Science Society

In this enlightening episode, Dr. Ceren Kabukcu takes us back to the Paleolithic era as she shares her groundbreaking research on hunter-gatherer diets. While the predominant narrative has focused on the consumption of animals, Dr. Kabukcu sheds light on the significant role plants, particularly those with bitter and astringent tastes, played in ancient cuisine.

Her team conducted an in-depth analysis of carbonised macro-remains of processed plants from Franchthi Cave in the Aegean Basin and Shanidar Cave in the north-west Zagros Mountains. Through microscopic examination of these charred food remains, they discovered the use of pounded pulses as a common ingredient in cooked plant foods.

In our discussion, we explore the implications of these findings in the broader context of regional archaeobotanical literature. Dr. Kabukcu argues that despite their unappealing flavors to the modern palate, bitter and astringent plants were key ingredients of Palaeolithic cuisines in South-west Asia and the Eastern Mediterranean.

Join us for this fascinating exploration of our dietary past, a journey that reveals how our ancestors turned nature's pantry into diverse and nourishing meals.

Key Words: Palaeolithic Diet, Hunter-Gatherer, Plant Foods, Archaeobotany, Franchthi Cave, Shanidar Cave, Pounded Pulses, Bitter and Astringent Plants, South-west Asia, Eastern Mediterranean.

Kabukcu, C. (2022). Cooking in caves: Palaeolithic carbonised plant food remains from Franchthi and Shanidar. Antiquity, 1-17. doi:10.15184/aqy.2022.143

In this enlightening episode, we travel back in time to unravel the mysteries of ancient Greek astronomy with Dr. Victor Gysembergh, a leading expert on the subject. The focus of our conversation is the recently discovered evidence for Hipparchus’ lost Star Catalogue, a breakthrough made possible through advanced multispectral imaging and meticulous interpretation of a palimpsest manuscript.

Dr. Gysembergh shares with us the significance of these findings, revealing that they represent the most authoritative evidence to date for Hipparchus' Star Catalogue. The discovery notably confirms that the Star Catalogue was originally composed in equatorial coordinates, a fact that profoundly influences our understanding of ancient astronomical practices.

Moreover, Dr. Gysembergh explains how the evidence reveals that Ptolemy’s Star Catalogue was not entirely based on data from Hipparchus' work, challenging long-standing assumptions in the field of historical astronomy.

Perhaps most fascinating, the numerical evidence suggests that Hipparchus' Star Catalogue may have been accurate within 1° of the real stellar coordinates, outperforming even Claudius Ptolemy's renowned work in precision.

Join us on this celestial journey as we explore the groundbreaking discoveries and delve into the precision and ingenuity of ancient astronomy. Uncover the complex narratives of knowledge transmission and scientific advancement that continue to resonate today.

Key Words: Hipparchus, Star Catalogue, Ancient Astronomy, Multispectral Imaging, Palimpsest Manuscript, Equatorial Coordinates, Ptolemy, Claudius Ptolemy, Greek Astronomy, Historical Astronomy.

New evidence for Hipparchus’ Star Catalogue revealed by multispectral imaging https://doi.org/10.1177/00218286221128289

This episode delves into the fascinating world of host-associated microbiotas with renowned scientist Dr. Eisen. His groundbreaking research uncovers how microbiotas guide the trajectory of developmental programs and influence social behavior.

Dr. Eisen's team discovered that the zebrafish microbiota is required for normal social behavior, revealing a molecular pathway that connects the microbiota, microglial remodeling of neural circuits, and social behavior. This exploration was conducted using the experimentally tractable model vertebrate, the zebrafish.

We discuss in depth how the microbiota restrains neurite complexity and targets forebrain neurons necessary for normal social behavior. We also delve into how the microbiota is crucial for localizing forebrain microglia, brain-resident phagocytes that remodel neuronal arbors.

Dr. Eisen's research indicates that the microbiota influences microglial molecular functions, promoting the expression of the complement signaling pathway and the synaptic remodeling factor c1q. He shares with us his intriguing finding that several distinct bacterial taxa are individually sufficient for normal microglial and neuronal phenotypes, suggesting that host neuroimmune development is sensitive to a feature common among many bacteria.

In this illuminating conversation, we explore how understanding the connection between microbiota and social behavior can open up pathways for new interventions in multiple neurodevelopmental disorders. Join us as we navigate this complex and intriguing interplay between our microbiota and our brains.

Key Words: Microbiota, Neurodevelopment, Social Behavior, Microglial Remodeling, Neural Circuits, Zebrafish, Neurite Complexity, Forebrain Neurons, Neuroimmune Development, Neurodevelopmental Disorders.

Eisen et al. (2022) The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons. doi:10.1371/journal.pbio.3001838

In this fascinating episode, we dive into the world of insects with Dr. Emonet, an expert in sensory processing and behavior. We explore how insects like Drosophila melanogaster, commonly known as the fruit fly, utilize odor plumes to navigate complex and rapidly changing environments in their quest for food and mates.

Odour plumes, Dr. Emonet explains, are volatile, multidimensional signals carried by turbulent airflows. Insects are capable of extracting and integrating several features of these odour signals, including their identity, intensity, and timing. They also incorporate other sensory inputs like mechanosensory and visual cues. However, the conventional model of insect odour navigation has largely centered around the wind providing the primary directional cue.

Dr. Emonet challenges this model, revealing that Drosophila melanogaster also uses another directional cue—the direction of motion of odors. This information is gathered using temporal correlations in the odor signal between the insect's two antennae. The processes employed, he elaborates, are akin to those used in visual-direction sensing.

With the help of high-resolution virtual-reality paradigms, simulations, theory, and experiments, Dr. Emonet illustrates how this odor-direction sensing plays a critical role in navigating naturalistic plumes. The odor motion holds valuable directional information that is absent from airflow alone, proving beneficial to both Drosophila and virtual agents.

This episode provides a glimpse into the elegant mechanisms at play in the insect world and raises exciting possibilities for the development of olfactory robot navigation in uncertain environments.

Key Words: Insect navigation, Odour plumes, Drosophila melanogaster, Sensory inputs, Visual-direction sensing, Mechanosensory cues, Olfactory robot navigation, Sensory processing, and behavior.

Kadakia, N., Demir, M., Michaelis, B.T. et al. Odour motion sensing enhances navigation of complex plumes. Nature (2022). https://doi.org/10.1038/s41586-022-05423-4

In this fascinating episode, we're joined by Dr. Mizuno, an expert in microbiology and biodiversity, who shares his recent discovery of a unique multicellular bacterium.

Dr. Mizuno and his team identified a bacterium, HS-3, from an underground stream, demonstrating an entirely new type of prokaryotic multicellularity. The bacterium self-organizes its filamentous cells into layer-structured colonies, exhibiting properties similar to a nematic liquid crystal.

The research team observed that these colonies mature into a semi-closed sphere containing clusters of coccobacillus daughter cells. Interestingly, the release of these cells is selective and happens upon contact with water.

This groundbreaking discovery challenges our understanding of bacterial multicellularity and indicates that a liquid-crystal status can support prokaryotic multicellular behavior.

Dr. Mizuno further delves into the ecological context of this phenomenon. He hypothesizes that the cyclic exposure of these colonies to the cave's water flow might have driven the evolutionary transition from unicellular to multicellular life forms.

The findings, while preliminary, have exciting implications for a wide range of scientific disciplines, including microbiology, evolutionary biology, geobiology, and biophysics.

Join us for this fascinating conversation as we explore the ecological contexts that foster multicellularity and the intriguing world of bacterial life with Dr. Mizuno.

Key Words: Multicellularity, Bacterial Life, Prokaryotes, Microbiology, Ecology, Evolution, Biophysics, Geobiology, HS-3 Bacterium, Liquid Crystal, Coccobacillus Daughter Cells.

Kouhei Mizuno et al. (2022) Novel multicellular prokaryote discovered next to an underground stream eLife 11:e71920 https://doi.org/10.7554/eLife.71920

In this episode, we are thrilled to have Dr. Xie, a notable figure in the intersection of computational biology and personalized medicine. His groundbreaking work focuses on developing innovative machine-learning models to predict patient-specific responses to new compounds, a key aspect of personalized drug discovery and development.

The main hurdle in this field is the scarcity of patient data, which makes training a generalized machine-learning model challenging. To overcome this, Dr. Xie and his team created the context-aware de-confounding autoencoder (CODE-AE). This model can extract intrinsic biological signals obscured by context-specific patterns and confounding factors.

In the course of our conversation, Dr. Xie shares the results of extensive comparative studies, showing that CODE-AE not only alleviated the out-of-distribution problem for model generalization but also significantly improved the accuracy and robustness in predicting patient-specific clinical drug responses. These results were achieved purely from cell-line compound screens, demonstrating the effectiveness of CODE-AE.

Using this approach, Dr. Xie's team screened 59 drugs for over 9,800 cancer patients. The results align well with existing clinical observations, underscoring the potential of CODE-AE in developing personalized therapies and identifying drug response biomarkers.

This episode is a must-listen for those interested in personalized medicine, computational biology, machine learning, and the future of drug discovery and development. Join us as we delve into the fascinating world of personalized medicine with Dr. Xie.

Key Words: Personalized Medicine, CODE-AE, Machine Learning, Drug Discovery, Drug Development, Computational Biology, Cell-Line Compound Screens, Drug Response Biomarkers, Cancer Treatment.

Xie et al. A context-aware de-confounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening Nat 2022 https://doi.org/10.1038/s42256-022-00541-0

In this riveting episode, we host Dr. Qiu, a distinguished researcher whose work focuses on understanding the unique developmental differentiation within ant colonies. Ant colonies, much like higher-level organisms, consist of specialized reproductive and non-reproductive individuals, a phenomenon Dr. Qiu compares to germ-soma segregation in bilateral Metazoa.

Dr. Qiu and his team have assembled more than 1,400 whole-genome transcriptomes to reconstruct the individual developmental trajectories of two ant species, Monomorium pharaonis, and Acromyrmex echinatior. Through this, they have been able to predict caste phenotypes with impressive accuracy using genome-wide transcriptome profiling.

In our conversation, Dr. Qiu explains their finding that caste differentiation in ants is increasingly canalized from early development onwards, particularly in germline individuals (gynes/queens). He delves into the vital role of the juvenile hormone signaling pathway in this process by regulating body mass divergence between castes.

Furthermore, they have identified and quantified gene-specific canalization levels and uncovered that canalized genes with gyne/queen-biased expression are linked to ovary and wing functions. On the other hand, canalized genes with worker-biased expression were enriched in brain and behavioral functions.

By suppressing Freja, a highly canalized gyne-biased ovary gene in gyne larvae, they also demonstrate that any disturbance in the developmental pathway induces non-adaptive intermediate phenotypes between gynes and workers.

Join us as Dr. Qiu takes us on a genomic journey exploring the intricate and fascinating world of ant colonies. This episode is a must-listen for anyone interested in genomics, developmental biology, and the sophisticated world of insect social structure.

Key Words: Ant colonies, Developmental Differentiation, Genomics, Transcriptomes, Germ-Soma Segregation, Juvenile Hormone Signaling, Caste Phenotypes, Canalization, Ant Behavior, Evolutionary Biology.

Qiu, B., Dai, X., Li, P. et al. Canalized gene expression during development mediates caste differentiation in ants. Nat Ecol Evol 6, 1753–1765 (2022). https://doi.org/10.1038/s41559-022-01884-y

We are excited to welcome Dr. Ando, an expert in phylogenetic reconstruction and evolutionary biology, in this episode. Dr. Ando's intriguing work centers on Ribonucleotide Reductases (RNRs) - essential enzymes used by all free-living organisms and many viruses in the biosynthesis of DNA precursors.

RNRs exhibit tremendous diversity in terms of primary sequence and cofactor requirements while retaining a conserved fold and a radical-based mechanism for nucleotide reduction. Dr. Ando and his team have pieced together the most extensive phylogeny of RNRs to date, including a whopping 6779 sequences that unite all extant classes of the RNR family.

During our discussion, Dr. Ando shares fascinating insights into their discovery of a novel, phylogenetically distinct clade that they have dubbed 'clade Ø'. This clade is ancestral to the classes I and II RNRs, and is a significant addition to our understanding of RNR evolution.

Through a combination of techniques, including small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2, the team delves into the structure of a member of clade Ø, presenting the most minimal RNR architecture known to date. Based on their thorough analyses, Dr. Ando puts forth an evolutionary model for the diversification in the RNR family and discusses how their phylogeny could serve as a roadmap for future studies.

Join us for this engrossing episode as we explore the fascinating evolution of the RNR family with Dr. Ando. This episode is an enlightening journey for anyone interested in evolutionary biology, phylogenetic reconstruction, structural biology, and the mechanisms of life at the molecular level.

Key Words: Ribonucleotide Reductases, Phylogeny, Evolutionary Biology, Structural Biology, AlphaFold2, Cryogenic-Electron Microscopy, Small-Angle X-ray Scattering, DNA Biosynthesis, Protein Family Evolution.

Nozomi Ando et al. (2022) Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade eLife 11:e79790 https://doi.org/10.7554/eLife.79790

In this episode, we welcome Dr. Cohen, a pioneer in the fascinating world of microscopic robots. Dr. Cohen's work aims to revolutionize fields such as medicine and environmental remediation by developing autonomous robots on a microscopic scale. These tiny systems, guided by onboard complementary metal oxide semiconductor electronics, have the potential to significantly impact a broad range of industries.

During our conversation, Dr. Cohen delves into the intricacies of integrating information systems with microactuators, a key challenge in the creation of microscopic robots. He explains his team's process, which successfully integrates electronics fabricated at commercial foundries with microactuators.

Dr. Cohen shares exciting details about the autonomous, untethered robots they've built, which range from 100 to 250 micrometers in size. Powered by light, these robots can walk at speeds greater than 10 micrometers per second. Notably, they've also demonstrated a microscopic robot capable of responding to an optical command.

Join us as Dr. Cohen unravels the future of microscopic robots, offering insights into their potential uses and the technological advances that made them possible. If you're interested in robotics, AI, nanotechnology, or the intersection of technology and healthcare, this episode is a must-listen.

Key Words: Microscopic Robots, Autonomous Robots, Complementary Metal Oxide Semiconductor Electronics, Microactuators, Robotics, Nanotechnology, Medicine, Environmental Remediation, Light-Powered Robots.

Microscopic robots with onboard digital control https://doi.org/10.1126/scirobotics.abq2296

In this episode, we are joined by the renowned scientist Dr. Jack Feldman, whose work on the complex neural control system of breathing has been groundbreaking. Breathing, though seemingly simple, is a rhythmically regulated behavior vital for life and has profound influences on our brain and body.

Dr. Feldman delves into the intricacies of the breathing central pattern generator (bCPG), a complex system that not only regulates gas exchange but also coordinates breathing with various behaviors. He sheds light on the role of the preBötzinger complex (preBötC), a central element of the bCPG, that drives inspiratory rhythm through an intricate emergent mechanism.

Our conversation takes us through the synchronization dynamics that underpin preBötC rhythmogenesis, granting the system robustness and lability. We discuss how these dynamics are influenced by inputs from all over the brain and generate rhythmic, patterned activity that is widely distributed.

Join us as Dr. Feldman elucidates the fascinating link between breathing, emotion, and cognition, backed by an emerging body of research. His insights hold promising implications for understanding function and dysfunction in breathing, as well as in other neural circuits of mammals.

Key Words: Breathing, Central Pattern Generator, preBötzinger Complex, Neural Control System, Rhythmic Motor Behavior, Neural Circuits, Emotion, Cognition.

Breathing Rhythm and Pattern and Their Influence on Emotion https://doi.org/10.1146/annurev-neuro-090121-014424