2024 Topic-Specific Grants and Descriptions

Brain circuits are composed by a myriad of interconnected inhibitory and excitatory neuronal cell types, which differ in connectivity, morphology, biophysics, and gene expression. Understanding the functional relevance of each of these circuit elements is fundamental problem in neuroscience. Are there genetically defined neuronal ensembles devoted to specific sensory, motor or cognitive functions? Is the function of each neural type conserved or flexibly repurposed across different brain areas? To what extent the properties of a neuron are plastic, shaped by development and learning, or statically defined by gene expression? 
To address these questions, this project will characterize the function large populations of cortical neurons in vivo, across cortical layers and brain areas, both during spontaneous behaviors (navigation, sleep) or during learning of adaptive visual tasks. To record and perturb the activity, we will leverage large scale two-photon calcium imaging, optogenetics, and targeted photoablation. Then, to classify the cell types, the project will pioneer and establish novel spatial transcriptomic methods to measure gene expression in situ and match it to the neurons recorded in vivo.
To complete this project, we are looking for candidates with an MSc in neuroscience, physics, engineering, or any STEM discipline to build our laboratory. Hands-on training in experimental neuroscience or molecular biology, and/or familiarity with programming (e.g. Python, Matlab), will be highly valued. Successful candidates will join a growing diverse, multidisciplinary and collegial group, will help build our new lab, and will be offered direct training, supervision and mentorship from the principal investigator. Additional training in spatial transcriptomics will be offered by our collaborators at University College London (UK) and INMED (Marseille). 

For more details, please see the lab webpage: https://www.rossilab.iit.it

Selected References:
Rossi, L. F., Harris, K. D. & Carandini, M. Spatial connectivity matches direction
selectivity in visual cortex. Nature, 2020

Bugeon, S., Duffield, J., Dipoppa, M. et al. A transcriptomic axis predicts state modulation of cortical interneurons. Nature, 2022

Rossi, L. F., Wykes, R. C., Kullmann, D. M. & Carandini, M. Focal cortical seizures
start as standing waves and propagate respecting homotopic connectivity. Nat Commun
2017.

Ye Z, Shelton AM, Shaker JR, Boussard J, Colonell J, Birman D, Manavi S, Chen S, Windolf C, Hurwitz C, Namima T, Pedraja F, Weiss S, Raducanu B, Ness TV, Jia X, Mastroberardino G, Rossi LF, Carandini M, Häusser M, Einevoll GT, Laurent G, Sawtell NB, Bair W, Pasupathy A, Lopez CM, Dutta B, Paninski L, Siegle JH, Koch C, Olsen SR, Harris TD, Steinmetz NA. Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings. bioRxiv, 2024

Pachitariu, M. et al. Suite2p beyond 10,000 neurons with standard two-photon
microscopy. biorXiv, 2016.

Carandini, M. et al. Imaging the awake visual cortex with a genetically encoded voltage
indicator. J Neurosci 2015.

Brondi, M., Sato, S. S., Rossi, L. F., Ferrara, S. & Ratto, G. M. Finding a Needle in a
Haystack: Identification of EGFP Tagged Neurons during Calcium Imaging by Means
of Two-Photon Spectral Separation. Front Mol Neurosci, 2012

Rossi, L. F., Kullmann, D. M. & Wykes, R. C. The Enlightened Brain: Novel Imaging
Methods Focus on Epileptic Networks at Multiple Scales. Front Cell Neurosci 2018.
 

To navigate the dynamic world, our brain needs to continuously update its representation of external information and generate predictions of future states. Without such predictions, there would be a substantial time lag between states in the real world and the perception of, and reaction to, these states. A fundamental assumption is that the brain constantly generates and updates internal models of the world. However, the representational nature of internal models at different processing levels, and how the dynamics of internal models temporally relate to (e.g. follow or predict) actual events in the real world, remains unknown. 

The objective of this PhD project is to investigate the representational dynamics in the brain in response to dynamic events using a novel, magnetoencephalography (MEG)-based approach – dynamic representational similarity analysis (dRSA hereafter). The innovation of the approach is to use temporally variable models of representational similarity to characterize representational content at each time point during temporally extended, unfolding events. This allows testing whether a given time point is represented in a lagged bottom-up manner or in a predictive top-down manner, that is, before it actually occurred (for reference to the method, see https://doi.org/10.1101/2022.09.02.506366). 

The successful candidate should have a background in cognitive neuroscience and neuroimaging (preferably M/EEG or fMRI, MVPA/RSA) and strong programming skills (preferably Matlab). For further information, candidates are strongly encouraged to get in contact with Moritz Wurm.

This project tests the hypothesis that cholinergic and noradrenergic activity cooperatively control the intrinsic dynamics of mammalian brain networks. The candidate will use fibre photometry, fMRI and functional ultrasound imaging to causally link neurotransmitter levels to brain networks dynamics in the living mouse brain.

Supervisor: Alessandro Gozzi, IIT

This project will entail the use of information theory methods to infer directed functional connectivity in resting brain networks of the mouse brain. The question we would like to address here, is whether resting brain networks exhibit a default directed information flow, or if instead, during rest, all brain regions reciprocally communicate in a balanced, and non-directional fashion.

Supervisor: Alessandro Gozzi, IIT

Brain network mapping in rodents has so far entailed the use of light anaesthesia to induce immobilization and prevent motion related artefacts. In this project we will leverage the portability and non-invasiveness of functional ultrasound imaging to implement brain network imaging in resting as well as behaviorally-operant mice.

Supervisor: Alessandro Gozzi, IIT

The Laboratory of Autism and Neurodevelopmental Disorders at IIT (IIT-LAND), directed by Dr. Michael Lombardo, at the Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, invites applications for 2 PhD scholarships to investigate early biomarkers behind autism subtypes. Our research aims to understand how autism may be split into distinctive types of autisms, characterized by distinctive phenotypic presentation, underlying neurobiological mechanisms, and differential responses to treatment. To answer these types of questions, we use a combination of approaches from neuroimaging (EEG, MRI), cognitive and computational neuroscience, and data science. Our work is primarily focused on human patients (i.e. autistic children), but we also collaborate with other groups on larger cross-cutting translational work focused on elucidating biological mechanisms in model systems. For more info, see:  https://land.iit.it.

We have 2 PhD positions focused on identifying biomarkers for different clinically and behaviorally distinctive subtypes of autism. The work heavily focuses on methodologies such as eye tracking, EEG, and MRI/fMRI. The datasets we work with are a combination of large publicly available datasets, datasets from international collaborators, as well as data coming from ongoing experiments run within IIT-LAND. The work will heavily rely on new or past stratification models of neural and phenotypically distinctive autism subtypes. The two positions are fully-funded off of an ERC Consolidator Grant to Dr. Michael Lombardo.

We are looking for talented and highly motivated individuals that can build on prior skill sets or knowledge within the core areas of our research - EEG, eye tracking, neuroimaging (MRI, fMRI), data science, and autism. Advanced understanding and conceptual thinking with regards to statistics and big data analysis is a plus, as is requisite computational and programming skills (e.g., R, Python, MATLAB) to implement such ideas. Ability to speak both Italian and English is highly prioritized. Good communication skills and ability to work within larger groups is also emphasized. Strong passion/desire to pursue an academic career focusing on neurodevelopmental disorders like autism is also a key characteristic we are looking for, as is an existing strong grasp of the literature on autism and neurodevelopmental disorders.

Successful candidates will join a growing diverse, multidisciplinary and collegial group, and will be offered direct training, supervision and mentorship from the principal investigator and other senior members of the lab. The work also offers up the possibility of working within a larger international context, as nearly all of the work we do on this topic is done with collaborations from colleagues in Europe and the USA. The position is a four-year scholarship in the international doctoral school in Cognitive and Brain Sciences (CIMEC) at the University of Trento. Candidates will join a diverse cohort of PhD students and receive multi-disciplinary training at the interface of computational, experimental and cognitive neuroscience across humans and animal models.

The IIT-CNCS in Rovereto is actively expanding its infrastructure for systems level neuroscience research. Our center is located in Trentino, a region of Northern Italy nested within the Dolomite mountains, offering easy access to spectacular natural beauty and mountaineering, vibrant culture and exceptional quality of life (https://www.iit.it/it-IT/cncs-unitn/).

Candidates can informally contact Dr Michael Lombardo (michael.lombardo [at] iit.it) to gather more information about the position, the project, the application procedure and the selection process.

Human beings are intricately connected with their surrounding environment, using their senses and physical abilities to perceive stimuli. The intricate relationship between cognitive processes, bodily states and surroundings continues to be a subject of ongoing debate. Grounded Cognition states that our cognitive processes are influenced by the external context in which we find ourselves. In essence, these theories propose that our perception is shaped by the environment. Consequently, exploring the impact of the external environment, comprising natural elements, on our cognition is of significant interest. This question was particularly well-suited to the unique capabilities and scope of terraXcube: performing experiments with subjects (ensuring safety) within simulated environments (extreme but under control). We conducted research on body thermal perception, which refers to our ability to detect changes in temperature. The four small climatic chambers in terraXcube were crucial. These chambers allowed us to obtain groundbreaking results on total body thermal perception, which were published in Scientific Reports (Battistel et al., 2023) and received significant media coverage (Alto Adige, Giornale Trentino, il Dolomiti, RaiNews … ). 

The present proposal aims to extend the obtained results and explore other factors affecting our perception such as humidity, lights and carbon dioxide concentrations. We recognize that these variables should be examined in pairs, such as temperature and lights, to ensure ecological validity in our tests. Ecological validity refers to how closely an experiment resembles real-world situations, and it is important for ensuring the applicability of our findings. To enhance the ecological validity of our tests, we are planning to incorporate virtual or mixed reality into terraXcube. Virtual reality provides a versatile and controlled platform for creating realistic experimental scenarios, overcoming the challenges often encountered in real-world observational studies. 

The candidate will focus on the following aspects:

•    Develop new protocols to study body perceptions related to humidity, lights, carbon dioxide, and their interplay.
•    Conduct extensive experimental campaigns, including cognition tests and EEG measurements.

The proposal not only maximizes the capabilities of our chambers but also it is aligned with a strategic pillar of our center: providing training for various public administrations, including healthcare, firefighters, and alpine rescuers. These training sessions take place in challenging environments where personnel often face difficulties in performing efficiently. The project holds the potential to offer valuable insights for enhancing performance and knowledge transfer during these demanding training scenarios.

The ideal candidate should hold a degree in Psychology or Cognitive Science or Cognitive Neuroscience or related areas and possess prior experience in conducting experimental research with participants. Additionally, a foundational understanding of R, MATLAB, and the Office package is necessary for the proposed research activities.

Supervisors: Massimiliano Zampini, Riccardo Parin

Declarative knowledge, meaning the portion of knowledge that we can consciously access and manipulate, is one of the most enduring mysteries of the human mind. How did it evolve? And what are the mechanisms behind it? One possibility is that the complex neural machinery that mammals evolved to navigate space has been recycled to “navigate” declarative knowledge. Research from single-cell recordings in rodents to brain imaging studies with humans is converging toward the fascinating hypothesis that conscious declarative knowledge is spatially organized, and can be stored, retrieved and manipulated through the same computations used to represent and navigate physical space. 
In the last few years my lab has been testing and developing this hypothesis, relying upon cutting-edge neuroimaging and analysis techniques. We provided evidence that conceptual knowledge is organized within cognitive maps across complementary allocentric and egocentric reference frames; We studied the role of vision in the development of cognitive maps, showing a different neural geometry underlying spatial navigation in Early Blind people; We provided evidence that abstract cognitive maps are navigated through internal attentional movements; among other contributions. 
In this new project, building upon our recent findings, we seek to crack the mental code that supports relational declarative memory, working at the intersection between attention, memory and consciousness studies. We will conduct our investigations using cutting-edge eye-tracking technology, multimodal neuroimaging (fMRI, MEG, iEEG) and deep neural networks. 
See below some of the recent publications from the lab:
Sigismondi, F., Xu, Y., Silvestri, M., & Bottini, R. (2024). Altered grid-like coding in early blind people Nature Communications
Dutriaux, L., Xu, Y., Sartorato, N., Lhuillier, S. & Bottini, R. (2024). Disentangling reference frames in the neural compass Imaging Neuroscience
Viganò, S., Bayramova, R., Doeller, C., & Bottini, R. (2024). Spontaneous eye movements reflect the representational geometries of conceptual spaces PNAS
Viganò, S., Bayramova, R., Doeller, C., & Bottini, R. (2023). Mental search of concepts is supported by egocentric vector representations and restructured grid maps Nature Communications
Giari G., Vignali L., Xu Y. & Bottini R. (2023). MEG frequency tagging reveals a grid-like code during attentional movements Cell Reports
Xu,Y., Vignali, L., Sigismondi, F., Crepaldi, D., Bottini, R., Collignon, O. (2023). Similar object shape representation encoded in the inferolateral occipitotemporal cortex of sighted and early blind people Plos Biology
Bottini, R., Doeller, FC. (2020). Knowledge across reference frames: Cognitive maps and image spaces Trends in Cognitive Sciences

Supervisor: Roberto Bottini

This project aims to investigate the functional architecture of neural circuits supporting appetitive behaviors in the mouse. The student will combine the investigation of ethological goal-driven behaviors in unrestrained mice with more controlled head-fixed paradigms whenever possible. During the project, the student will have the possibility to employ a comprehensive suite of cutting-edge neurotechnological methods for recording and manipulating neural activity during behavior, including super-high-density electrophysiology (e.g., Neuropixels 2.0), two-photon microscopy, one-photon miniscope, fiber photometry, optogenetics, intersectional viral tracing, and automated behavioral measurements (MoSeq).

Supervisor: Giuliano Iurilli

The candidate will be involved in a research program focused on the use of archer fish as animal models to investigate cognitive abilities, with particular reference to cognition of quantity (both discrete, countable, and continuous) and the possibility to learn to associate it with arbitrary symbols. The studies are planned to be mainly behavioural, though development of neurobiological assays is foreseen. Experience in research on cognitive abilities in animals, and especially in fish (ideally in archer fish) would be appreciated.

Supervisor: Giorgio Vallortigara

Honeybees are fundamental for our ecosystem, but they are more and more subjected to multiple environmental stressors such as bacteria, viruses but also temperature, humidity, nutrients availability, and pesticides, all exacerbated by climate change. To improve the welfare of Apis mellifera we need to better understand its neurobiology and to study the interactions with the environments in order to promote a more resilient beekeeping. This project aims at understanding the effect of the environmental stressors identified above on honeybees’ behaviour and cognitive abilities also through the alteration of their microbiota. This research will include behavioural studies (in the laboratory and in the field), electrophysiological measurements and neuroimaging to investigate the immunity, the wellness, the nutrition, and the resistance of Apis mellifera in different environmental scenarios that characterize the climate change we are going through.

Supervisors: Elisa Frasnelli and Albrecht Haase. Corresponding research areas: Animal Cognition, Animal Behaviour, Pollinators, Honeybee, Brain sciences, Neuroimaging, Environmental stress, Microbiota, Climate change

Spatial hearing is critical for orientation in space and navigation. It furthermore helps to selectively direct attention to relevant sound cues in complex acoustic situations. The loss of spatial hearing as a result of deafness not only leads to a reduced quality of life, but also contributes to potential danger in everyday situations. The PhD project is part of the multidisciplinary MSCA Doctoral Network 'CherISH', Cochlear Implants and Spatial Hearing (CORDIS; CherISH website), that combines approaches from medicine, biomedical engineering and psychology to optimally  improve the restoration of hearing after deafness by combining next generation’s cochlear implant (CI) technology with innovative rehabilitation approaches. The PhD project DC7, will examine to what extent and under which neurocognitive principles acting upon sounds and acting to  move sounds in space can change perceptual and meta-cognitive experiences of sound position. In addition, you will study how this active approach to spatial hearing could be exploited when aiming to re-learn or consolidate sound localization skills, especially in cochlear implant users.  The DC (Doctoral Candidate) will be contractually employed for 48 months by University of Trento (36 months paid by the CherISH project, and 12 months paid by the University of Trento) and will be covered under the Italian social security scheme. This research will be carried out as a doctoral candidate within the PhD programme in Cognitive and Brain Sciences. Therefore, in addition to their individual scientific projects, the successful candidate will benefit from further continuing education, which includes a variety of training modules, as well as  courses on transferable skills and active participation in workshops and Conferences. Secondment periods are anticipated.

Supervisor: Francesco Pavani. Corresponding research areas: Attention, Brain sciences, Cochlear implants, Cognitive processes, Deafness, Experimental psychology, Multisensory perception, Neuroplasticity, Neuropsychology, Psychology, Spatial perception, Spatial representation