Kavli Blog

Requests for Applications (RFAs) for the NIH BRAIN Initiative® continue to address critical components of the BRAIN 2025 Report, including novel tools to explore brain microconnectivity and non-neuronal cells, technology integration and dissemination, neuroethics, non-invasive human brain imaging, invasive human neuroscience, and team-based research on neural systems and circuits.

For Fiscal Year (FY) 2018, NIH announces 11 funding opportunity announcements (FOAs) for the BRAIN Initiative. Three new FOAs call for the development of tools for facilitating high-throughput microconnectivity analysis, methods to characterize non-neuronal cells in the brain, and resource grants for technology integration and dissemination. Additionally, several FY17 FOAs are being re-issued for research on ethical issues associated with advancements supported by the BRAIN Initiative, human brain imaging, various projects exploring neural circuits, invasive human neuroscience, and research fellowships for postdoctorates.


New FOAs for FY18:

RFA-MH-18-505 Tools to Facilitate High-Throughput Microconnectivity Analysis (R01)

  • This FOA provides resources for development and validation of novel tools to facilitate the detailed analysis of brain microconnectivity. Primarily, this FOA seeks to provide techniques and resources for examining complex circuits at the level of synaptic connections, alone or in combination with methods for identifying important cellular and circuit features. Technologies such as electron microscopy, nanoscale imaging, and newer methodologies including expansion microscopy and array tomography, as well as barcode-based tagging of synaptic connection may make it possible to map brain connectivity at the synapse resolution. The goal of this proposed effort is to produce next-generation, novel technologies for analysis of the microconnectome. Therefore, proposed methods should be transformative in scope and innovative in approach to studying molecular and cellular mechanisms of neural activity, particularly in analysis of micro- and macro-circuits. Plans to validate the tool/technology will also be essential. The application receipt date for this FOA is December 7, 2017.


RFA-DA-18-018 Tools to target, identify and characterize non-neuronal cells in the brain (R01)

  • This FOA is designed to stimulate the development and validation of technologies, tools, and methods for a detailed inventory and analysis of non-neuronal cells within the brain and to understand their contribution to the function of neural circuits underlying complex behaviors. The unique properties of non-neuronal cells limit the usefulness and applicability of tools developed to study neurons, and sites of neuro-glio-vascular interactions can be difficult to isolate experimentally. This FOA complements existing cell-census and tools development efforts initiated under RFA-MH-14-215 and RFA-MH-14-216 and is designed to develop new tools providing access to individual and defined groups of non-neuronal cells. Proposed tools or technologies should be transformative, high-risk, and aimed to overcome technical and analytical barriers to bridging experimental scales. Therefore, interdisciplinary collaborations such as with nanobiologists, computational and material scientists, and engineers are encouraged. The application receipt date for this FOA is February 1, 2018; clinical trials are not allowed.


RFA-NS-18-005 Research Resource Grants for Technology Integration and Dissemination (U24)

  • This U24 mechanism seeks to accelerate the scientific impact of the BRAIN Initiative by rapidly disseminating developed and validated technologies and resources to the broader neuroscience community. Proposed techniques, resources, or approaches should be at a well-validated stage wherein their value in research has already been demonstrated; proposals focused solely on development are not responsive to this FOA. Representative examples of projects responsive to this FOA include: a consortium for voltage sensors that detect changes in membrane potential, imaging services for large-scale recording or neural activity from multiple brain areas, and a resource that gathers and streamlines the distribution of transgenic mouse models for research. The application receipt date for this FOA is February 9, 2018; clinical trials are not allowed.


FOAs Re-issued for FY18:

RFA-MH-18-500 Research on the Ethical Implications of Advancements in Neurotechnology and Brain Science (Re-issue of MH-17-260; R01)

  • This R01 mechanism provides opportunities to consider the integration of ethical issues with BRAIN-supported scientific advances, specifically research involving human subjects and resulting from emerging technologies and research advancements. Examples of application topics include those focusing on: risk analyses, consent issues, privacy, ethical implications of neuromodulation and neuroimaging technologies, and issues associated with predictive/diagnostic research. Individuals interested in applying are encouraged to contact the scientific co-leads to discuss application ideas. The application receipt date for this FOA is December 7, 2017.


RFA-EB-17-005 Theories, Models and Methods for Analysis of Complex Data from the Brain (Re-issue of EB-15-006; R01)

  • This RFA utilizes a R01 mechanism to solicit new theories, computational models, and statistical tools to derive understanding of brain function from complex neuroscience data. A variety of approaches are applicable: the creation of new theories, ideas, and conceptual frameworks to organize/unify data and infer general principles of brain function; new computational models to develop testable hypotheses and design/drive experiments; and new mathematical and statistical methods to support or refute a stated hypothesis about brain function, and/or assist in detecting dynamical features and patterns in complex brain data. NIH expects that the tools developed under this FOA will be made widely available to the neuroscience research community. The application receipt dates for this FOA are December 15, 2017, October 17, 2018, and October 17, 2019.


RFA-EB-17-003 Proof of Concept Development of Early Stage Next Generation Human Brain Imaging (Re-issue of EB-17-001; R01)

  • This RFA uses a R01 mechanism to solicit unusually bold and potentially transformative approaches, including proof-of-concept development of brain imaging based on innovative and/or unconventional concepts aimed at revolutionizing the way non-invasive human neuroimaging is conducted. Tools and technologies can span a wide array of approaches including hardware, software, or imaging probes addressing any of the steps of the image acquisition and analysis process. Creative efforts to bridge scales from the micro- to meso- to macro-level in the brain are especially encouraged. The application receipt dates for this FOA are December 20, 2017 and December 11, 2018.


RFA-EB-17-004 Development of Next Generation Human Brain Imaging Tools and Technologies (Re-issue of EB-17-002; U01)

  • This RFA uses an U01 mechanism to support the full-scale development of novel imaging technologies beyond the proof of concept stage for noninvasive imaging of human brain processes in ways that are currently unachievable in healthy persons. NIH expects successful projects supported under the previous RFAs to be the basis for some of the applications submitted in response to this announcement, but previous support is not a requirement. This FOA supports an open competition for the best ideas for the full development of innovative and compelling new or next-gen non-invasive brain imaging technologies, with the intent of delivering working tools within the time frame of the BRAIN Initiative. The application receipt dates for this FOA are December 20, 2017 and December 11, 2018.


RFA-NS-18-008 Exploratory Team-Research BRAIN Circuit Programs – eTeamBCP (Re-issue of NS-15-005; U01)

  • This RFA uses an U01 mechanism and is part of a family of “Integrated Approaches” NIH BRAIN FOAs. This FOA promotes the integration of experimental, analytic, and theoretical capabilities for the large-scale analyses of neural systems and circuits, through interdisciplinary teams of experts who plan to conduct exploratory studies. These studies should incorporate information on cell-types and circuit function/connectivity, and be performed alongside analyses of complex, ethologically relevant behaviors. Successful exploratory studies should lead to subsequent competing applications for team-based research projects. The application receipt date for this FOA is December 15, 2017.


RFA-NS-18-009 Targeted BRAIN Circuits Projects – TargetedBCP (Re-issue of NS-17-014; R01)

  • This RFA uses a R01 mechanism and is part of a family of “Integrated Approaches” NIH BRAIN FOAs. The primary goal of this FOA is to solicit research projects using innovative, methodologically-integrated approaches to understand how circuit activity gives rise to mental experience and behavior. This RFA may support individual laboratories or small multi-PD/PI groups, and applications should offer specific, feasible research goals as endpoints to understand brain circuit function at cellular and sub-second levels of resolution in ethologically relevant behaviors within a 5-year term. The application receipt dates for this FOA are December 8, 2017 and March 15, 2018.


RFA-NS-18-010 Exploratory Research Opportunities Using Invasive Neural Recording and Stimulating Technologies in the Human Brain (Re-issue of NS-17-019; U01)

  • This RFA uses an U01 mechanism and addresses the BRAIN 2025 Report recommendation to “Advance Human Neuroscience.” This FOA seeks applications to assemble integrated, multi-disciplinary teams to tackle barriers inherent to human studies using invasive technologies and experimental protocols via exploratory research and planning activities to establish feasibility, proof-of-principle, and early stage development studies that might later compete for continued BRAIN Initiative funding. Successful projects will maximize opportunities to conduct innovative neuroscience research from invasive surgical procedures, and may incorporate methods of temporally-linked brain-behavior quantification. Note that awardees are expected to join a consortium work group to identify data standards and aggregate data for broad dissemination. The application receipt date for this FOA is January 19, 2018.


RFA-MH-18-510 BRAIN Initiative Fellows: Ruth L. Kirschstein National Research Service Award (NRSA) Individual Postdoctoral Fellowship (Re-issue of MH-17-250; F32)

  • The purpose of the BRAIN Initiative Fellows (F32) program is to enhance the research training of promising postdoctorates, early in their postdoctoral training period, who have the potential to become productive investigators in research areas that will advance the goals of the BRAIN Initiative. Applications are encouraged in any research area that is aligned with the BRAIN Initiative, including neuroethics. Applicants are expected to propose research training in an area that clearly complements their predoctoral research. Formal training in analytical tools appropriate for the proposed research is expected to be an integral component of the proposed research training plan. In order to maximize the training potential of the F32 award, this program encourages applications from individuals who have not yet completed their terminal doctoral degree and who expect to do so within 12 months of the application due date. On the application due date, candidates may not have completed more than 12 months of postdoctoral training. The application receipt dates for this FOA are: March 15, 2018; December 7, 2018; August 7, 2019; April 7, 2020.


Please visit our Active Funding Opportunities page for more details on these and other RFAs for the BRAIN Initiative.


Enhancement of a new DNA-based bioimaging technique… Method allowing near-simultaneous imaging of several thousand neurons in awake behaving mice… Imaging method to overcome biological tissue refractive index inhomogeneity increases large-field-of-view imaging depth… Open-source software package for working with microscopy images boosts high-throughput, single-cell analysis …

Improved DNA conjugation method enhances the achievable labeling density and spatial accuracy of highly multiplexed Exchange-PAINT imaging

Recent developments in high-resolution fluorescence imaging methods have overcome the limits of light diffraction. However, these techniques are challenged by their limited multiplexing capability, which hinders researchers’ understanding of multi-protein interactions at the nanoscale level. Exchange-PAINT (i.e., Points Accumulation in Nanoscale Topography), a new DNA-based approach, boosts multiplexing capabilities by sequentially imaging target molecules using orthogonal, dye-labeled DNA strands. Although very promising for bioimaging, the widespread application of this approach has been limited by the availability of DNA-conjugated ligands for protein labeling. At Harvard University, Dr. Peng Yin and colleagues have developed a new labeling platform for Exchange-PAINT that efficiently conjugates DNA oligonucleotides to various labeling probes (e.g., antibodies, nanobodies, and small molecules). By designing and testing the conjugation of 52 oligonucleotides to labeling probes like nanobodies, the group successfully enhanced the achievable labeling density and spatial accuracy of Exchange-PAINT. Finally, they demonstrated high-resolution cellular imaging with their labeling platform. The DNA conjugation method is simple to perform and the group anticipates that this general framework for labeling protein targets will make Exchange-PAINT accessible to a broader scientific community.

High-resolution image of proteins in HeLa cells acquired using nine rounds of Exchange-PAINT. The target proteins were labeled with DNA-conjugated antibodies using direct immunostaining. Complementary DNA strands were sequentially introduced to the sample for imaging. Post-acquisition, a washing buffer with reduced ionic strength was introduced to remove all DNA strands. Nine imaging rounds were performed using orthogonal DNA strands conjugated to the same dye.

Novel calcium imaging technique with a two-photon light-sculpting system enables fast volumetric imaging across multiple cortical layers

Calcium imaging in mouse hippocampus. (a) Schematic of the window preparation (red box represents imaging volume). (b) Time-averaged image (100μm depth). (c) Calcium traces of individual neurons imaged at 158fps in a single plane. (d) 3D rendering of time-averaged image (0.5 mm × 0.5 mm × 0.2 mm).

Advancing techniques for imaging the mammalian brain requires developing tools that record the activity of all neurons within a functional network at single-neuron resolution and over physiologically relevant time scales. Despite the recent introduction of various high-speed calcium imaging techniques, it remains a challenge to image the functional dynamics of large-scale neuronal circuits in awake-behaving mammals at high resolution. ­­At the Rockefeller University and the University of Vienna, Dr. Alipasha Vaziri and colleagues reveal a new calcium imaging method that utilizes a two-photon light-sculpting system. They updated their previously developed methods by tailoring the microscope to view the typical size of neuronal cell bodies in the mouse cortex. These changes allowed for the samplings of larger volumes with minimal numbers of excitation voxels at near-single-cell resolution. The signal-to-noise ratio was maximized using a fiber-based laser amplifier that synchronized pulses to the imaging voxel speed. The overall approach enabled near-simultaneous calcium imaging of several thousand neurons, across cortical layers (0.5 mm × 0.5 mm × 0.5 mm) and in the hippocampus of awake behaving mice. This exciting new method presents the opportunity to test experimentally a variety of theoretical models of information processing in the mammalian neocortex.

Large-field-of-view imaging by multi-pupil adaptive optics allows position-dependent correction of biological tissue optical distortion

The refractive index inhomogeneity within biological tissue presents challenges for in vivo optical imaging. Adaptive optics (AO) has corrected some of the distor­tions caused by this lack of homogeneity. However, the limited field-of-view (FOV) of current methods reduces imaging speed across larger areas, since distor­tion varies spatially and needs to be corrected accordingly. Approaches that provide simultaneous large-FOV distortion correction, and hence enable imaging of fast dynamics, are needed. At Purdue University, Dr. Meng Cui and colleagues developed multi-pupil adaptive optics (MPAO), which enables simultaneous, position-dependent correction over a 450 × 450 μm2 FOV and expands the correction area to nine times that of previous methods. In conventional AO, the correction measured from one region is applied to the entire image, improving imaging performance within a limited FOV. In MPAO, the imaging procedure is similar to conventional sys­tems, but independent correction for all regions is achieved. By implementing MPAO with imaging of in vivo mouse microglia dynamics, the group demonstrated improved quality compared with conventional AO. They next performed calcium imaging of neurons and astrocytes at 450 μm depth, achieving high-resolution images with full correction. Compared to typical techniques that provide imaging at 200-300 μm depths, large-FOV imaging at ~650 μm depth is possible using MPAO. Finally, with spatially independent distortion control, MPAO also enables nonplanar microscopy (i.e., brings 3D features at different depths into one imaging plane), which the group demonstrated by imaging 3D neurovasculature dynamics in anesthetized mice. This technique can aid high-spatiotemporal-resolution microscopy in various biological systems.

Calcium imaging at 450 μm depth with MPAO. (a,b) Astrocytes at 436-465 μm under the dura with full (a) and system (b) correction. (c,d) Zoomed-in view of the central area in a and b. (e,f) Standard deviation of the time-lapse images of neurons with full (e) and system (f) correction. The images in cf are from the same area. (g) Astrocytes (magenta) and neurons (green) at 450 μm depth. (h) Regions of interest (ROIs) for computing calcium transients. (i) Calcium transients with full and system correction.

A Python platform for image-guided mass spectrometry profiling facilitates sequential multi-technique analysis of each target in a biological sample

Sequential analysis of the same rat cerebellum-derived cell using MS instruments with different capabilities; MALDI-TOF followed by MALDI-FT-ICR.  Once a cell is located in the optical image, its location remains fixed through multiple analyses. MALDI-TOF provides high-throughput screening of thousands of cells to highlight rare or representative individuals. FT-ICR provides exact mass measurement for elemental composition analysis. Such a workflow facilitates exhaustive cell population analysis while efficiently utilizing the FT-ICR instrument.

Image-guided mass spectrometry (MS) profiling is a methodology for analyzing samples ranging from single cells to tissue sections. The workflow uses whole-slide microscopy to select targets, determine their locations, and perform MS analysis at those locations. This framework provides a link between the spatial dimensions in an image and the physical location of a sample. Single-cell MS has attracted substantial interest due to its sensitivity. Biomolecules within cells are detectible with MS, facilitating discovery of single-cell heterogeneity and enhancing understanding of the relationship between cellular chemical contents and their functions. However, limitations in MS imaging for high-throughput, single-cell analysis have stimulated efforts to develop methods that improve efficiency and resolution. At the University of Illinois at Urbana–Champaign, Dr. Jonathan Sweedler and colleagues have developed an open-source software package for working with microscopy images called microMS. The new platform permits effortless sequential analysis, enabling each cell to be scrutinized by multiple techniques. Targets can be automatically located, filtered, and stratified before MS. Specific MS systems are implemented through a novel abstract base class and software architecture, offering impressive simplification of the connection of microMS to new instruments and facilitating more efficientsequential analysis of the same target. The group believes that the ease of extending microMS to a variety of mass spectrometers and other instruments will help advance single-cell profiling.

Intracranial electrical recordings and neuro-stimulation of neurosurgical patients have made fundamental contributions to our understanding of vision, speech, decision making, memory, and sensorimotor processing. The use of these methods has burgeoned over the last decade due to technological advances and an increase in the number of patients undergoing neurosurgery for different neurological disorders. Intracranial electrophysiological research is performed only in patients who are scheduled to undergo neurosurgery, but the combination of treatment with research raises neuroethical issues around informed consent and risk assessment.

The Neuroethics Division of the NIH BRAIN Initiative Multi-Council Working Group (MCWG) serves as a resource of expertise to help navigate ethical considerations associated with cutting-edge science supported under the NIH BRAIN Initiative, such as intracranial electrophysiological research. Dr. Winston Chiong, an assistant Professor in the UCSF Department of Neurology Memory and Aging Center and member of the Neuroethics Division, recently published a paper in Neurosurgery with colleagues Drs. Matthew Leonard and Edward Chang. The group identified ethical dilemmas involved in intracranial electrophysiology research and proposed ethical standards for resolving potential issues.

For instance, patients may be unable to distinguish between clinical treatment and research participation, believing that their treatment is conditional on their participation and therefore making it difficult for them to know when they can refuse participation. Furthermore, the ability of these patients to give consent and understand treatment and research may be impaired by the disorder for which they are being treated, or by psychiatric comorbidities. Participants may also struggle to give informed consent in extra-operative procedures (i.e., testing that continues outside the operating room), as they experience changes in their physical or emotional state or in their medications.

Another ethical theme identified in the paper concerns the dual role of the physician as both clinician and investigator. This dual role may confuse patients about not only the distinction between research and treatment, but also the motivation behind a physician’s recommendations. The authors emphasize the value of strong communication between clinical and research teams and critically, among these teams, patients, and patients’ families. Furthermore, the authors point to the importance of determining how the costs of research will be distinguished from the costs of treatment.

The authors propose modifications to informed consent procedures, including that institutional review boards determine who should obtain consent on a case-by-case basis, and that appropriate methods ensure patient understanding that care is not conditional on participation. They encourage the creation of improved procedures to ensure patients understand the difference between treatment and research and can therefore give informed consent. They state that subject selection should be based on clinical determinations, not research ones. If there is any debate about the proper course of treatment for a subject, they suggest the inclusion of clinicians who are not involved in the research in order to come to a decision. Finally, they encourage the inclusion of bioethics specialists on research teams, to ensure maximized benefits and minimized risks for patients.

As invasive neurosurgical procedures and research become more prevalent, the authors emphasize the importance of adequately addressing these themes, to ensure that we continue making strides in understanding how the brain works while also protecting patients and research participants. Indeed, the NIH BRAIN Initiative emphasizes addressing neuroethical issues associated with neurotechnological advances. On October 26th, the NIH Clinical Center Department of Bioethics in association with the Neuroethics Division of the MCWG of the NIH BRAIN Initiative will host a one-day workshop entitled Ethical Issues in Research with Invasive and Non-Invasive Neural Devices in Humans (details, including a videocast link, will be made available here). These and other efforts can help scientists navigate the novel ethical concerns often raised by breakthrough neuroscience research.