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The neuroscience of mind-body techniques for pain relief: Chronic pain appears to be associated with a dysregulation in the stress response. Diffrenet mind-body techniques derived from complementary medicine (such as meditation or hypnosis) as well as modern tools such as biofeedback or vagus nerve stimulation could help with the regulation of this response. These techniques have only little been investigated from this mechanistic perspective in patients with chronic pain. Our lab has developped a specific stress induction technique that allows to expand on this line of research, using psychophysical monitoring (HRV, GSR, EEG), questionnaires and biological markers. Furthermore, clinical populations in acute situations of physiological stress (surgery, ICU) will be investigated in parallel with similar perspectives and questions regarding stress resiliance.

Inter-organelle communication, translational research in aging and muscle metabolism: Novel highlights in the role and function of perilipid droplet mitochondria and other tethers

Study of the pathophysiological mechanims promoting protection against heart failure: Investigating the molecular basis of cardiac repair in injured and stressed hearts.

Bioengineering, Stem Cell Biology and Regenerative Medicine: Developing A Novel Stem Cell Bandage For Bone Repair

The role of lipid droplets in the healthy and aging brain 

Glia-neuron communication in the regulation of energy balance: Investigating tanycyte-dependant synaptic plasticity on hypothalamic neurons regulating food intake in mice

Cell-penetrating peptide and homeoprotein uptake mechanisms: The current focus of our laboratory is to characterize the mechanism of CPP cell entry via direct translocation or via endocytosis and how they escape endosomes when they use this later entry route. We also investigate how physiological molecules that naturally bear cell-penetrating sequences, such as homeoproteins, enter cells

Evolution of neural circuit structure and function

Center for Integrative Genomics

Deciphering the genetic and anatomic complexity of hypothalamic circuits: Sexually dimorphic development of hypothalamic feeding-circuits

Light and temperature regulated plant development

Molecular basis of gene regulation specificity: Regulatory elements that activate or silence gene transcription are promiscuous and can act over long genomic distances in animals. We study how chromosome folding in 3D correctly wires regulatory elements to their target promoters.

RNA biology and circadian clocks: Different topics available in the larger context of post-transcriptional / translational regulation of gene expression and circadian timekeeping. Projects can go from in vitro to cellular models and animal work (mice), as well as bioinformatics - depending on interest and qualifications.

Dissecting genetic networks during stem cell development in crops: The aim of this PhD project will be to identify and characterize genes and gene networks that are involved in stem cell control and were selected during crop domestication and breeding.

Systematic analysis of genetic interactions: The deleteriousness of a mutation can depend upon the genetic background. For example, two patients carrying the same disease causal mutation may experience differences in disease severity. By mapping the effects of single and double mutants on a large scale, the student will try to understand when and how such genetic interactions occur.

Sensory processing across conscious and unconscious state in humans (coma, sleep): Encoding of global auditory regularities in unconscious states

Herbette Sonia (**)

Cognitive neurosciences, stroke and brain reorganization: Modulation of brain activation and structure by cognitive training in stroke patients and healthy subjects

Computational Oncology: Cancer Evolution / Cancer cell plasticity / Genome 3D architecture

Ecology of Microbial Systems. WE ask: Can we predict the dynamics of microbial systems if we know how the individual cells interact? We address this question with single-cell experiments and mathematical modeling. 

Reconstructing ancestral eukaryotic genomes by integrating large-scale genomic data: At the interface between biology and computer science, our laboratory seeks to better understand evolutionary and functional relationships between genes, genomes, and species. We have a number of ongoing projects in the lab—the research project will be discussed depending on the skills and interests of the candidates. More information on projects are available here: https://lab.dessimoz.org/research.

Molecular mechanisms of neuronal secretion

Exploring epigenetic and transcriptional plasticity confering resistance in skin cancer: Using high-throughput sequencing techniques (scRNAseq, spatial transcriptomics, RNA-, ATAC- and CHIP-sequencing) and computational modelling, we attempt to identify the transcription factors/epigenetic regulators of non-melanoma skin cancer progression. Our main interest is the study of the epigenetic and transcriptional mechanisms implicated in tumor plasticity and resistance to targeted therapy, with an emphasis on translational validation in both preclinical (mouse genetic models) and clinical (human samples) models.

Social evolution in ants: Evolutionary genomics of social behaviour. Evolution of a supergene controlling social organization in ants. Behavioural and genetic underpinnings of queen number variation in ants

Environmental DNA Conservation genetics and genomics Biodiversity monitoring

Population Genetics & Genomics: Barn owl population genomics

Genomics of social behaviour Division of labour in social insects

Evolution of plant sexual systems and range margins

Evolutionary bioinformatics: Sexual differentiation and evolution of gene expression in fishes

Navigation ecology in the barn owl

Evolution of reproductive and genetic systems

Evolutionary Conservation Biology: Evolutionary consequences of unintended artificial selection in fish

Genetics of Inherited Neuroendocrine Reproductive Disorders

Control of chromosome replication and impact chromosome methylation in bacteria: I propose to study the impact of DNA methylation on the replication and the expression of the Agrobacterium tumefaciens multi-partite genome, combining classical genetics, transcriptomic, biochemitry and single-cell microscopy experiments.

Microbiome research and animal-microbe symbiosis: Metabolic crosstalk between the gut microbiota and the host; Ecology and evolution of the gut microbiota; Wet lab and bioinformatics; Multi-omics analyses

Chromosome organization and segregation by SMC complexes and related proteins: How do Wadjet SMC defense systems recognize and restrict plasmid?

Artificial selection of small bacterial communities

Quantitative signal transduction in single cells: we use budding yeast as a model system to study the dynamics of signal transduction in the conserved MAPK pathways. We develop quantitative fluorescent reporters to monitor cellular activities in single cells. Our objective is to understand how cells respond to extra-cellular signals and switch cellular fate.

Bacterial synthetic biology:  diverse projects in bacterial synthetic biology, including CRISPR-based circuits, optogenetics, circuits  for pattern formation, distributed computing and engineered living materials

Molecular mechanisms underlying antibiotic resistance development in human pathogens

Molecular mechanisms, Brain Circuitries and Social behaviour in Autism Spectrum Disorders: Mechanisms orchestrating synapse formation, plasticity and social behaviours in Autism.

Study of the neural circuits underlying motivated behaviours: Neuronal dynamics for adult-newborn interactions.

Forward- and reverse-genetics of neurodegeneration: Dissecting the survival function of Rop/STXBP1 in the fruitfly

Computational oncoimmunology: We are developing machine learning tools to study and predict TCR-peptide-MHC interactions, including TCRs recognizing specific neo-antigens in cancer.

Vascular and Tumor Biology: 
1. Cross-talk of intestinal stem cells and vessels
2. Organ chemo-injury  and treatment responses in cancer 

Molecular virology and pathogenesis of hepatitis C and E: Investigating the host factors required for hepatitis E virus (HEV) life cycle

Immunobiology

Mitochondria & Energy Metabolism Lab

Fibroblasts of lymphoid organs as novel regulators of adaptive immunity

Mechanisms of autoinflammation: Study the activation of the inflammasome in autoinflammatory diseases

Immunogenetics of infectious diseases: Immunogenetics of infections due to human herpes simplex viruses

Harnessing innate immune training to improve sepsis management.

Decision making processes in the human and the small rodents, thalamocortical interactions, neural networks dynamics

Impact of stress and trauma on mental health in the perinatal period: Childbirth-related posttraumatic stress disorder and other perinatal mental health problems among mothers and co-parents from pregnancy to the first year of parenthood: a comparison between high-risk and community samples

Neuromuscular plasticity in response to exercise and disease: Any topic covering neuromuscular plasticity and involving non-invasive characterization of neural / contractile properties in response to acute / chronic exercise in healthy or clinical populations. The precise topic will be discussed with any potential interested PhD candidate.

Epidemiology, public health: Sleep genetics and variability: do they influence degenerative diseases? Abstract provided upon request

Hall Diana (**)

Alternative genetic markers for forensic analysis and prenatal paternity testing: Identification of miRNAs for forensic body fluid identification.

HIV-host interactions : characterization of candidate cellular factors and their role during HIV life cycle: Investigation of the role of candidate factors on HIV replication identified upon differential methylation and gene expression analysis, i.e. upon epitranscriptomic and transcripomtic charaterization of HIV-infected cells. Development of new single cell tools to assess HIV life cycle, in particular integration. 

Identification and characterization of new factors involved in cell envelope homeostasis in Gram negative bacteria: Cell envelope and cell division factors as new antimicrobial targets in Pseudomonas aeruginosa

Tuberculosis: diagnostic, treatment and antibiotic resistance: Antibiotic resistance and in vitro biomarkers of treatment efficacy towards tuberculosis

A new fully autologous human iPSC-based platform to assess both CNS-specific CD8+ T cells and antibodies: To assess antigenic specificity of CNS-autoreactive antibodies in MS patients

Epigenetics in Brain Cancer: Targeting pathway vulnerabilities induced by epigenetic disturbance in glioblastoma

Infection and human reproduction: Vaginal microbiota: from functional characterization to treatment options

Objectively measured eating behavior and brain responses to food viewing in pregnancy and postpartum: Analysing brain responses in obese and non-obese subjects and in women with gestational diabetes

Exploiting tumor microenvironment factors to enhance engineered T cell therapies for cancer

Antigen discovery for development of personalized cancer immunotherapy

Gene therapy of retinal disease

Uncovering the cell signaling mechanisms during pollen cell expansion: In flowering plants, sexual reproduction depends on the directional, long-distance growth of pollen tubes that deliver sperm cells to the female gametophytes. The polarized and rapid growth of the pollen tube cell depends on the highly dynamic communication and remodeling of its cell-wall. Key genes in controlling this process are RALF signaling peptides that are sensed by two distinct receptor families:  malectin membrane receptor kinases and the cell-wall monitoring leucine-rich repeat (LRR) extensin proteins (LRXs). Recently we have dissected in molecular terms how these RALF signaling peptides, are distinctly perceived by these two protein families, to regulate cell wall integrity and pollen tube growth in plants (Moussu et al, PNAS, 2020). The structure determination and functional studies on these cell-wall motoring systems sets an important pillar in the field and allow us to investigate new avenues to uncover the molecular mechanisms that link the cell-wall integrity process with the cell machinery to orchestrate plant cell expansion and development. 

Machine learning for medical image analysis: Development of AI image reconstruction and segmentation methods for the assessment of brain MRI, with focus on domain adaptation from different magnetic fields (ultra-low, 1.5T, 3T). 

Sensory and multisensory processes in humans across the lifespan

Richiardi Jonas (*)

Machine learning on medical images and -omics data for diagnosis, prognosis, and treatment planning: Deep learning for imaging genetics

Innate and adaptive immune determinants of graft rejection and tolerance after solid organ transplantation: Immune profiling of rejection episodes and outcome after kidney transplantation

Development and implementation of innovative clinical tools in family medicine: Effectiveness and implementation of point-of-care procalcitonin embedded in a multifaceted implementation strategy to reduce antibiotic prescription in Swiss primary care: the ImpPro hybrid trial

New treatments and approaches for the management of peripheral arterial diseases and aortic aneurysm: Role of cars2 in vascular remodeling in peripheral arterial disease