Science Society

In this episode, we're joined by Dr. Rai, who enlightens us about the exciting field of precision protein engineering and its potential applications.

Precision engineering of native proteins is akin to maintaining machinery – both necessitate an operational understanding and a robust set of tools for repair. Dr. Rai presents a technology that offers substantial control over various aspects of protein manipulation, including reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. This technology is known as cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K).

The strength of this user-friendly protocol lies in its ability to achieve quantitative conversions within an hour, leveraging chemically orthogonal C-S bond-formation and bond-dissociation. Interestingly, it offers the capacity to target a single lysine residue of a single protein in a complex biomolecular mixture, yielding an analytically pure single-site probe-engineered protein bioconjugate.

The LDMC-K technique also enables the creation of homogeneous antibody conjugates, which demonstrate highly selective anti-proliferative activity towards breast cancer cells.

Join us as we explore the depths of precision protein engineering, its implications, and its future prospects.

Key Words: Precision Protein Engineering, LDMC-K, Reactivity, Chemoselectivity, Site-selectivity, Protein-selectivity, Breast Cancer, Antibody Conjugates.

Reddy, N.C., Molla, R., Joshi, P.N. et al. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nat Commun (2022). https://doi.org/10.1038/s41467-022-33772-1

This episode features Dr. Kole, who shares fascinating insights into the world of myelination in parvalbumin-expressing (PV+) basket cells, a type of fast-spiking inhibitory interneurons vital for regulating local circuit activity and oscillations.

PV+ axons are often myelinated, but the electrical and metabolic implications of interneuron myelination remain an open question in neuroscience. To delve deeper into this, Dr. Kole and his team developed viral constructs for cell type-specific investigation of mitochondria using genetically encoded fluorescent probes.

Their investigations revealed a selective clustering of mitochondria to myelinated segments of PV+ basket cells. Interestingly, while the mitochondrial density increases in excitatory axons, cuprizone-induced demyelination erased mitochondrial clustering in PV+ axons.

When the myelin basic protein was genetically deleted, they still observed mitochondrial clustering at internodes wrapped by noncompacted myelin, signifying that myelin compaction is not mandatory for this process.

In the final part of their study, two-photon imaging was used to monitor action potential-evoked calcium (Ca2+) responses, which revealed that interneuron myelination reduces both the cytosolic and mitochondrial Ca2+ transients.

These findings propose a unique role of oligodendrocyte ensheathment of PV+ axons in assembling mitochondria to selectively fine-tune metabolic demands. Join us as we uncover the mysteries of interneuron myelination with Dr. Kole.

Key Words: Parvalbumin-expressing Basket Cells, Myelination, Mitochondrial Clustering, Cuprizone-induced Demyelination, Two-photon Imaging, Calcium Transients, Oligodendrocyte Ensheathment.

Kole, K., et al. Parvalbumin basket cell myelination accumulates axonal mitochondria to internodes. Nat Commun 13, 7598 (2022). https://doi.org/10.1038/s41467-022-35350-x

This episode features Dr. McWilliam, who discusses the intricate microbial immune-detection system in mammals revolving around MR1, a highly conserved protein. MR1 plays a crucial role in capturing vitamin B-related metabolite antigens from various microbes and displaying them at the cell surface to stimulate MR1-restricted lymphocytes, including mucosal-associated invariant T (MAIT) cells.

This process of MR1 presentation and MAIT cell recognition aids in maintaining homeostasis through host defense and tissue repair mechanisms. However, the cellular mechanisms that regulate MR1 cell surface expression, which are critical for its function and MAIT cell recognition, remain largely unexplored.

Dr. McWilliam and his team report that human MR1 is equipped with a tyrosine-based motif in its cytoplasmic domain that facilitates low-affinity binding with the endocytic adaptor protein 2 (AP2) complex. This interaction regulates the rate of MR1 internalization from the cell surface and restricts recycling.

They propose that MR1 utilizes AP2 endocytosis to determine the duration of antigen presentation to MAIT cells and the detection of a microbial metabolic signature by the immune system. Join us in this episode to delve deeper into the exciting world of MR1 and MAIT cells with Dr. McWilliam.

Key Words: MR1, Microbial Immune-Detection, Mucosal-Associated Invariant T Cells, Endocytic Adaptor Protein 2, Antigen Presentation, Host Defense.

McWilliam et al. A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells. doi: 10.1083/jcb.202110125. Epub 2022 Sep 21. PMID: 36129434; PMCID: PMC9499830.

In this episode, Dr. Luque delves into the fascinating realm of exoplanets and their composition. With the majority of known temperate exoplanets orbiting red dwarf stars, these celestial bodies present an intriguing field for exploration and research.

Dr. Luque and his colleague Pallé have been analyzing the masses and radii of these small transiting planets. Their research reveals three distinct populations - rocky, water-rich, and gas-rich. Contrary to the previously accepted bimodal radius distribution theory, which suggested atmospheric loss of a hydrogen/helium envelope, Dr. Luque proposes a new interpretation.

Their findings suggest a density gap that separates rocky exoplanets from water-rich ones. This division could shed light on the planets' formation, possibly linked to their location within their planetary systems before orbital migration. According to their model, rocky planets form within the snow line, while water-rich planets form outside it and later migrate inward.

Join us for an in-depth discussion with Dr. Luque as we delve into the intricacies of exoplanets, their formation, and the implications for our understanding of the universe.

Key Words: Exoplanets, Red Dwarf Stars, Planet Composition, Planet Formation, Orbital Migration, Density Gap.

Density, not radius, separates rocky and water-rich small planets orbiting M dwarf stars https://doi.org/10.1126/science.abl7164

DNA's mechanical and structural properties, dictated by local sequence and epigenetic modifications, have significant influence over a variety of DNA-deforming processes. However, comprehending this 'mechanical code' has been a complex task due to the lack of high-throughput experimental methods. Dr. Basu's research endeavors to unlock this intricate code.

In this episode, we delve into Dr. Basu's groundbreaking research. Utilizing high-throughput measurements of DNA bendability through loop-seq, a technology developed by his team, Dr. Basu reveals how the occurrence and spatial distribution of dinucleotides, tetranucleotides, and methylated CpG influence DNA bendability.

Building on these findings, Dr. Basu's team developed a physical model that captures the sequence and methylation dependence of DNA bendability. The model was further validated by using loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites.

The conversation also explores how the model was applied to test the predictions of all-atom molecular dynamics simulations and show that sequence and epigenetic modifications can mechanically encode regulatory information in various contexts.

Join us as we traverse the fascinating terrain of DNA's mechanical code with Dr. Basu, opening up new avenues in our understanding of genetics and molecular biology.

Key Words: DNA Bendability, Mechanical Code, Loop-seq, Dinucleotides, Tetranucleotides, Methylated CpG, All-atom Molecular Dynamics Simulations, Epigenetic Modifications.

Basu, A., Bobrovnikov, D.G., Cieza, B. et al. Deciphering the mechanical code of the genome and epigenome. Nat Struct Mol Biol 29, 1178–1187 (2022). https://doi.org/10.1038/s41594-022-

-6

The three-dimensional folding of genes within the nuclear space is integral to understanding gene function and regulation, moving beyond the linear DNA sequence. Dr. Neguembor presents immuno-OligoSTORM, a revolutionary imaging strategy that super-resolves the distribution of nucleosomes within specific genes by simultaneously visualizing DNA and histones.

In this episode, we dive into the technology behind immuno-OligoSTORM and how it integrates with restraint-based and coarse-grained modeling approaches to sync super-resolution imaging data with Hi-C contact frequencies and deconvoluted micrococcal nuclease-sequencing information. This results in Modeling immuno-OligoSTORM, a method that allows for quantitative modeling of genes with nucleosome resolution and reveals information about chromatin accessibility for regulatory factors, like RNA polymerase II.

Join us as Dr. Neguembor elucidates how Modeling immuno-OligoSTORM allows exploration of intercellular variability, transcriptional-dependent gene conformation, and the folding of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells. This conversation promises to provide the highest degree of data integration on this subject so far.

Key Words: immuno-OligoSTORM, Super-Resolution Imaging, Chromatin Architecture, DNA Folding, Nucleosomes, Restraint-based Modeling, Coarse-Grained Modeling, Hi-C Contact Frequencies, Micrococcal Nuclease-Sequencing, RNA Polymerase II.

Neguembor, et al. MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution. Nat Struct Mol Biol 29, (2022). https://doi.org/10.1038/s41594-00839-y

Title: "Exploring Tumour Neo-Innervation and Anti-Tumour Immunity with Dr. Talbot"

Description:

The innervation of solid tumors by pain-initiating sensory neurons or nociceptors and its implications on cancer immunosurveillance is a subject of immense interest. In this episode, we're joined by Dr. Talbot, who discusses how melanoma cells interact with nociceptors, leading to their increased neurite outgrowth, sensitivity to noxious ligands, and neuropeptide release.

Dr. Talbot delves into how Calcitonin Gene-Related Peptide (CGRP), a nociceptor-produced neuropeptide, can directly amplify the exhaustion of cytotoxic CD8+ T cells, limiting their ability to eliminate melanoma. Strategies like the genetic ablation of the TRPV1 lineage, local pharmacological silencing of nociceptors, and antagonism of the CGRP receptor RAMP1 all showed promising results in reducing leukocyte exhaustion and tumor growth, significantly increasing the survival rate of melanoma-bearing mice.

Further, the conversation shifts to a critical finding: the reversal of CD8+ T cell exhaustion in sensory-neuron-depleted mice treated with local recombinant CGRP. Single-cell RNA sequencing of biopsies from melanoma patients further reveals the link between RAMP1-expressing CD8+ T cells and exhaustion, with RAMP1 overexpression correlating to a poorer prognosis.

Join us as Dr. Talbot proposes a novel approach to improve anti-tumour immunity: curtailing the release of CGRP from tumor-innervating nociceptors to negate the immunomodulatory effects on cytotoxic CD8+ T cells.

Key Words: Solid Tumours, Nociceptor Neurons, Cancer Immunosurveillance, Melanoma, Calcitonin Gene-Related Peptide (CGRP), CD8+ T Cells, TRPV1 Lineage, RAMP1, Anti-Tumour Immunity.

Balood, M., Ahmadi, M., Eichwald, T. et al. Nociceptor neurons affect cancer immunosurveillance. Nature 611, 405–412 (2022). https://doi.org/10.1038/s41586-022-05374-w

The long childhood characteristic of our species is hypothesized to have evolved for learning complex foraging skills. This episode features Dr. Ilaria Pretelli, who investigates the connection between the development of foraging proficiency and the complexity of the foraging niche. Using published records of child and adolescent foragers from 28 different societies, Dr. Pretelli explores how skill-intensive different resources are and assess whether children’s proficiency increases more slowly for these resources.

The discussion reveals that foraging returns for more skill-intensive and difficult-to-extract resources like tubers and game increase slowly, with peak productivity reached only in adulthood. In contrast, returns for easier-to-extract resources like fruit and fish/shellfish increase rapidly during childhood, achieving adult levels of productivity by adolescence.

Dr. Pretelli's findings support the hypothesis that long childhoods evolved to allow extended periods for learning to extract complex resources characteristic of the human foraging niche. Join us in this episode as we delve into the intricate relationship between human development and the acquisition of crucial survival skills.

Key Words: Human Development, Foraging Skills, Childhood Learning, Niche Complexity, Skill-intensive Resources, Foraging Returns, Evolution.

Foraging complexity and the evolution of childhood https://doi.org/10.1126/sciadv.abn9889

In this enlightening episode, we delve into the realm of integrating neurons into digital systems with Dr. Kagan. Dr. Kagan presents his innovative development, DishBrain, which uses in vitro neural networks from human or rodent origins, integrated with in silico computing through a high-density multielectrode array. This fusion of biology and technology represents a significant leap towards creating synthetic biological intelligence.

By embedding these cultures in a simulated game world, mimicking the arcade game "Pong," Dr. Kagan and his team observe learning within five minutes of real-time gameplay that is not seen in control conditions. The research demonstrates the importance of closed-loop structured feedback in eliciting learning over time.

Dr. Kagan explains that these neural networks display the ability to self-organize activity in a goal-directed manner, responding to sparse sensory information about the consequences of their actions. This exploration of what the team has termed synthetic biological intelligence might offer valuable insights into the cellular correlates of intelligence, and it has the potential to revolutionize our understanding of both biological and artificial intelligence.

Key Words: Synthetic Biological Intelligence, Neuron Integration, Digital Systems, DishBrain, In Vitro Neural Networks, In Silico Computing, Multielectrode Array, Active Inference, Free Energy Principle, Cellular Correlates of Intelligence.

In vitro neurons learn and exhibit sentience when embodied in a simulated game world https://doi.org/10.1016/j.neuron.2022.09.001

In this compelling episode, Dr. Weijian Yang introduces us to a breakthrough in computational imaging: a compact and learnable lensless 3D camera capable of real-time photorealistic imaging. This technological innovation holds great promise in revolutionizing how we capture and interpret our world.

The device, developed by Dr. Yang and his team, replaces traditional bulky optics with customized thin optical masks, making it lightweight and portable. Contrary to existing lensless imaging methods that require extensive calibration and heavy computational resources, this lensless 3D camera overcomes these challenges. Dr. Yang discusses the custom design and fabrication of the optical phase mask, optimized for spatial frequency support and axial resolving ability.

The team has developed a robust physics-aware deep learning model with an adversarial learning module that allows for real-time depth-resolved photorealistic reconstructions. The ability of this lensless imager to resolve depth and "see-through" opaque obstacles offers transformative potential across a range of computational imaging applications.

Join us as we delve into the future of imaging technology and its implications for a variety of fields, from medical imaging to remote sensing and beyond.

Key Words: Computational Imaging, Lensless 3D Camera, Real-Time Imaging, Photorealistic Reconstruction, Optical Phase Mask, Physics-Aware Deep Learning, Adversarial Learning, Depth Resolution, See-Through Imaging.

Tian F, Yang W. Learned lensless 3D camera. Opt Express. 2022 Sep 12;30(19):34479-34496. doi: 10.1364/OE.465933. PMID: 36242459; PMCID: PMC9576281.