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Introduction to protocols.io: Scientific collaboration through open protocols
Research articles and laboratory protocol organization often lack detailed instructions for replicating experiments. protocols.io is an open-access platform where researchers collaboratively create dynamic, interactive, step-by-step protocols that can be executed on mobile devices or the web. Researchers can easily and efficiently share protocols with colleagues, collaborators, the scientific community, or make them public. Real-time communication and interaction keep protocols up to date. Public protocols receive a DOI and enable open communication with authors and researchers to foster efficient experimentation and reproducibility.
Introduction to protocols.io: Scientific collaboration through open protocols
Research articles and laboratory protocol organization often lack detailed instructions for replicating experiments. protocols.io is an open-access platform where researchers collaboratively create dynamic, interactive, step-by-step protocols that can be executed on mobile devices or the web. Researchers can easily and efficiently share protocols with colleagues, collaborators, the scientific community, or make them public. Real-time communication and interaction keep protocols up to date. Public protocols receive a DOI and enable open communication with authors and researchers to foster efficient experimentation and reproducibility.
Face matching and decision making: The influence of framing, task presentation and criterion placement
Many situations rely on the accurate identification of people with whom we are unfamiliar. For example, security at airports or in police investigations require the identification of individuals from photo-ID. Yet, the identification of unfamiliar faces is error prone, even for practitioners who routinely perform this task. Indeed, even training protocols often yield no discernible improvement. The challenge of unfamiliar face identification is often thought of as a perceptual problem; however, this assumption ignores the potential role of decision-making and its contributing factors (e.g., criterion placement). In this talk, I am going to present a series of experiments that investigate the role of decision-making in face identification.
Evolution of convulsive therapy from electroconvulsive therapy to Magnetic Seizure Therapy; Interventional Neuropsychiatry
In April, we will host Nolan Williams and Mustafa Husain. Be prepared to embark on a journey from early brain stimulation with ECT to state-of-the art TMS protocols and magnetic seizure therapy! The talks will be held on Thursday, April 25th at noon ET / 6PM CET. Nolan Williams, MD, is an associate professor of Psychiatry and Behavioral Science at Stanford University. He developed the SAINT protocol, which is the first FDA-cleared non-invasive, rapid-acting neuromodulation treatment for treatment-resistant depression. Mustafa Husain, MD, is an adjunct professor of Psychiatry and Behavioral Sciences at Duke University and a professor of Psychiatry and Neurology at UT Southwestern Medical Center, Dallas. He will tell us about “Evolution of convulsive therapy from electroconvulsive therapy to Magnetic Seizure Therapy”. As always, we will also get a glimpse at the “Person behind the science”. Please register va talks.stimulatingbrains.org to receive the (free) Zoom link, subscribe to our newsletter, or follow us on Twitter/X for further updates!
Astrocyte reprogramming / activation and brain homeostasis
Astrocytes are multifunctional glial cells, implicated in neurogenesis and synaptogenesis, supporting and fine-tuning neuronal activity and maintaining brain homeostasis by controlling blood-brain barrier permeability. During the last years a number of studies have shown that astrocytes can also be converted into neurons if they force-express neurogenic transcription factors or miRNAs. Direct astrocytic reprogramming to induced-neurons (iNs) is a powerful approach for manipulating cell fate, as it takes advantage of the intrinsic neural stem cell (NSC) potential of brain resident reactive astrocytes. To this end, astrocytic cell fate conversion to iNs has been well-established in vitro and in vivo using combinations of transcription factors (TFs) or chemical cocktails. Challenging the expression of lineage-specific TFs is accompanied by changes in the expression of miRNAs, that post-transcriptionally modulate high numbers of neurogenesis-promoting factors and have therefore been introduced, supplementary or alternatively to TFs, to instruct direct neuronal reprogramming. The neurogenic miRNA miR-124 has been employed in direct reprogramming protocols supplementary to neurogenic TFs and other miRNAs to enhance direct neurogenic conversion by suppressing multiple non-neuronal targets. In our group we aimed to investigate whether miR-124 is sufficient to drive direct reprogramming of astrocytes to induced-neurons (iNs) on its own both in vitro and in vivo and elucidate its independent mechanism of reprogramming action. Our in vitro data indicate that miR-124 is a potent driver of the reprogramming switch of astrocytes towards an immature neuronal fate. Elucidation of the molecular pathways being triggered by miR-124 by RNA-seq analysis revealed that miR-124 is sufficient to instruct reprogramming of cortical astrocytes to immature induced-neurons (iNs) in vitro by down-regulating genes with important regulatory roles in astrocytic function. Among these, the RNA binding protein Zfp36l1, implicated in ARE-mediated mRNA decay, was found to be a direct target of miR-124, that be its turn targets neuronal-specific proteins participating in cortical development, which get de-repressed in miR-124-iNs. Furthermore, miR-124 is potent to guide direct neuronal reprogramming of reactive astrocytes to iNs of cortical identity following cortical trauma, a novel finding confirming its robust reprogramming action within the cortical microenvironment under neuroinflammatory conditions. In parallel to their reprogramming properties, astrocytes also participate in the maintenance of blood-brain barrier integrity, which ensures the physiological functioning of the central nervous system and gets affected contributing to the pathology of several neurodegenerative diseases. To study in real time the dynamic physical interactions of astrocytes with brain vasculature under homeostatic and pathological conditions, we performed 2-photon brain intravital imaging in a mouse model of systemic neuroinflammation, known to trigger astrogliosis and microgliosis and to evoke changes in astrocytic contact with brain vasculature. Our in vivo findings indicate that following neuroinflammation the endfeet of activated perivascular astrocytes lose their close proximity and physiological cross-talk with vasculature, however this event is at compensated by the cross-talk of astrocytes with activated microglia, safeguarding blood vessel coverage and maintenance of blood-brain integrity.
Fidelity and Replication: Modelling the Impact of Protocol Deviations on Effect Size
Cognitive science and cognitive neuroscience researchers have agreed that the replication of findings is important for establishing which ideas (or theories) are integral to the study of cognition across the lifespan. Recently, high-profile papers have called into question findings that were once thought to be unassailable. Much attention has been paid to how p-hacking, publication bias, and sample size are responsible for failed replications. However, much less attention has been paid to the fidelity by which researchers enact study protocols. Researchers conducting education or clinical trials are aware of the importance in fidelity – or the extent to which the protocols are delivered in the same way across participants. Nevertheless, this idea has not been applied to cognitive contexts. This seminar discusses factors that impact the replicability of findings alongside recent models suggesting that even small fidelity deviations have real impacts on the data collected.
Protocols for the social transfer of pain and analgesia in mice
We provide protocols for the social transfer of pain and analgesia in mice. We describe the steps to induce pain or analgesia (pain relief) in bystander mice with a 1-h social interaction with a partner injected with CFA (complete Freund’s adjuvant) or CFA and morphine, respectively. We detail behavioral tests to assess pain or analgesia in the untreated bystander mice. This protocol has been validated in mice and rats and can be used for investigating mechanisms of empathy. Highlights • A protocol for the rapid social transfer of pain in rodents • Detailed requirements for handling and housing conditions • Procedures for habituation, social interaction, and pain induction and assessment • Adaptable for social transfer of analgesia and may be used to study empathy in rodents https://doi.org/10.1016/j.xpro.2022.101756
NMC4 Short Talk: Systematic exploration of neuron type differences in standard plasticity protocols employing a novel pathway based plasticity rule
Spike Timing Dependent Plasticity (STDP) is argued to modulate synaptic strength depending on the timing of pre- and postsynaptic spikes. Physiological experiments identified a variety of temporal kernels: Hebbian, anti-Hebbian and symmetrical LTP/LTD. In this work we present a novel plasticity model, the Voltage-Dependent Pathway Model (VDP), which is able to replicate those distinct kernel types and intermediate versions with varying LTP/LTD ratios and symmetry features. In addition, unlike previous models it retains these characteristics for different neuron models, which allows for comparison of plasticity in different neuron types. The plastic updates depend on the relative strength and activation of separately modeled LTP and LTD pathways, which are modulated by glutamate release and postsynaptic voltage. We used the 15 neuron type parametrizations in the GLIF5 model presented by Teeter et al. (2018) in combination with the VDP to simulate a range of standard plasticity protocols including standard STDP experiments, frequency dependency experiments and low frequency stimulation protocols. Slight variation in kernel stability and frequency effects can be identified between the neuron types, suggesting that the neuron type may have an effect on the effective learning rule. This plasticity model builds a middle ground between biophysical and phenomenological models allowing not just for the combination with more complex and biophysical neuron models, but is also computationally efficient so can be used in network simulations. Therefore it offers the possibility to explore the functional role of the different kernel types and electrophysiological differences in heterogeneous networks in future work.
OpenFlexure
OpenFlexure is a 3D printed flexure translation stage, developed by a group at the Bath University. The stage is capable of sub-micron-scale motion, with very small drift over time. Which makes it quite good, among other things, for time-lapse protocols that need to be done over days/weeks time, and under space restricted areas, such as fume hoods.
Addgene AAV data hub
The Addgene AAV Data Hub was launched to help scientists share data and protocols obtained from AAV experiments. Our longterm goal is to provide scientists with a resource to help guide AAV selection and use by providing data from individual labs on AAV performance.
Untangling the web of behaviours used to produce spider orb webs
Many innate behaviours are the result of multiple sensorimotor programs that are dynamically coordinated to produce higher-order behaviours such as courtship or architecture construction. Extendend phenotypes such as architecture are especially useful for ethological study because the structure itself is a physical record of behavioural intent. A particularly elegant and easily quantifiable structure is the spider orb-web. The geometric symmetry and regularity of these webs have long generated interest in their behavioural origin. However, quantitative analyses of this behaviour have been sparse due to the difficulty of recording web-making in real-time. To address this, we have developed a novel assay enabling real-time, high-resolution tracking of limb movements and web structure produced by the hackled orb-weaver Uloborus diversus. With its small brain size of approximately 100,000 neurons, the spider U. diversus offers a tractable model organism for the study of complex behaviours. Using deep learning frameworks for limb tracking, and unsupervised behavioural clustering methods, we have developed an atlas of stereotyped movement motifs and are investigating the behavioural state transitions of which the geometry of the web is an emergent property. In addition to tracking limb movements, we have developed algorithms to track the web’s dynamic graph structure. We aim to model the relationship between the spider’s sensory experience on the web and its motor decisions, thereby identifying the sensory and internal states contributing to this sensorimotor transformation. Parallel efforts in our group are establishing 2-photon in vivo calcium imaging protocols in this spider, eventually facilitating a search for neural correlates underlying the internal and sensory state variables identified by our behavioural models. In addition, we have assembled a genome, and are developing genetic perturbation methods to investigate the genetic underpinnings of orb-weaving behaviour. Together, we aim to understand how complex innate behaviours are coordinated by underlying neuronal and genetic mechanisms.