Biology subjects

Kobayashi, R.

Publications and source records attributed to Kobayashi, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Engineering robust cardiomyocyte differentiation from iPSCs through WNT-mediated process window expansion

Lack of robustness and high variability in cardiomyocyte (CM) differentiation from human induced pluripotent stem cells (hiPSCs) remain critical challenges for cardiac regenerative medicine and biological research. Guided by developmental principles of lineage specification, we investigated whether early WNT inhibition could expand the process window of CM differentiation and thereby improve robustness. To test this, we compared early WNT inhibition from days 1--5 with standard inhibition from days 3--5 following a 1-day CHIR99021 (CHIR) treatment for WNT activation. Focusing on CHIR concentration as a critical parameter, we found that early WNT inhibition substantially broadened the concentration window yielding [≥]80% differentiation efficiency across distinct hiPSC lines. Extending the analysis to a two-dimensional parameter space incorporating cell density revealed a markedly expanded [≥]80% process window. Temporal analysis of lineage-specific transcription factor expression showed that early WNT inhibition suppressed paraxial mesoderm (PM) specification, likely through MSGN1 suppression, in the range of high initial WNT activation that otherwise favored PM fate, thereby extending the process window. It also suppressed definitive endoderm (DE) specification within the expanded window, promoting a more favorable lateral plate mesoderm/cardiac fate. We further demonstrated substantially reduced variability under parameter perturbations and across wells and batches, accompanied by higher differentiation efficiency, without compromising CM phenotypes. These findings demonstrate early WNT inhibition as an effective strategy for expanding the process window of CM differentiation and improving robustness, while exemplifying the process engineering principle that a broader window can support more robust differentiation, with potential relevance to stem cell--based bioprocesses.

bioengineering↗

bioRxiv2026

Engineering a highly active thermophilic F1-ATPase by homolog-guided exploration and machine-learning-assisted prioritization

The rotary motor F1-ATPase has been extensively studied as a model molecular machine, yet rational engineering of its catalytic activity remains challenging because ATP hydrolysis is regulated by long-range intersubunit allostery and large conformational transitions. Here, we developed a homolog-guided engineering strategy to increase the maximum rotation rate of the thermophilic Bacillus PS3 F1-ATPase (TF1). Candidate mutation sites were first identified by comparing TF1 with the homologous enzymes bovine mitochondrial F1 (bMF1) and Paracoccus denitrificans F1 (PdF1), both of which exhibit higher maximum rotation rates than TF1. Systematic exploration of these sites identified four activity-enhancing hotspots, followed by focused hotspot exploration and machine-learning-assisted prioritization of combinatorial mutants. The best mutant, TF1({beta}Y313L/{beta}E332S), exhibited a 1.8-fold higher maximum rotation rate than TF1(WT) while retaining its functional thermostability. Interestingly, activity-enhancing substitutions were not limited to the residues conserved in both bMF1 and PdF1, indicating that the bMF1-PdF1 consensus substitutions effectively identify activity-enhancing hotspots rather than uniquely defining the optimal amino acid. Machine-learning-assisted exploration efficiently prioritized highly active mutants, although the predictive performance was limited by the relatively small training dataset and epistatic interactions among mutations. Kinetic and structural comparisons further provided mechanistic insights into the enhanced catalytic activity of the engineered mutant. Together, these results establish a practical strategy for engineering complex molecular motors by combining homolog-guided hotspot identification with focused hotspot exploration.

biophysics↗

bioRxiv2026

In-Cell Protein Crystallization via a Locally Flexible 24-mer Assembly Precursor

In-cell protein crystallization (ICPC) produces ordered protein crystals within living cells, but the mechanisms used by proteins to acquire long-range crystalline order in the cellular environment remains poorly understood. Here, we define the assembly pathway of CipB, a crystalline inclusion protein from Photorhabdus luminescens. CipB crystals formed in cells dissolve under mild acidic conditions into a predominant 24-mer species, supporting a model in which an in-cell crystal is built from a discrete 24-mer assembly precursor rather than through direct packing of smaller oligomeric states. Structural analysis of recrystallized CipB shows that the same 24-mer architecture packs into a body-centered cubic lattice, consistent with the lattice observed for the in-cell crystals. Cryo-EM and molecular dynamics analyses indicate that the 24-mer assembly precursor preserves its overall architecture while retaining local conformational flexibility at the N-terminal and surface-loop regions. Mutation analyses further link the N-terminal region to the formation of the 24-mer precursor and surface residues to lattice assembly. These observations support a stepwise crystallization model in which N-terminal flexibility facilitates the formation of an assembly-competent 24-mer precursor, whereas defined hydrophobic surface contacts subsequently organize these precursors into a long-range-ordered lattice.

biophysics↗

bioRxiv2026

High-fat diet-induced obesity differentially alters circadian gene expression across peripheral tissues

Circadian rhythms regulate diverse physiological processes, including metabolism, and their disruption has been implicated in metabolic disorders such as obesity. However, the tissue-specific effects of obesity on peripheral circadian clocks remain incompletely understood. Here, we investigated the impact of high-fat diet (HFD)-induced obesity on circadian gene expression in skeletal muscle, liver, and white adipose tissue (WAT). Mice were fed either a regular diet (RD) or HFD for 6 weeks, followed by tissue collection at 4-hour intervals over a 24-hour period. Under RD conditions, key circadian regulators and their downstream targets exhibited robust 24-hour oscillations across all tissues. In contrast, HFD feeding induced distinct, tissue-specific alterations. In the liver, Per2, Dbp, and Rev-erb showed phase-advanced expression patterns, whereas in WAT, rhythmic expression was markedly attenuated. Notably, skeletal muscle largely preserved circadian gene expression patterns, indicating relative resistance to HFD-induced circadian disruption. In addition, HFD feeding altered metabolic gene expression in adipose tissue, characterized by reduced Pgc1 expression and increased Leptin expression. Together, these findings demonstrate that HFD-induced obesity differentially disrupts peripheral circadian clocks in a tissue-specific manner and highlight skeletal muscle as a relatively resilient tissue. These results provide insight into how circadian dysregulation contributes to metabolic abnormalities in obesity.

physiology↗

bioRxiv2025

Sequence-encoded conformational biases shape self-assembly modes of intrinsically disordered proteins

Self-assembly of intrinsically disordered proteins (IDPs) underlies cellular functions and disease pathogenesis. This process is mediated by two intermolecular interaction modes: transient point-to-point contacts described by the sticker-and-spacer framework, and persistent surface-to-surface contacts proposed in the cross-{beta} hypothesis. We investigated the molecular basis of these modes in the context of conformational biases, defined as sequence-encoded structural preferences of local segments. Using a five-residue model, we generated lag-series IDPs from the TIA-1 prion-like domain by systematically modulating conformational biases while preserving amino acid composition. The lag-series IDPs demonstrated distinct condensate properties and varying capacities for amyloid fibril formation. Their structural analyses revealed that strongly biased regions preferentially adopt extended structures, including {beta}-strands, and the spacing between these regions influences metastable {beta}-sheet formation. Our findings demonstrate that local conformational biases shape interaction modes of IDPs, thereby linking sequence to condensate properties and amyloid fibril formation. Significance StatementProteins fold into three-dimensional structures defined by their amino acid sequences. In contrast, intrinsically disordered proteins (IDPs) lack stable structures, yet their sequences encode unique self-assembly behaviors, including phase separation and amyloid fibril formation. Can such behaviors be explained within structure-based frameworks? Using a five-residue model, we showed that IDP sequences encode local structural preferences, termed conformational biases, within short segments. These biases determine whether segments engage in transient point-to-point interactions driving phase separation or persistent surface-to-surface interactions leading to amyloid fibril formation. By bridging sequence, structure, and interaction modes, our work provides a comprehensive mechanism for self-assembly and conceptual tools for understanding IDP-related biological functions and disease mechanisms.

biophysics↗

bioRxiv2025

Cell-Free Protein Crystallization Enables Rapid Structure Determination of Disaccharides and Trisaccharides Using Galectin-10 Crystals

It is critical to understand the conformational selection and dynamics of flexible saccharides via protein-ligand interactions in efforts to elucidate their biofunctional roles. Protein crystals can serve as scaffolds to immobilize small molecules, enabling structural and dynamic analysis of saccharides that are difficult to study by conventional approaches. However, constructing versatile scaffold crystals for high-throughput structural analysis remains challenging because this work involves laborious protein production and crystallization workflows. Here, we report rapid crystallization and structural analysis of saccharide-bound scaffolds by applying cell-free protein crystallization (CFPC) to galectin-10 (Gal-10), a lectin known to crystallize spontaneously in vivo. Using CFPC-generated Gal-10 crystals, we obtained the first atomic-resolution structures of melezitose, one of the trisaccharide, bound to the protein scaffold, revealing binding modes inaccessible by conventional approaches. Normalized B-factor analysis combined with molecular dynamics simulations reveals how the binding-site architecture modulates saccharide flexibility and immobilization. This platform can be extended to other flexible ligands and fragment-based screening.

biophysics↗

bioRxiv2025

Temporary parasitic ants modify nestmate discrimination patterns of host workers

Social insects rely on nestmate discrimination systems to maintain highly organized societies. Some social parasites can evade these systems to exploit their hosts. In this study, we report that the temporarily socially parasitic ant Lasius umbratus may modify the nestmate discrimination patterns of its host, L. japonicus. Aggression assays revealed that unparasitized hosts exhibited high aggression toward non-nestmate conspecifics and parasites. In contrast, parasitized hosts showed significantly lower aggression toward non-nestmate conspecifics and parasites, while maintaining considerable aggression toward a non-parasitic congener as a positive control. This suggests that parasites modify the nestmate discrimination patterns of the hosts rather than merely suppressing aggression. Furthermore, chemical analysis of cuticular hydrocarbons revealed that hosts from mixed-species colonies of hosts and parasites had profiles resembling those of unparasitized hosts, whereas parasites from mixed-species and parasite-only colonies showed distinct profiles. Notably, parasites from mixed-species colonies had hydrocarbon profiles resembling those of their hosts, indicating that L. umbratus employs chemical mimicry to alter host behaviour. Our findings shed light on the intricate strategies of social parasites and the behavioural and chemical mechanisms sustaining highly organized ant societies.

animal behavior and cognition↗

bioRxiv2024

Rotation-direction-dependent regulation of ATPase inhibitory factor 1 for mitochondrial ATP synthase from atomistic simulation

ATPase inhibitory factor 1 (IF1) is an endogenous regulatory protein for mitochondrial FoF1-ATP synthase. It blocks the catalysis and rotation of the F1 part by deeply inserting itself into the rotor-stator interface. Recent single-molecule manipulation experiments have elucidated that forcible rotations only in the ATP-synthesis direction eject IF1, rescuing F1 from the IF1-inhibited state. However, the molecular mechanism of the rotation-direction-dependent process at an atomic resolution is still elusive. Here, we have performed all-atom molecular dynamics (MD) simulations of the IF1-bound F1 structure with a torque applied to the rotor {gamma} subunit. In the torque-applying simulations, we first found that the core part of the {gamma} subunit rotated more in response to an external torque in the synthesis direction than in the hydrolysis direction. Further rotations of the {gamma} subunit up to 120{degrees} revealed that the conformational change of the IF1-bound {beta} was only allowed in the synthesis direction. Also, the 120{degrees} rotation in the synthesis direction disrupted its contacts with IF1, destabilizing the short helix of IF1. After additional rotation up to the synthetic 240{degrees} state, the closed-to-open conformational change of the IF1-bound {beta} subunit pulled IF1 outwardly, deforming the long helix of IF1. These stepwise destabilizations of the IF1 helices should be crucial for IF1 ejection. Our simulations also provided insight into the nullification mechanism of the hydrolytic rotation, highlighting the steric clash between F22 of IF1 and the {beta}TP subunit. Finally, we discussed a sufficient proton motive force to rescue FoF1-ATP synthase from the IF1-inhibited state. Significance statementFoF1-ATP synthase is crucial for cellular energy production. However, its reverse reaction as an ATPase can be harmful, particularly in mammalian cells. This study reveals how ATPase inhibitory factor 1 (IF1) controls the catalysis of mitochondrial ATP synthase and provides the atomic-level description of the rotation-direction-dependent regulation using molecular dynamics simulation. ATP-synthetic {gamma} rotation dissociates IF1 from the complex, thereby recovering active ATP synthesis. However, IF1 completely suppresses the {gamma} rotation through multiple mechanisms to prevent wasteful ATP consumption in ATP-hydrolysis mode. Our analysis also reveals that sufficient torque in the synthesis direction is required to rescue FoF1-ATP synthase from the IF1-inhibited state. These findings offer valuable insights for developing inhibitors by leveraging the structural and functional similarities with IF1.

biophysics↗

bioRxiv2024

Branched-chain amino acid metabolism is a crucial modulator of cellular senescence

Cellular senescence is a complex stress response that results in the permanent arrest of cell proliferation. The accumulation of senescent cells occurs during aging in living organisms, and contributes to tissue dysfunction. Although there are growing lines of evidence that various metabolic changes occur in senescent cells, the link between cellular metabolism and senescence is not yet fully understood. In this study, we demonstrate that alterations in the metabolism of branched-chain amino acids (BCAAs) play a crucial role in establishing cellular senescence. Furthermore, we identified mitochondrial BCAA transamination as a crucial step in this process. Our findings show that various types of cellular stress lead to a reduction in the expression of BCAA aminotransferase 2 (BCAT2), one of the BCAA catabolic enzymes, resulting in decreased catabolism of BCAAs and reduced synthesis of glutamate. The reduction of BCAA catabolites, together with the consequent limitation in glutathione production from glutamate, triggers cellular senescence. Furthermore, we demonstrate that a reduction in BCAT2 levels alone is sufficient to induce cellular senescence, both in cultured cells and in mice. Additionally, our results demonstrate that aging alters BCAA metabolism in both mice and humans. Our findings provide new insights into the metabolic mechanisms underlying cellular senescence, with a particular focus on the role of BCAAs.

cell biology↗

bioRxiv2024

Sleep homeostasis in lizards and the role of cortex

Although their phenotypes are diverse, slow-wave sleep (SWS) and rapid eye movement sleep (REMS) are the two primary components of electrophysiological sleep (e-sleep) in mammals and birds. Slow waves in the cortex not only characterize SWS but are also used as biological markers for sleep homeostasis, given their rebound after sleep deprivation (SD). Recently, it has been reported that the Australian dragon Pogona vitticeps exhibits two-stage sleep pattern in the dorsal ventricular ridge (DVR), which includes a homologue of the mammalian claustrum (CLA). It remains unclear whether reptilian e-sleep, which has been characterized by activity outside the cortex, compensates for sleep loss, as observed in mammals. We here report a significant rebound in the local field potential (LFP) after 7 hours of SD, during both SWS and REMS. Meanwhile, the cycle and mean bout length of SWS/REMS remained unaffected. We further investigated a possible role of the cortex in e-sleep regulation and homeostasis in Pogona and found that, although a corticotomy had no obvious effect on the LFP features investigated, it abolished LFP power rebound in the CLA/DVR after SD. These findings suggest that e-sleep homeostasis is a common feature in amniotes, and that cortex is involved in regulating activity rebounds in reptiles and mammals.

neuroscience↗

bioRxiv2024

Laminar endocytic machinery revealed by quantitative multiplexed super-resolution imaging

Super-resolution microscopy achieves a few nanometers resolution, but protein quantification and colocalization is limited by its labeling density. Here we present a method to map molecular complexes using the multiplexed data of IRIS super- resolution imaging. We developed antiserum-derived Fab IRIS probes for high- density labeling of endogenous targets, and image analysis, Protein Cluster coloring (PC-coloring), which employs pixel-based principal component analysis and clustering. PC-coloring was first used to map regions of distinct ratios of targets on the image. The molecular complex formation was then evaluated by correlation between all combinations of two proteins in each PC-colored region. We elucidate receptor recruitment and the complex formation in a clathrin-coated structure (CCS) which is pre-assembled prior to endocytosis. Upon EGF stimulation, EGFR-, EGFR-Grb2-complex- and Grb2-dominant regions lined up from the CCS rim. Along the interior of Grb2-dominant regions, Eps15, FCHo1/2 and intersectin-1 formed a complex with Grb2. The interior of Eps15-FCHo1/2 complexes was lined with Eps15-intersectin-1 complexes. The results reveal a laminar complex formation of EGFR, Grb2 and CCS components at the recruitment sites.

cell biology↗

bioRxiv2024

TAU FILAMENTS WITH THE CHRONIC TRAUMATIC ENCEPHALOPATHY FOLD IN A CASE OF VACUOLAR TAUOPATHY WITH VCP MUTATION D395G

Dominantly inherited mutation D395G in the gene encoding valosin-containing protein causes vacuolar tauopathy, a type of behavioural-variant frontotemporal dementia, with marked vacuolation and abundant filamentous tau inclusions made of all six brain isoforms. Here we report that tau inclusions were concentrated in layers II/III of the frontotemporal cortex in a case of vacuolar tauopathy. By electron cryo-microscopy, tau filaments had the chronic traumatic encephalopathy (CTE) fold. Tau inclusions of vacuolar tauopathy share this cortical location and the tau fold with CTE, subacute sclerosing panencephalitis and amyotrophic lateral sclerosis/parkinsonism-dementia complex, which are believed to be environmentally induced. Vacuolar tauopathy is the first inherited disease with the CTE tau fold.

neuroscience↗

bioRxiv2024

Induction of NASH and vacuolar structures in the Nwd1-/- mouse liver via SERCA2-dependent endoplasmic reticulum stress

The endoplasmic reticulum (ER) stores Ca2+ and plays crucial roles in protein folding, lipid transfer, and its perturbations trigger an ER stress. In the liver, chronic ER stress is involved in the pathogenesis of nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). Previous studies revealed that dysfunction of sarco/endoplasmic reticulum calcium ATPase (SERCA2), a key regulator of Ca2+ transport from the cytosol to the ER, is associated with the induction of ER stress and lipid droplet formation. We previously identified NACHT and WD repeat domain-containing protein 1 (Nwd1), which is localized in the ER and mitochondria. However, the physiological significance of Nwd1 outside the central nervous system remains unclear. In this study, we revealed that Nwd1 knockout mice exhibited pathological manifestations comparable to NASH. Nwd1 interacts with SERCA2 near ER membranes. Nwd1-/- livers exhibited reduced SERCA2 ATPase activity and a smaller Ca2+ pool in the ER, leading to an exacerbated state of ER stress. These findings highlight the importance of SERCA2 activity mediated by Nwd1 in the pathogenesis of NASH. HighlightsO_LINwd1-/- mice exhibited NASH-like liver steatosis. C_LIO_LIElevated ER stress, fibrosis, and pyroptosis were observed in Nwd1-/- livers. C_LIO_LINwd1 interacts with SERCA2, an ER membrane Ca2+ pump. C_LIO_LINwd1-/- livers exhibited reduced SERCA2 activity and smaller Ca2+ pools in the ER. C_LI

molecular biology↗

bioRxiv2023

High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization

Intrinsically disordered proteins (IDPs) play a crucial role in various biological phenomena, dynamically changing their conformations in response to external environmental cues. To gain a deeper understanding of these proteins, it is essential to identify the determinants that fix their structures at the atomic level. Here, we developed a pipeline for rapid crystal structure analysis of IDP using a cell-free protein crystallization (CFPC) method. Through this approach, we successfully demonstrated the determination of the structure of an IDP to uncover the key determinants that stabilize its conformation. Specifically, we focused on the 11-residue fragment of c-Myc, which forms an -helix through dimerization with a binding partner protein. This fragment was strategically fused with an in-cell crystallizing protein and was expressed in a cell-free system. The resulting crystal structures of the c-Myc fragment were successfully determined at a resolution of 1.92 [A] and we confirmed that they are identical to the structures of the complex with the native binding partner protein. This indicates that the environment of the scaffold crystal can fix the structure of c-Myc. Significantly, these crystals were obtained directly from a small reaction mixture (30 L) incubated for only 72 hours. Analysis of 8 crystal structures derived from 22 mutants revealed two hydrophobic residues as the key determinants responsible for stabilizing the -helical structure. These findings underscore the power of our CFPC screening method as a valuable tool for determining the structures of challenging target proteins and elucidating the essential molecular interactions that govern their stability.

biophysics↗

bioRxiv2023

Fibroblast Nrf2 inhibits profibrotic transcription with Ddx54 and mitigates pathological fibrosis in the mouse heart and kidney

BackgroundTissue fibrosis is a common feature of many organ dysfunctions, such as heart failure and chronic kidney disease. However, no fundamental treatment has been developed. This study aims to identify novel molecular mechanisms for antifibrotic intervention, focusing on fibroblast activation. MethodsWe performed a forward genetic screen using a genome-wide CRISPR library in the context of transforming growth factor {beta} (TGF-{beta})-mediated connective tissue growth factor (CTGF) expression, and used unbiased techniques such as Cleavage Under Targets and Tagmentation (CUT&Tag) and proximity-dependent biotin labeling by TurboID to reveal the detailed molecular mechanisms. ResultsCRISPR library screening identified a number of players in both the canonical Smad pathway and the non-canonical pathway. In addition to the known factors, the Keap1-Nrf2 pathway was identified as a predominant regulator of TGF-{beta}-mediated CTGF expression. Keap1 deletion and consequent Nrf2 activation broadly suppressed profibrotic gene expression, independently of conventional antioxidant effects. CUT&Tag revealed that Nrf2 bound to the proximity of fibrosis-related genes including Ctgf and Fn1. Subsequent individual analysis revealed Smad3 and RNA polymerase II binding to the Nrf2 peak site, which was attenuated by Keap1 deletion. TurboID experiments further discovered that Nrf2 interacts with Ddx54, which acts as a corepressor. Consistently, Keap1 deletion-mediated repression of profibrotic gene expression was reversed by additional Ddx54 deletion. The impact of the Keap1-Nrf2 pathway on pathological fibrosis was examined using tamoxifen-inducible fibroblast-specific Keap1 knockout mice. Pressure overload for 4 weeks robustly induced cardiac hypertrophy, fibrosis and contractile dysfunction. However, deletion of Keap1 in the Postn lineage attenuated these cardiac pathologies. The anti-fibrotic effects of Keap1 deletion were also confirmed in renal fibrosis in the unilateral ureteral obstruction (UUO) model. ConclusionsFibroblast Nrf2 transcriptionally represses fibrosis-related genes in cooperation with the corepressor Ddx54. Fibroblast-specific deletion of Keap1 attenuated pathological fibrosis in pressure overload heart failure and renal fibrosis.

cell biology↗

bioRxiv2023

Integration of shoot-derived polypeptide signals by root TGA transcription factors is essential for survival under fluctuating nitrogen environments

Unlike plants in the field, which experience significant temporal fluctuations in environmental conditions, plants in the laboratory are typically grown in controlled, stable environments. Therefore, signaling pathways evolved for survival in continuously fluctuating environments often remain functionally latent in laboratory settings. Here, we show that TGA1 and TGA4 act as hub transcription factors through which the expression of genes involved in high-affinity nitrate uptake are regulated in response to shoot-derived phloem mobile polypeptides, CEP DOWNSTREAM 1 (CEPD1), CEPD2 and CEPD-like 2 (CEPDL2) as nitrogen (N) deficiency signals, and Glutaredoxin S1 (GrxS1) to GrxS8 as N sufficiency signals. CEPD1/2/CEPDL2 and GrxS1-S8 competitively bind to TGA1/4 in roots, with the former acting as transcription coactivators that enhance the uptake of nitrate, while the latter function as corepressor complexes together with TOPLESS to limit nitrate uptake. Arabidopsis plants deficient in TGA1/4 maintain basal nitrate uptake and exhibit growth similar to wild-type plants in a stable N environment, but were impaired in regulation of nitrate acquisition in response to shoot N demand, leading to defective growth under continuously fluctuating N environments where rhizosphere nitrate ions switch periodically between deficient and sufficient states. TGA1/4 are crucial transcription factors that enable plants to survive under fluctuating and challenging N environmental conditions.

plant biology↗

bioRxiv2023

Statistical mining of triple-negative breast cancer-specific nanobodies among huge libraries from immunized alpacas

Breast cancer can be classified into several types according to the expression patterns of human epidermal growth factor receptor 2 (Her2), oestrogen receptor (ER), and progesterone receptor (PgR) proteins. The prognosis of patients with tumors showing low Her2 expression and no ER and PgR expression--categorized as triple-negative breast cancer (TNBC)--is worst among these groups. Due to the lack of specific antibodies for TNBC, curative treatments for TNBC remain limited. Antibodies targeting TNBC have potential as diagnostic and therapeutic tools. Here, we generate a panel of nanobodies targeting TNBC cell lines by immunizing alpacas and subsequently panning the resulting phage libraries with TNBC cell lines. We show that several clones exclusively stain Her2-negative cells in tissues of breast cancer patients, and a few clones stain both Her2-positive and Her2-negative regions in these tissues. These clones can be applied to patient-specific therapies using drug-conjugated antibodies, radiolabelled antibodies, chimaera antigen receptor T cells, or drug delivery components, as well as to TNBC diagnosis.

cancer biology↗

bioRxiv2021

Theoretical investigation of active listening behavior based on the echolocation of CF-FM bats

Bats perceive the three-dimensional (3D) environment by emitting ultrasound pulses from their nose or mouth and receiving echoes through both ears. To detect the position of a target object, it is necessary to know the distance and direction of the target. Certain bat species synchronize the movement of their pinnae with pulse emission, and it is this behavior that enables 3D direction detection. However, the significance of bats ear motions remains unclear. In this study, we construct a model of an active listening system including the motion of the ears, and conduct mathematical investigations to clarify the importance of ear motion in 3D direction detection. The theory suggests that only certain ear motions, namely three-axis rotation, accomplish accurate and robust 3D direction detection. Our theoretical analysis also strongly supports the behavior whereby bats move their pinnae in the antiphase mode. In addition, we provide the conditions for ear motions to ensure accurate and robust direction detection, suggesting that simple shaped hearing directionality and well-selected uncomplicated ear motions are sufficient to achieve precise and robust 3D direction detection. Our findings and mathematical approach have the potential to be used in the design of active sensing systems in various engineering fields. Author SummaryMany mammals use visual sensing for primary perception of their surroundings, whereas bats accomplish spatial perception by active acoustic sensing. In particular, by emitting ultrasound pulses and listening to the echoes, bats localize reflective objects, a process known as echolocation. Certain bat species move both of their ears while receiving the echoes, but the essential theory behind this ear movement remains unclear. This paper describes a simple mathematical model for investigating the active listening strategy employed by bats. The theory suggests that the ear motions employed by bats enables highly accurate direction detection that is robust to observation errors. In addition, we determine what kind of ear motions are optimal for 3D direction detection. This study not only reveals the significance of pinnae motions in bats, but also opens up the possibility of engineering applications for active listening systems.

animal behavior and cognition↗