y sus consecuencias en la modulación del "fitness" del VIH-1. / Human Immunodeficiency Virus Tipo-1 (HIV-1) is the agent responsible of Acquired Immunodeficiency Syndrome (AIDS). This illness is characterized by a long-term loss of CD4+T cells producing a global alteration of the immune system leading to the dead of the individual.From the introduction of Zidovudine in 1986 to Highly Active Antiretroviral Therapies (HAART) (combinations of at least 3 antiretroviral drugs), in 1996 it has been approved a total of 19 new drugs against HIV. These regimens have contributed to decrease mortality and morbidity among HIV-1 infected patients. However, in the course of treatment drug resistant HIV-1 variants often emerge as a result of impotent regimens, suboptimal adherence, pharmacological hurdles or ineffectively treated compartments, which has been a major factor contributing to treatment failure. Our research begins for the interest in study changes in HIV-1 replicative capacity or viral fitness associated with the acquisition of resistance mutations. The relationship between the maintenance of viral strains with low viral fitness and high resistance with a better clinical outcome is one of the mains objectives in the studies of viral fitness. In this thesis we will resume the knowledge from the last years in the studies of HIV-1: its basic structure and aspect associated this thesis, the processes of resistance and their consequences in changes of viral fitness.

La presencia de arsénico en aguas potables y de riego es un problema económico, social y ambiental de extrema importancia, especialmente en varios países de América Latina (principalmente en el Norte de Chile y de Argentina). Los microorganismos respiradores que reducen As(V) a arsenito As(III) son diversos y pueden estar implicados en la movilización del arsénico del sedimento a fuentes de agua potable. Para entender cómo contribuye este metabolismo a la biogeoquímica del arsénico la presente tesis explora, por un lado, tanto la diversidad de comunidades microbianas en ambientes naturales salinos con presencia (p.ej. el Salar de Ascotán) o ausencia (Laguna Tebenquiche) de arsénico, como la distribución y diversidad de los genes involucrados en este metabolismo (arsenato reductasa arrA y arsC) y, por el otro, el aislamiento y caracterización de cultivos puros y su implicación en la formación de minerales sulfurosos de arsénico en estos ambientes salinos.Con la construcción de bibliotecas genéticas se pudo caracterizar la diversidad microbiana del gen ribosómico 16S rRNA, encontrando diferencias marcadas entre las bacterias presentes en ambientes salinos con y sin arsénico. La diversidad de genes involucrados en la reducción del As(V), se estudió con cebadores específicos descritos en estudios previos pero optimizando su aplicación a muestras naturales con contenidos elevados de arsénico. Se estudió el gen arrA presente en microorganismos que respiran arsenato y lo reducen a arsenito y el gen arsC que está ligado a la detoxificación del arsénico denle el citoplasma y su expulsión mediante bombas de excreción ligadas a la membrana. La mayoría de las secuencias recuperadas formaron grupos nuevos pero relacionados con los clones obtenidos en ambientes similares pero de menor concentración de arsénico reportados en la literatura, y emparentados con el grupo Firmicutes. Observamos que, tanto por el estudio de los genes 16S rRNA como de los genes funcionales de As, los grupos más abundantes siempre fueron Firmicutes y Gammaproteobacteria en muestras de agua y de sedimento del Salar de Ascotán.En un conjunto de muestras naturales con diferentes concentraciones de arsénico encontramos una relación entre la concentración de arsénico y la presencia, mediante la técnica del número más probable, de bacterias reductoras de arsénico muy abundantes a mayores concentraciones y ausentes a bajas concentraciones. La presencia del gen arrA se detectó a lo largo de todo el gradiente. En cambio, el gen arsC sólo fue encontrado en muestras con bajas concentraciones de arsénico. Estos datos indican la presencia en estos sistemas de bacterias relacionadas con la reducción del arsénico sugiriendo un papel importante en su movilización a fuentes de aguas naturales.Finalmente, los estudios de cultivos de enriquecimientos y aislamiento de cepas procedentes del Salar de Ascotán, nos permitió disponer de una nueva cepa del genéro Shewanella capaz de reducir As y sulfato en forma anaeróbica, una peculiaridad que la diferencia de otras Shewanella spp. aisladas previamente de ambientes contaminados con arsénico. Además, estos estudios nos ayudaron a comprender mejor el ciclo biogeoquímico del arsénico a nivel geológico, ya que se demostró que la presencia y actividad de bacterias reductores de arsenato está ligada a la formación de minerales sulfurados de arsénico a gran escala, confirmando el origen biológico de estos minerales. / Presence of arsenic in drinking and irrigation waters is a serious concern of great economic, social, and environmental importance in numerous locations across South America (mainly in the Northern Chile and Argentina). As respiring microorganisms that reduce As(V) to As(III) are diverse and can be involved in the As mobilization from the sediment to drinking water sources. The present PhD thesis explores the links between the microbial metabolism and the biogeochemical cycling of As in saline systems of Northern Chile. On the one hand, the microbial diversity and the distribution and diversity of arsenic functional genes (i.e., arsenate reductases arrA and arsC) were studied in saline environments with high (e.g., Salar de Ascotán) and low (e.g., Laguna Tebenquiche) As concentrations. On the other hand, characterization of microbial enrichments and bacterial pure cultures were carried out to link bacterial activity and the origin of arsenic minerals in the environment. The 16S rRNA gene clone libraries showed consistent differences in bacterial community composition in saline environments with high and low concentrations of As. As functional genes were amplified with specific primers previously described in the literature and methodological improvements were conducted in this work to optimize the amplification in hypersaline, As-rich natural samples. The gen arrA is present in anaerobic microorganims that respire As (V) to As (III). The gen arsC, in turn, is used for detoxification trough membrane pumps. Most of the sequences found formed new clusters distantly related to previously known sequences obtained from environments with presence of As, within the Firmicutes. Both 16S rDNA and arsenic functional genes showed Firmicutes and Gammaproteobacteria as the predominant bacterial groups in water and sediment samples of Salar de Ascotán.Along a set of natural samples with increasing arsenic concentrations we found a positive relationship between arsenic concentration and abundance of arsenic reducing bacteria determined by MPN. The gen arrA was detected throughout the gradient. Conversely, the gen arsC was only found in the samples with the lowest arsenic concentrations. These data showed a widespread occurrence of bacteria related to the arsenic cycling, suggesting a key role of arsenic reducing bacteria in the arsenic mobilization to the aqueous phase.Finally, through classical microbiology studies we obtained a new strain of Shewanella from sediments of Ascotán that reduced both As and sulfate under anaerobic conditions, a specific trait not previously reported in other Shewanella spp isolated from environments contaminated with arsenic. In addition, these studies gave further clues for a better comprehension of the arsenic cycle at the geological level. We showed that the presence and activity of arsenic reducing bacteria was linked to the formation of sulfurous arsenic minerals at a large scale, giving further evidence for the biological origin of the wide arsenic mineral layers found in Salar de Ascotán.

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Four glycoproteins (gD, gB, gH, and gL) are required for herpes simplex virus (HSV) entry into the cell and for cell-cell fusion in transfected cells. gD serves as the receptor-binding glycoprotein and as the trigger of fusion; the other three glycoproteins execute fusion between the viral envelope and the plasma or endocytic membranes. Little is known on the interaction of gD with gB, gH, and gL. Here, the interactions between herpes simplex virus gD and its nectin1 receptor or between gD, gB, and gH were analyzed by complementation of the N and C portions of split enhanced green fluorescent protein (EGFP) fused to the glycoproteins. Split EGFP complementation was detected between proteins designated gDN + gHC, gDN + gBC, and gHN + gBC + wtgD, both in cells transfected with two or tree glycoproteins and in cells transfected with the four glycoproteins, commited to form syncytia. The in situ assay provides evidence that gD interacts with gH and gB independently one of the other. We further document the interaction between gH and gB. To elucidate which portions of the glycoproteins interact with each other we generated mutants of gD and gB. gD triggers fusion through a specialised domain, named pro-fusion domain (PFD), located C-terminally in the ectodomain. Here, we show that PFD is made of subdomains 1 and 2 (amino acids 260–285 and 285–310) and that each one partially contributed to herpes simplex virus infectivity. Chimeric gB molecules composed of HSV and human herpesvirus 8 (HHV8) sequences failed to reach the cell surface and to complement a gB defective virus. By means of pull down experiments we analyzed the interactions of HSV-HHV8 gB chimeras with gH or gD fused to the strep-tag. The gB sequence between aa residues 219-360 was identified as putative region of interaction with gH or critical to the interaction.

Herpes simplex virus 1 (HSV-1) infects oral epitelial cells, then spreads to the nerve endings and estabilishes latency in sensory ganglia, from where it may, or may not reactivate. Diseases caused by virus reactivation include mild diseases such as muco-cutaneous lesions, and more severe, and even life-threatening encephalitis, or systemic infections affecting diverse organs. Herpes simplex virus represents the most comprehensive example of virus receptor interaction in Herpesviridae family, and the prototype virus encoding multipartite entry genes. In fact, it encodes 11-12 glycoproteins and a number of additional membrane proteins: five of these proteins play key roles in virus entry into subsceptible cells. Thus, glycoprotein B (gB) and glycoprotein C (gC) interact with heparan sulfate proteoglycan to enable initial attachment to cell surfaces. In the next step, in the entry cascade, gD binds a specific surface receptor such as nectin1 or HVEM. The interaction of glycoprotein D with the receptor alters the conformation of gD to enable the activation of gB, glycoprotein H, and glycoprotein L, a trio of glycoproteins that execute the fusion of the viral envelope with the plasma membrane. In this thesis, I described two distinct projects: I. The retargeting of viral tropism for the design of oncolytic Herpesviruses: • capable of infecting cells through the human epitelial growth factor receptor 2 (HER2), overexpressed in highly malignant mammary and ovarian tumors and correlates with a poor prognosis; • detargeted from its natural receptors, HVEM and nectin1. To this end, we inserted a ligand to HER2 in gD. Because HER2 has no natural ligand, the selected ligand was a single chain antibody (scFv) derived from MAb4D5 (monoclonal antibody to HER2), herein designated scHER2. All recombinant viruses were targeted to HER2 receptor, but only two viruses (R-LM113 and R-LM249) were completely detargeted from HVEM and nectin1. To engineer R-LM113, we removed a large portion at the N-terminus of gD (from aa 6 to aa 38) and inserted scHER2 sequence plus 9-aa serine-glycine flexible linker at position 39. On the other hand, to engineer R-LM249, we replaced the Ig-folded core of gD (from aa 61 to aa 218) with scHER2 flanked by Ser-Gly linkers. In summary, these results provide evidence that: i. gD can tolerate an insert almost as big as gD itself; ii. the Ig-like domain of gD can be removed; iii. the large portion at the N-terminus of gD (from aa 6 to aa 38) can be removed without loss of key function; iv. R-LM113 and R-LM249 recombinants are ready to be assayed in animal models of mammary and ovary tumour. This finding and the avaibility of a large number of scFv greatly increase the collection of potential receptors to which HSV can be redirected. II. The production and purification of recombinant truncated form of the heterodimer gHgL. We cloned a stable insect cell line expressing a soluble form of gH in complex with gL under the control of a metalloprotein inducible promoter and purified the heterodimer by means of ONE-STrEP-tag system by IBA. With respect to biological function, the purified heterodimer is capable: • of reacting to antibodies that recognize conformation dependent epitopes and neutralize virion infectivity; • of binding a variety cells at cell surface. No doubt, the availability of biological active purified gHgL heterodimer, in sufficient quantities, will speed up the efforts to solve its crystal structure and makes it feasible to identify more clearly whether gHgL has a cellular partner, and what is the role of this interaction on virus entry.

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The first part of the research project of the Co-Advisorship Ph.D Thesis was aimed to select the best Bifidobacterium longum strains suitable to set the basis of our study. We were looking for strains with the abilities to colonize the intestinal mucosa and with good adhesion capacities, so that we can test these strains to investigate their ability to induce apoptosis in “damaged” intestinal cells. Adhesion and apoptosis are the two process that we want to study to better understand the role of an adhesion protein that we have previously identified and that have top scores homologies with the recent serpin encoding gene identified in B. longum by Nestlè researchers. Bifidobacterium longum is a probiotic, known for its beneficial effects to the human gut and even for its immunomodulatory and antitumor activities. Recently, many studies have stressed out the intimate relation between probiotic bacteria and the GIT mucosa and their influence on human cellular homeostasis. We focused on the apoptotic deletion of cancer cells induced by B. longum. This has been valued in vitro, performing the incubation of three B.longum strains with enterocyte-like Caco- 2 cells, to evidence DNA fragmentation, a cornerstone of apoptosis. The three strains tested were defined for their adhesion properties using adhesion and autoaggregation assays. These features are considered necessary to select a probiotic strain. The three strains named B12, B18 and B2990 resulted respectively: “strong adherent”, “adherent” and “non adherent”. Then, bacteria were incubated with Caco-2 cells to investigate apoptotic deletion. Cocultures of Caco-2 cells with B. longum resulted positive in DNA fragmentation test, only when adherent strains were used (B12 and B18). These results indicate that the interaction with adherent B. longum can induce apoptotic deletion of Caco-2 cells, suggesting a role in cellular homeostasis of the gastrointestinal tract and in restoring the ecology of damaged colon tissues. These results were used to keep on researching and the strains tested were used as recipient of recombinant techniques aimed to originate new B.longum strains with enhanced capacity of apoptotic induction in “damaged” intestinal cells. To achieve this new goal it was decided to clone the serpin encoding gene of B. longum, so that we can understand its role in adhesion and apoptosis induction. Bifidobacterium longum has immunostimulant activity that in vitro can lead to apoptotic response of Caco-2 cell line. It secretes a hypothetical eukaryotic type serpin protein, which could be involved in this kind of deletion of damaged cells. We had previously characterised a protein that has homologies with the hypothetical serpin of B. longum (DD087853). In order to create Bifidobacterium serpin transformants, a B. longum cosmid library was screened with a PCR protocol using specific primers for serpin gene. After fragment extraction, the insert named S1 was sub-cloned into pRM2, an Escherichia coli - Bifidobacterium shuttle vector, to construct pRM3. Several protocols for B. longum transformation were performed and the best efficiency was obtained using MRS medium and raffinose. Finally bacterial cell supernatants were tested in a dotblot assay to detect antigens presence against anti-antitrypsin polyclonal antibody. The best signal was produced by one starin that has been renamed B. longum BLKS 7. Our research study was aimed to generate transformants able to over express serpin encoding gene, so that we can have the tools for a further study on bacterial apoptotic induction of Caco-2 cell line. After that we have originated new trasformants the next step to do was to test transformants abilities when exposed to an intestinal cell model. In fact, this part of the project was achieved in the Department of Biochemistry of the Medical Faculty of the University of Maribor, guest of the abroad supervisor of the Co-Advisorship Doctoral Thesis: Prof. Avrelija Cencic. In this study we examined the probiotic ability of some bacterial strains using intestinal cells from a 6 years old pig. The use of intestinal mammalian cells is essential to study this symbiosis and a functional cell model mimics a polarised epithelium in which enterocytes are separated by tight junctions. In this list of strains we have included the Bifidobacterium longum BKS7 transformant strain that we have previously originated; in order to compare its abilities. B. longum B12 wild type and B. longum BKS7 transformant and eight Lactobacillus strains of different sources were co-cultured with porcine small intestine epithelial cells (PSI C1) and porcine blood monocytes (PoM2) in Transwell filter inserts. The strains, including Lb. gasseri, Lb. fermentum, Lb. reuterii, Lb. plantarum and unidentified Lactobacillus from kenyan maasai milk and tanzanian coffee, were assayed for activation of cell lines, measuring nitric oxide by Griess reaction, H202 by tetramethylbenzidine reaction and O2 - by cytochrome C reduction. Cytotoxic effect by crystal violet staining and induction on metabolic activity by MTT cell proliferation assay were tested too. Transepithelial electrical resistance (TER) of polarised PSI C1 was measured during 48 hours co-culture. TER, used to observe epithelium permeability, decrease during pathogenesis and tissue becomes permeable to ion passive flow lowering epithelial barrier function. Probiotics can prevent or restore increased permeability. Lastly, dot-blot was achieved against Interleukin-6 of treated cells supernatants. The metabolic activity of PoM2 and PSI C1 increased slightly after co-culture not affecting mitochondrial functions. No strain was cytotoxic over PSI C1 and PoM2 and no cell activation was observed, as measured by the release of NO2, H202 and O2 - by PoM2 and PSI C1. During coculture TER of polarised PSI C1 was two-fold higher comparing with constant TER (~3000 ) of untreated cells. TER raise generated by bacteria maintains a low permeability of the epithelium. During treatment Interleukin-6 was detected in cell supernatants at several time points, confirming immunostimulant activity. All results were obtained using Lactobacillus paracasei Shirota e Carnobacterium divergens as controls. In conclusion we can state that both the list of putative probiotic bacteria and our new transformant strain of B. longum are not harmful when exposed to intestinal cells and could be selected as probiotics, because can strengthen epithelial barrier function and stimulate nonspecific immunity of intestinal cells on a pig cell model. Indeed, we have found out that none of the strains tested that have good adhesion abilities presents citotoxicity to the intestinal cells and that non of the strains tested can induce cell lines to produce high level of ROS, neither NO2. Moreover we have assayed even the capacity of producing certain citokynes that are correlated with immune response. The detection of Interleukin-6 was assayed in all our samples, including B.longum transformant BKS 7 strain, this result indicates that these bacteria can induce a non specific immune response in the intestinal cells. In fact, when we assayed the presence of Interferon-gamma in cells supernatant after bacterial exposure, we have no positive signals, that means that there is no activation of a specific immune response, thus confirming that these bacteria are not recognize as pathogen by the intestinal cells and are certainly not harmful for intestinal cells. The most important result is the measure of Trans Epithelial Electric Resistance that have shown how the intestinal barrier function get strengthen when cells are exposed to bacteria, due to a reduction of the epithelium permeability. We have now a new strain of B. longum that will be used for further studies above the mechanism of apoptotic induction to “damaged cells” and above the process of “restoring ecology”. This strain will be the basis to originate new transformant strains for Serpin encoding gene that must have better performance and shall be used one day even in clinical cases as in “gene therapy” for cancer treatment and prevention.