Protein molecules and their interactions via protein-protein interactions (PPIs) are at the core of cellular functions. While such global PPI networks have been useful for analyzing gene function and effects of genetic variants, they do not resolve tissue and cell-typespecific interactions. Here we leverage recent advances in single-cell RNA sequencing (scRNA-seq) to reconstruct cell-type-specific PPI networks across different tissues to enable a context-sensitive analysis of immune cells’ gene-protein pathways. Targeting B cells, T cells, and macrophage cells as a proof-of-principle, we used scRNA-seq data across different tissues from the Tabula Muris mouse consortium. We mapped the protein-coding DEGs to a protein-protein interaction network database (STRING v.11). Topological and global similarity analysis of the networks revealed distinct properties between tissues highlighting tissue-specific behaviors for each cell type. For example, we found that degree and clustering coefficients distributions were tissue-specific. Different cell types and tissues displayed specific characteristics, and in particular, the splenic PPI networks were different compared to other analyzed tissues for all the immune cell types examined. For example, the pairwise comparison of the Jaccard index for node similarity and the mantel test correlation analysis showed that the spleen’ node and PPI networks are more different than any other tissues for each cell type examined. The physiological and anatomical properties that distinguish the spleen from other examined tissues might explain why the splenic PPI networks tend to be less similar compared to other tissues. The cell-type-specific network analyses using the different distance measures between the adjacency matrices on the hub nodes such as Euclidean, Manhattan, Jaccard, and Hamming distances showed a macrophage-specific behavior not observed in B cells and T cells, confirming their lineage differences. Finally, we explored the rewiring of selected hub nodes and transcription factors in the PPI networks along with their biological enrichments to validate our observations. The suggested biological validity of our results confirms the relevance of data-driven reconstruction of these context-sensitive networks using more advanced network inference algorithms. In conclusion, scRNA-seq enables the reconstruction of global unspecific PPI networks into cell and tissue-specific networks, thereby providing an increased resolution of the biological context.

In this thesis, a novel single molecule technique will be presented that will, for the first time, give direct access to the interaction energy landscapes of small molecules. The technique relies on the interpretation of thermal position fluctuations of a colloidal probe particle tethered to the molecular complex of interest and a geometrical amplification effect that converts Ångstrom scale fluctuations of the ligand in the binding pocket of the receptor to tens of nanometer fluctuation of the bead. The position of the bead is measured with 0.5 MHz bandwidth and 2 nm spatial resolution. The surface characteristic of the substrate was found to be critical for this new technique and various surface effects were observed. Methods were developed to block nonspecific interaction between the surfaces. The mobility of specifically bound particles was found to depend strongly on the density of specific bonds and the length of the molecular complex; low concentration and short linker lead to slow ligand-receptor mediated surface diffusion, high concentration and/or long linkers to an immobilization of the particle. Transient bond formation was observed for the intermediate range. Details of the interaction energy landscape were not resolved. However, a systematic change in the linker length from 22 Å to 29 Å led to a corresponding change in the lateral position fluctuations from 12.9 nm to 13.2 nm in excellent agreement with our theoretical calculations, confirming the geometrical amplification effect. Also, a new phenomenon of nanometer scale friction in the gap between the bead and the surface was discovered. In summary, the results underline that the novel technique might be able to measure details of the interaction energy landscape of a specific ligand-receptor bond and thus test theoretical predictions for its shape. / text

Les dendrimères sont des entités chimiques "arborescentes" multi-ramifiées. Cette famille de polymères non linéaires comporte des applications dans différents domaines. Un dendrimère nommé ABP a montré des propriétés immuno-modulatrices sur le système immunitaire humain in vitro. Ce dendrimère comporte le profil d'un nouvel agent thérapeutique pour être utilisé dans le traitement de maladies inflammatoires chez l'homme. Parmi les cellules mononucléaires du sang humain, le dendrimère ABP cible principalement les monocytes et induit une activation anti-inflammatoire de ces cellules. Cette nouvelle étude a visé à comprendre l'interaction entre le dendrimère ABP et les monocytes humains. De manière intéressante, une interaction spécifique a été observée. En utilisant des expériences de modélisation, de physico-chimie et de biologie moléculaire, nous démontrons que le dendrimère ABP induit une activation anti-inflammatoire des monocytes humains par l'intermédiaire d'un ou de récepteur (s). / Dendrimers are multi-branched "tree-like" chemical entities. This family of non-linear polymers has already been applied in different fields. A dendrimer named ABP has shown some immuno-modulatory properties toward the Human immune system in vitro. This dendrimer is at the dawn to become a new therapeutic agent by itself for the treatment of inflammatory diseases in Human. Among human Peripheral Blood Mononuclear Cells (PBMC), the ABP dendrimer selectively targets human monocytes and induces an anti-inflammatory activation of these cells. This new study aims at understanding the interaction between the ABP dendrimer and human monocytes. Interestingly, a specific interaction was observed. Using, biological, physico-chemical and molecular modelling experiments we demonstrated that the ABP dendrimer triggers monocyte activation through receptor(s) recognition.

Os bandos mistos de aves são agregações sociais complexas estáveis durante o tempo e espaço. Até hoje, a estrutura social dessas espécies foi descrita a partir de estudos subjetivos de campo ou a partir de compilações do número e intensidade das interações a nível de todo o grupo, sem considerar as interações par-a-par individualmente. Nossos objetivos foram buscar evidências de associações não-randômicas entre pares de espécies de aves, delimitar os grupos a partir das espécies com as associações mais fortes e verificar se há diferenças na estrutura social entre os habitat de floresta primária e secundária. Utilizamos dados de ocorrência das espécies coletados a partir de redes de neblina e gravação de vocalizações para identificar pares de espécies que foram co-detectadas mais frequentemente do que o esperado a partir do modelo nulo e compararamos a força dessa interação entre as florestas tropicais primária e secundária Amazônicas. Nós também utilizamos as associações par-a-par para construir as redes de interação social e suas mudanças entre os tipos de habitat. Nós encontramos muitas interações positivas fortes entre as espécies, mas nenhuma evidência de repulsão. As análises das redes de interação revelaram vários grupos de espécies que corroboram com grupos ecológios descritos na literatura. Além disso, tanto a estrutura da rede de interação como a força da interação se alteraram drasticamente com a perturbação do habitat, com formação de algumas associações novas, mas uma tendência geral para quebra de associações entre as espécies. Nossos resultados mostram que as interações sociais entre essas aves podem ser fortemente afetados pela degradação do habitat, sugerindo que a estabilidade das interações desenvolvida entre espécies é ameaçada pelos distúrbios causados pelo homem. / Inter-specific associations of birds are complex social phenomena, frequently detected and often stable over time and space. So far, the social structure of these associations has been largely deduced from subjective assessments in the field or by counting the number of inter-specific encounters at the whole-group level, without considering changes to individual pairwise interactions. Here, we look for evidence of non-random association between pairs of bird species, delimit groups of more strongly associated species and examine differences in social structure between old growth and secondary forest habitat. We used records of bird species detection from mist-netting capture and from acoustic recordings to identify pairwise associations that were detected more frequently than expected under a null distribution, and compared the strength of these associations between old-growth and secondary forest Amazonian tropical forest. We also used the pairwise strength associations to visualize the social network structure and its changes between habitat types. We found many strongly positive interactions between species, but no evidence of repulsion. Network analyses revealed several modules of species that broadly agree with the subjective groupings described in the ornithological literature. Furthermore, both network structure and association strength changed drastically with habitat disturbance, with the formation of a few new associations but a general trend towards the breaking of associations between species. Our results show that social grouping in birds is real and may be strongly affected by habitat degradation, suggesting that the stability of the associations is threatened by anthropogenic disturbance.

Os bandos mistos de aves são agregações sociais complexas estáveis durante o tempo e espaço. Até hoje, a estrutura social dessas espécies foi descrita a partir de estudos subjetivos de campo ou a partir de compilações do número e intensidade das interações a nível de todo o grupo, sem considerar as interações par-a-par individualmente. Nossos objetivos foram buscar evidências de associações não-randômicas entre pares de espécies de aves, delimitar os grupos a partir das espécies com as associações mais fortes e verificar se há diferenças na estrutura social entre os habitat de floresta primária e secundária. Utilizamos dados de ocorrência das espécies coletados a partir de redes de neblina e gravação de vocalizações para identificar pares de espécies que foram co-detectadas mais frequentemente do que o esperado a partir do modelo nulo e compararamos a força dessa interação entre as florestas tropicais primária e secundária Amazônicas. Nós também utilizamos as associações par-a-par para construir as redes de interação social e suas mudanças entre os tipos de habitat. Nós encontramos muitas interações positivas fortes entre as espécies, mas nenhuma evidência de repulsão. As análises das redes de interação revelaram vários grupos de espécies que corroboram com grupos ecológios descritos na literatura. Além disso, tanto a estrutura da rede de interação como a força da interação se alteraram drasticamente com a perturbação do habitat, com formação de algumas associações novas, mas uma tendência geral para quebra de associações entre as espécies. Nossos resultados mostram que as interações sociais entre essas aves podem ser fortemente afetados pela degradação do habitat, sugerindo que a estabilidade das interações desenvolvida entre espécies é ameaçada pelos distúrbios causados pelo homem. / Inter-specific associations of birds are complex social phenomena, frequently detected and often stable over time and space. So far, the social structure of these associations has been largely deduced from subjective assessments in the field or by counting the number of inter-specific encounters at the whole-group level, without considering changes to individual pairwise interactions. Here, we look for evidence of non-random association between pairs of bird species, delimit groups of more strongly associated species and examine differences in social structure between old growth and secondary forest habitat. We used records of bird species detection from mist-netting capture and from acoustic recordings to identify pairwise associations that were detected more frequently than expected under a null distribution, and compared the strength of these associations between old-growth and secondary forest Amazonian tropical forest. We also used the pairwise strength associations to visualize the social network structure and its changes between habitat types. We found many strongly positive interactions between species, but no evidence of repulsion. Network analyses revealed several modules of species that broadly agree with the subjective groupings described in the ornithological literature. Furthermore, both network structure and association strength changed drastically with habitat disturbance, with the formation of a few new associations but a general trend towards the breaking of associations between species. Our results show that social grouping in birds is real and may be strongly affected by habitat degradation, suggesting that the stability of the associations is threatened by anthropogenic disturbance.

Os bandos mistos de aves são agregações sociais complexas estáveis durante o tempo e espaço. Até hoje, a estrutura social dessas espécies foi descrita a partir de estudos subjetivos de campo ou a partir de compilações do número e intensidade das interações a nível de todo o grupo, sem considerar as interações par-a-par individualmente. Nossos objetivos foram buscar evidências de associações não-randômicas entre pares de espécies de aves, delimitar os grupos a partir das espécies com as associações mais fortes e verificar se há diferenças na estrutura social entre os habitat de floresta primária e secundária. Utilizamos dados de ocorrência das espécies coletados a partir de redes de neblina e gravação de vocalizações para identificar pares de espécies que foram co-detectadas mais frequentemente do que o esperado a partir do modelo nulo e compararamos a força dessa interação entre as florestas tropicais primária e secundária Amazônicas. Nós também utilizamos as associações par-a-par para construir as redes de interação social e suas mudanças entre os tipos de habitat. Nós encontramos muitas interações positivas fortes entre as espécies, mas nenhuma evidência de repulsão. As análises das redes de interação revelaram vários grupos de espécies que corroboram com grupos ecológios descritos na literatura. Além disso, tanto a estrutura da rede de interação como a força da interação se alteraram drasticamente com a perturbação do habitat, com formação de algumas associações novas, mas uma tendência geral para quebra de associações entre as espécies. Nossos resultados mostram que as interações sociais entre essas aves podem ser fortemente afetados pela degradação do habitat, sugerindo que a estabilidade das interações desenvolvida entre espécies é ameaçada pelos distúrbios causados pelo homem. / Inter-specific associations of birds are complex social phenomena, frequently detected and often stable over time and space. So far, the social structure of these associations has been largely deduced from subjective assessments in the field or by counting the number of inter-specific encounters at the whole-group level, without considering changes to individual pairwise interactions. Here, we look for evidence of non-random association between pairs of bird species, delimit groups of more strongly associated species and examine differences in social structure between old growth and secondary forest habitat. We used records of bird species detection from mist-netting capture and from acoustic recordings to identify pairwise associations that were detected more frequently than expected under a null distribution, and compared the strength of these associations between old-growth and secondary forest Amazonian tropical forest. We also used the pairwise strength associations to visualize the social network structure and its changes between habitat types. We found many strongly positive interactions between species, but no evidence of repulsion. Network analyses revealed several modules of species that broadly agree with the subjective groupings described in the ornithological literature. Furthermore, both network structure and association strength changed drastically with habitat disturbance, with the formation of a few new associations but a general trend towards the breaking of associations between species. Our results show that social grouping in birds is real and may be strongly affected by habitat degradation, suggesting that the stability of the associations is threatened by anthropogenic disturbance.

abstract: Protein-surface interactions, no matter structured or unstructured, are important in both biological and man-made systems. Unstructured interactions are more difficult to study with conventional techniques due to the lack of a specific binding structure. In this dissertation, a novel approach is employed to study the unstructured interactions between proteins and heterogonous surfaces, by looking at a large number of different binding partners at surfaces and using the binding information to understand the chemistry of binding. In this regard, surface-bound peptide arrays are used as a model for the study. Specifically, in Chapter 2, the effects of charge, hydrophobicity and length of surface-bound peptides on binding affinity for specific globular proteins (&beta-galactosidase and &alpha1-antitrypsin) and relative binding of different proteins were examined with LC Sciences peptide array platform. While the general charge and hydrophobicity of the peptides are certainly important, more surprising is that &beta-galactosidase affinity for the surface does not simply increase with the length of the peptide. Another interesting observation that leads to the next part of the study is that even very short surface-bound peptides can have both strong and selective interactions with proteins. Hence, in Chapter 3, selected tetrapeptide sequences with known binding characteristics to &beta-galactosidase are used as building blocks to create longer sequences to see if the binding function can be added together. The conclusion is that while adding two component sequences together can either greatly increase or decrease overall binding and specificity, the contribution to the binding affinity and specificity of the individual binding components is strongly dependent on their position in the peptide. Finally, in Chapter 4, another array platform is utilized to overcome the limitations associated with LC Sciences. It is found that effects of peptide sequence properties on IgG binding with HealthTell array are quiet similar to what was observed with &beta-galactosidase on LC Science array surface. In summary, the approach presented in this dissertation can provide binding information for both structured and unstructured interactions taking place at complex surfaces and has the potential to help develop surfaces covered with specific short peptide sequences with relatively specific protein interaction profiles. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2014

The phase behavior of CO2 + polymer systems is of interest in polymer synthesis, flue and natural gas processing, polymer foam and nanoparticle processing, and drug delivery. Theoretical and experimental evidence suggests that CO2 is able to interact with electron donating functional groups in polymers to form weak Lewis acid – base or EDA (Electron Donor Acceptor) complexes. These complexes can have a significant effect on the phase behavior of associated CO2 + polymer systems. In spite of this, however, the phase equilibria of only a few associated CO2 + polymer systems have been measured. Some success in modeling the phase behavior of polymer solutions has been achieved by various versions of the Statistical Association Fluid Theory (SAFT), as well as by several Lattice Models. However, many of these models incorporate two to four adjustable parameters that often depend on temperature (T), pressure (P), and/or molecular weight (MW). As a result, a large amount of experimental data is required to apply these models. The goal of the present work was therefore to develop a new thermodynamic model for associating systems that would include no more than two temperature-independent adjustable parameters. The new model presented in this work is based on the Guggenheim-Huggins-Miller lattice and includes complex formation in the development of the partition function. The EOS obtained from the resulting partition function includes two mixture parameters – the enthalpy of association or complex formation and a reference value of the equilibrium constant for complex formation . Most importantly, can be obtained from in situ Attenuated Total Reflection Fourier Transform Infrared (ATR – FTIR) measurements. This work therefore demonstrates the use of ATR – FTIR spectra to obtain molecular level information regarding the interaction of CO2 and electron donating functional groups in polymers. Unlike other studies, this work uses the bending vibration of CO2 to estimate the enthalpies of association ( ) of CO2 + polymer systems. Values of were directly incorporated in the new model and were found to lie between -7 and -12 kJ/mol for the systems investigated in this work. They increased (i.e. became more negative) in the order: CO2 + PS-co-PMMA < CO2 + PMMA <CO2 + PBMA < CO2 + PSF < CO2 + PVAc < CO2 + EVA40 < CO2 + PEG. Values of the second parameter in the new EOS ( ) were obtained by fitting solubility data at one temperature. Both and were found to be temperature independent. The application of the new EOS was demonstrated by calculating the solubility (sorption) of CO2 in polymers, the extent of swelling of polymers due to CO2, and the solubility of polymers in CO2 (cloud points). Both sorption and cloud point behavior in CO2 + polymer systems could be calculated using a single value of for each binary system. Ionic Liquids (ILs) can also incorporate electron donating functional groups in their structure. Evidence for the interaction of such ILs with CO2 can be found in the large values of the enthalpies of absorption of CO2 in these ILs. The ALF EOS was therefore extended to CO2 + IL systems using the enthalpy of absorption as a measure of association ( ) in these systems. was again treated as an adjustable parameter in the calculation of the CO2 solubility in ILs. A single value of was sufficient to predict swelling in these systems within experimental error.

Tigers (Panthera tigris Linnaeus, 1758) are in danger of extinction. Their populations have declined from ~100,000 to only ~3,000 individuals in a century and their habitat has shrunk to less than 7% of the historic range. Of the five extant tiger subspecies, the Sumatran tiger (Panthera tigris sumatrae Pocock, 1929) is the most seriously threatened. Currently determined as Critically Endangered under IUCN criteria, the Sumatran tiger is likely to become extinct unless effective conservation measures are enacted. Threats to the tiger include habitat destruction, killing due to conflict with humans and livestock, and poaching for illegal wildlife trade. Long-term survival of Sumatran tigers depends largely on the effectiveness of current conservation efforts in every tiger landscape. Successful conservation and management require accurate information on ecology of the species upon which decisions can be based. This study investigated basic ecological aspects of tigers and developed strategies for management and restoration to improve tiger viability in the Central Sumatra landscape. This landscape is comprised of natural forests and plantations managed for timber and agricultural commodities. The first chapter assesses the variation in tiger abundance across forest types in Southern Riau, and over time in Tesso Nilo National Park, all in Central Sumatra. Using camera traps, my team and I systematically sampled five blocks representing three major forest types in the region: peat land, flat lowland, and hilly lowland. I found that tiger abundance varied by forest type and through time. Excluding two sampling blocks where no tigers were photographed, the lowest tiger density was in peat land forest of Kerumutan, and the highest density was in the flat lowland forest of Tesso Nilo. Repeated sampling in the newly established Tesso Nilo National Park documented a trend of increasing tiger density (SE) from 0.90 (0.38) individuals/100 km2 in 2005 to 1.70 (0.66) individuals/100 km2 in 2008. Overall, tiger densities from this study were lower than most previous estimates from other parts of Sumatra. The trend of increasing tiger density in Tesso Nilo, however, suggests that the tiger population could be augmented by protection of habitats that were previously logged and severely disturbed. The second chapter examines the occupancy and habitat-use of the tiger across the major landcover types (natural forest, acacia plantation, oilpalm plantation, rubber plantation, and mixed agriculture). I found that tigers used some plantation areas, although they significantly preferred forests over plantations. In all landcover types, sites with tiger detections had thicker understory cover than sites without tiger detection. Modeling tiger occupancy while recognizing that probability of detection is not always perfect, I found that tiger occupancy covaried positively and significantly with altitude and negatively, but not significantly, with distance-to-forest-cores. Probability of habitat use by tigers covaried positively and significantly with understory cover and altitude, and negatively and significantly with human settlement and landcover rank. The results suggested that with adjustments in plantation management, tigers could use or roam through plantations within the habitat mosaic provided that the plantations had adequate understory cover and low level of human activity. They also could use riparian forests (as corridors) and smaller forest patches (as stepping stones) to travel between the main habitat patches across the forest and plantation landscape. The third chapter investigates the ecological characteristics and possible inter-specific interactions among wild felids, including tigers and smaller cats, based on data collected using systematic camera trapping in combination with information on their natural history. I found that despite overlap in resource needs of the five felid species, each appears adapted to specific environmental conditions allowing coexistence with other felids. The five felid species used statistically different elevations, with the golden cat found to inhabit the highest elevation. Two-species occupancy models showed that only leopard cats were found to co-occur with other felid species more frequently than expected by chance under independence. Species of similar size or eating similar-sized prey generally tended to have low coefficients of temporal activity overlap, suggesting avoidance. Temporal avoidance is likely occurring in three pairs of felids, namely clouded leopards and golden cats, clouded leopards and marbled cats, and marbled cats and leopard cats. Based on the differences in morphological and ecological characteristics, and on patterns of spatial and temporal occurrence, I identified six possible mechanisms by which felids in Central Sumatra maintain coexistence. I discussed the implications of this study for management, focusing on how to balance diversity and abundance of felids. The fourth chapter presents the tiger distribution models as a case study to illustrate the importance of accounting for uncertainty in species distribution mapping. I applied four modeling approaches, differing in how the response variable (tiger presence) is constructed and used in the models. I compared the performance and output of different models based on the relative importance of variables, descriptive statistics of the predictions, cross comparison between models using an error matrix, and validation using tiger presence data collected from independent surveys. All models consistently identified forest area within the grid as one of the most important variables explaining tiger probability of occurrence. Three models identified altitude as another important factor. While the four models were consistent in predicting relatively high probability of tiger occurrence for high elevation forest areas such as Rimbang Baling and Bukit Tigapuluh, they generally had a lower level of agreement in predictions for low elevation areas, particularly the peat land in the northeastern part of the study area. Based on the results of cross evaluation of the predictions among models and validation with the independent data, I considered the occupancy model to be superior to the others. If data collection format permits, I advocate the use of occupancy instead of the other modeling techniques to develop predictive species distribution maps. The last chapter constructs a strategy to restore the tiger population across the ecosystem of Central Sumatra through integration of knowledge on tiger ecology from previous chapters with consideration of the ecological conditions of the landscape in the region. The strategy combines existing knowledge of tiger conservation and regional ecosystem restoration. It recognizes the limitations and challenges of traditional nature protection and considers existing and new opportunities. Emerging opportunities and new mechanisms, such as direct and indirect economic incentives for nature conservation and restoration, are taken into account. These, coupled with increased awareness of the stakeholders, better policies and implementation of good governance, and the willingness and know-how to maintain coexistence with wildlife among the local people, are expected to support and accelerate the recovery of tigers and their ecosystem. / Ph. D.