Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial cell fate manipulation of human pluripotent stem cells by controlling the microenvironment using photocurable hydrogel

Human pluripotent stem cells (hPSCs) dynamically respond to their chemical and physical microenvironment, dictating their behavior. However, conventional in vitro studies predominantly employ plastic culture wares, which offer a simplified representation of the in vivo microenvironment. Emerging evidence underscores the pivotal role of mechanical and topological cues in hPSC differentiation and maintenance. In this study, we cultured hPSCs on hydrogel substrates with spatially controlled stiffness. The use of culture substrates that enable precise manipulation of spatial mechanical properties holds promise for better mimicking in vivo conditions and advancing tissue engineering techniques. We designed a photocurable polyethylene glycol–polyvinyl alcohol (PVA-PEG) hydrogel, allowing for spatial control of surface stiffness and geometry at a micrometer scale. This versatile hydrogel can be functionalized with various extracellular matrix (ECM) proteins. Laminin 511-functionalized PVA-PEG gel effectively supports the growth and differentiation of hPSCs. Moreover, by spatially modulating the stiffness of the patterned gel, we achieved spatially selective cell differentiation, resulting in the generation of intricate, patterned structures. Summary statement A new hydrogel substrate enables spatial control of surface stiffness at the micrometer level, enabling local differentiation of hPSC and facilitating complex pattern formation.
On the Reliability of Wearable Technology: A Tutorial on Measuring Heart Rate and Heart Rate Variability in the Wild

Wearable sensors are quickly making their way into psychophysiological research, as they allow collecting longitudinal and ecologically valid data. The present tutorial considers fidelity of physiological measurement with wearable sensors, focusing on reliability. We elaborate why ensuring reliability for wearables is important and offer statistical tools for assessing wearable reliability for between participants and within-participant designs. The framework offered here is illustrated using several brands of commercially available heart rate sensors. Our hope is that by systematically quantifying measurement reliability, researchers will be able to make informed choices about specific wearable devices and measurement procedures that meet their research goals.
What moves when mice move a single whisker to touch? Individuality and stereotypy in behavior

A key function of the brain is to move the body through a rich, complex environment. When rodents engage their environment, they move their whiskers as they extract tactile information. Even though the study of whisking has a long history, the details of what mice move when they move a whisker actively to touch are still unknown. Here we trained head fixed mice in a simple go-cue task to move a whisker on one side of the face to touch a sensor and tracked facial movements. Our analysis shows that mice specifically control the movement of the whisker they use to touch and that as they move their whiskers, they move their nose and apply forces on the head-post in a manner that reflects the behavioral epoch. Importantly, mice controlled the setpoint, amplitude and frequency of movement of whiskers bilaterally and individually. Additionally, even though mice achieved the goal of the task -- to touch the sensor within 2 seconds -- how they did so, how they coordinated movement of the nose and forces on head post with movement of individual whiskers was stereotyped, specific and related to the distance they needed to move a whisker to touch the sensor. Our work shows how stereotyped mouse behavior can be, and it emphasizes both the level of fine motor control mice can exert over individual whiskers and the extent of facial movements in a goal directed whisking-to-touch task.
Midbody proteins display distinct temporal dynamics during cytokinesis

The midbody is an organelle that forms between the two daughter cells during cytokinesis. It co-ordinates the abscission of the nascent daughter cells and is composed of a multitude of proteins that are meticulously arranged into distinct temporal and spatial localization patterns. However, very little is known about the mechanisms that regulate the localization and function of midbody proteins. Here, we analyzed the temporal and spatial profiles of key midbody proteins during mitotic exit under normal conditions and after treatment with drugs that affect phosphorylation and proteasome-mediated degradation to decipher the impacts of post-translational modifications on midbody protein dynamics. Our results highlighted that midbody proteins show distinct spatio-temporal dynamics during mitotic exit and cytokinesis that depend on both ubiquitin-mediated proteasome degradation and phosphorylation/de-phosphorylation. They also identified two discrete classes of midbody proteins: ‘transient’ midbody proteins - including Anillin, Aurora B and PRC1- which rapidly accumulate at the midbody after anaphase onset and then slowly disappear, and ‘stable’ midbody proteins - including CIT-K, KIF14 and KIF23- which instead persist at the midbody throughout cytokinesis and also post abscission. These two classes of midbody proteins display distinct interaction networks with ubiquitylation factors, which could potentially explain their different dynamics and stability during cytokinesis.
Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates

Differentiation of B cells into antibody-secreting cells (ASCs) is a key process to generate protective humoral immunity. A detailed understanding of the cues controlling ASC differentiation is important to devise strategies to modulate antibody formation. Here, we dissected differentiation trajectories of human naive B cells into ASCs using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from an in vitro model with ex vivo B cells and ASCs, we uncovered a novel pre-ASC population present ex vivo in lymphoid tissues. For the first time, a germinal-center-like population is identified in vitro from human naive B cells and possibly progresses into a memory B cell population through an alternative route of differentiation, thus recapitulating in vivo human GC reactions. Our work allows further detailed characterization of human B cell differentiation into ASCs or memory B cells in both healthy and diseased conditions.
BK channels of five different subunit combinations underlie the de novo KCNMA1 G375R channelopathy

The molecular basis of a severe developmental and neurological disorder associated with a de novo G375R variant of the tetrameric BK channel is unknown. Here we address this question by recording from single BK channels expressed for a heterozygous G375R mutation. Five different types of functional BK channels were observed: 3% were WT, 12% were homomeric mutant, and 85% were three different types of hybrid channels. All channel types except WT showed a marked gain-of-function in voltage activation and a smaller loss-of-function in single channel conductance, with both becoming more pronounced as the number of mutant subunits per tetrameric channel increased. The molecular phenotype suggested codominance for the two homomeric channels and partial dominance for the hybrid channels. A model in which BK channels are randomly assembled from mutant and WT subunits, with each subunit contributing increments of activation and conductance, approximated the molecular phenotype of the heterozygous G375R mutation.
Functional genomics of cattle through integration of multi-omics data

Functional annotation of the bovine genome was performed by characterizing the spectrum of RNA transcription using a multi-omics approach, combining long- and short-read transcript sequencing and orthogonal data to identify promoters and enhancers and to determine boundaries of open chromatin. A total number of 171,985 unique transcripts (50% protein-coding) representing 35,150 unique genes (64% protein-coding) were identified across tissues. Among them, 159,033 transcripts (92% of the total) were structurally validated by independent datasets such as PacBio Iso-seq, ONT-seq, de novo assembled transcripts from RNA-seq, or Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive independent data from different technologies such as WTTS-seq, RAMPAGE, ChIP-seq, and ATAC-seq. A large proportion of identified transcripts (69%) were novel, of which 87% were produced by known genes and 13% by novel genes. A median of two 5’ untranslated regions was detected per gene, an increase from Ensembl and NCBI annotations (single). Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as non-coding genes in fetal tissues, but as protein coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 known gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available QTL data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. These validated results show significant improvement over current bovine genome annotations.
Atypical peripheral actin band formation via overactivation of RhoA and nonmuscle myosin II in mitofusin 2-deficient cells

Cell spreading and migration play central roles in many physiological and pathophysiological processes. We have previously shown that MFN2 regulates the migration of human neutrophillike cells via suppressing Rac activation. Here, we show that in mouse embryonic fibroblasts, MFN2 suppresses RhoA activation and supports cell polarization. After the initial spreading period, the wild-type cells polarize and migrate, whereas the Mfn2-/- cells maintain a circular shape. Increased cytosolic Ca2+ resulting from the loss of Mfn2 is directly responsible for this phenotype, which can be rescued by expressing an artificial tether to bring mitochondria and ER to close vicinity. Elevated cytosolic Ca2+ activates Ca2+/calmodulin-dependent protein kinase II, RhoA, and Myosin light-chain kinase, causing an over-activation of non-muscle myosin II and a formation of a prominent F-actin ring at the cell periphery and increased cell contractility. The formation of the peripheral actin band alters cell physics and is dependent on substrate rigidity. Our results provide a novel molecular basis to understand how MFN2 regulates distinct signaling pathways in different cells and tissue environments, which is instrumental in understanding and treating MFN2-related diseases.
Heterosynaptic Plasticity of the Visuo-auditory Projection Requires Cholecystokinin released from Entorhinal Cortex Afferents

The entorhinal cortex is involved in establishing enduring visuo-auditory associative memory in the neocortex. Here we explored the mechanisms underlying this synaptic plasticity related to projections from the visual and entorhinal cortices to the auditory cortex, using optogenetics of dual pathways. High-frequency laser stimulation (HFLS) of the visuo-auditory projection did not induce long-term potentiation (LTP). However, after pairing with sound stimulus, the visuo-auditory inputs were potentiated following either infusion of cholecystokinin (CCK) or HFLS of the entorhino-auditory CCK-expressing projection. Combining retrograde tracing and RNAscope in situ hybridization, we show that CCK expression is higher in entorhinal cortex neurons projecting to the auditory cortex than in those originating from the visual cortex. In the presence of CCK, potentiation in the neocortex occurred when the pre-synaptic input arrived 200 ms before post-synaptic firing, even after just five trials of pairing. Behaviorally, inhibition of CCK signaling blocked the generation of associative memory. Our results indicate that neocortical visuo-auditory association is formed through heterosynaptic plasticity, which depends on release of CCK in the neocortex mostly from entorhinal afferents.
A graph-matching based metric of functional connectome distance between pairs of individuals varies with their ages, cognitive performances and familial relationships

Functional connectomes (FCs), represented by networks or graphs that summarize coactivation patterns between pairs of brain regions, have been related at a population level to age, sex, cognitive/behavioral scores, life experience, genetics and disease/disorders. However, quantifying FC differences between pairs of individuals also provides a rich source of information with which to map to differences in those individuals’ biology, experience, genetics or behavior. In this study, graph matching is used to create a novel inter-individual FC metric, called swap distance, that quantifies the distance between pairs of individuals’ FCs. We apply graph matching to align FCs between pairs of individuals from the the Human Connectome Project (N = 997) and find that swap distance i) increases with increasing familial distance, ii) increases with subjects’ ages, iii) is smaller for pairs of females compared to pairs of males, and iv) is larger for females with lower cognitive scores compared to females with larger cognitive scores. Regions that contributed most to individuals’ swap distances were in higher-order networks, i.e. default-mode and fronto-parietal, that underlie executive function and memory. These higher-order networks’ regions also had swap frequencies that varied monotonically with familial relatedness of the individuals in question. We posit that the proposed graph matching technique provides a novel way to study inter-subject differences in FC and enables quantification of how FC may vary with age, relatedness, sex and behavior.
Enhanced charge stripe order of superconducting La(2-x)Ba(x)CuO(4) in a magnetic field

The effect of a magnetic field on the charge stripe order in La(2-x)Ba(x)CuO(4) has been studied by means of high energy (100 keV) x-ray diffraction for charge carrier concentrations ranging from strongly underdoped to optimally doped. We find that charge stripe order can be significantly enhanced by a magnetic field applied along the c-axis, but only at temperatures and dopings where it coexists with bulk superconductivity at zero field. The field also increases stripe correlations between the planes, which can result in an enhanced frustration of the interlayer Josephson coupling. Close to the famous x=1/8 compound, where zero field stripe order is pronounced and bulk superconductivity is suppressed, charge stripe order is independent of a magnetic field. The results imply that static stripe order and three-dimensionally coherent superconductivity are competing ground states.
Atypical NMDA Receptors Limit Synaptic Plasticity in the Adult Ventral Hippocampus

N-methyl-D-aspartate receptors (NMDARs) assemble as functionally diverse heterotetramers. Incorporation of the GluN3A subunit into NMDARs alters conventional NMDAR properties by reducing both magnesium sensitivity and calcium permeability. GluN1 together with GluN3A can also form functional receptors that lack a glutamate binding site and instead serve as excitatory glycine receptors (eGlyRs). GluN3A expression is high in early development but naturally declines to low levels in most brain regions by adulthood. Interestingly, GluN3A expression remains elevated in the CA1 of the adult ventral hippocampus (VH), but not in the dorsal hippocampus (DH). The DH and VH are now well-understood to play very different functional roles, with the DH being primarily involved in cognitive functions and the VH in emotional processing. Why GluN3A persists in the adult VH, and the impact its presence has on glutamatergic neurotransmission in the VH is currently unknown. Here, we show that GluN3A remains elevated both at synaptic and extrasynaptic locations in the adult VH, assembling as GluN1/GluN2/GluN3A NMDARs with reduced magnesium sensitivity, as well as GluN1/GluN3A eGlyRs. By comparing various synaptic properties in the DH and VH of wild-type (WT) and GluN3A knockout (KO) mice, we demonstrate that GluN3A persistence in the VH attenuates glutamate release, limits postsynaptic calcium influx through NMDARs, and reduces the magnitude of NMDAR-dependent long-term potentiation. In comparison, GluN3A KO had relatively little effect on these same properties in the DH. In all, our data demonstrate that GluN3A persistence in the VH represents a key modulator of VH excitability and therefore may play a central role in emotional processing.
Insect homolog of oxytocin/vasopressin associated with parenting of males but not females in a subsocial beetle

Parental care is thought to evolve through modification of behavioral precursors, which predicts that the mechanistic changes occur in the genes underlying those traits. The duplicated gene system of oxytocin/vasopressin has been broadly co-opted across vertebrates to influence parenting, from a pre-duplication ancestral role in water balance. It remains unclear whether co-option of these genes for parenting is limited to vertebrates. Here, we experimentally tested for associations between inotocin gene expression and water balance, parental acceptance of offspring, and active parenting in the subsocial beetle Nicrophorus orbicollis, to test whether a single copy homologue, inotocin, has similarly been co-opted for parental care in a species with elaborate parenting. As expected, inotocin was associated with water balance in both sexes. Inotocin expression increased around sexual maturation in both males and females, although more clearly in males. Finally, we found that expression of inotocin was not associated with acceptance of larvae but was associated with a transition to male but not female parenting. Moreover, level of offspring provisioning behavior and gene expression were positively correlated in males but uncorrelated in females. Our results suggest a broad co-option of this system for parenting that may have existed prior to gene duplication, and that inotocin may be associated with flexibility in parenting behavior. Impact Summary Oxytocin/vasopressin are amongst the most studied neuropeptides in vertebrates, influencing water balance, mating interactions, and most notably, social bonding. This gene pair evolved from a duplication in the vertebrate lineage of an ancestral vasopressin-like gene. Are the multiple social effects in vertebrates due to this duplication, or are social influences also ancestral? Here, we demonstrate that, in a biparental social beetle with a single copy, inotocin is associated with social interactions between fathers and offspring as well as being associated with the ancestral role of water balance in both males and females. In vertebrates, both oxytocin and vasopressin have been shown to impact social interactions in both sexes, although often showing sex-specificity in their action within species. Our results suggest that this system may have been co-opted for parenting prior to gene duplication and may facilitate flexibility in caring behavior.
Myosin-binding protein C stabilizes, but is not the sole determinant of SRX myosin in cardiac muscle

The myosin Super Relaxed (SRX) state is central to striated muscle metabolic and functional regulation. In skeletal muscle, SRX myosin are predominantly colocalized with Myosin-Binding Protein C (MyBP-C) in the C-zone, proximal to the sarcomere center. To define how MyBP-C and its specific domains contribute to stabilizing the SRX state in cardiac muscle, we took advantage of transgenic MyBP-C null mice and those expressing MyBP-C with a 271 residue N-terminal truncation. Utilizing super-resolution microscopy, we determined the lifetime and sub-sarcomeric location of individual fluorescent-ATP turnover events within isolated cardiac myofibrils. The proportion of SRX myosin was highest in the C-zone (71±6%) and lower in the D-zone (45±10%) which lies farther from the sarcomere center and lacks MyBP-C, suggesting a possible role for MyBP-C in stabilizing the SRX state within the C-zone. However, myofibrils from MyBP-C null mice demonstrated an ~40% SRX reduction, not only within the now MyBP-C-free C-zone (49±9% SRX), but also within the D-zone (22±5% SRX). These data suggest that the influence of MyBP-C on the SRX state is not limited to the C-zone, but extends along the thick filament. Interestingly, myofibrils with N-terminal truncated MyBP-C had an SRX content and spatial gradient similar to the MyBP-C null, indicating that the N terminus of cardiac MyBP-C is necessary for MyBP-C’s role in establishing SRX along the entire thick filament. Given that SRX myosin are enriched in the C-zone, even in the absence of MyBP-C or its N-terminus, an inherent bias must exist in the structure of the thick filament to stabilize the SRX state. One candidate may be a differential in the super repeats of titin that interact with MyBP-C and myosin and which template the thick filament.
Tunable image-mapping optical coherence tomography

We present tunable image-mapping optical coherence tomography (TIM-OCT), which can provide optimized imaging performance for a given application by using a programmable phase-only spatial light modulator in a low-coherence full-field spectral-domain interferometer. The resultant system can provide either a high lateral resolution or a high axial resolution in a snapshot without moving parts. Alternatively, the system can achieve a high resolution along all dimensions through a multiple-shot acquisition. We evaluated TIM-OCT in imaging both standard targets and biological samples. Additionally, we demonstrated the integration of TIM-OCT with computational adaptive optics in correcting sample-induced optical aberrations.
A novel nuclease is the executing part of a bacterial plasmid defense system

Cells are continuously facing the risk of taking up foreign DNA that can compromise genomic and cellular integrity. Therefore, bacteria are in a constant arms race with mobile genetic elements such as phages, transposons and plasmids. They have developed several active strategies against invading DNA molecules that can be seen as a bacterial ‘innate immune system’. Anti-phage systems are usually organized in ‘defense islands’ and can consist of restriction-modification (R-M) systems, CRISPR-Cas, and abortive infection (Abi) systems. Despite recent advances in the field, much less is known about plasmid defense systems. We have recently identified the MksBEFG system in Corynebacterium glutamicum as a novel plasmid defense system which comprises homologues of the condensin system MukFEB. Here, we investigated the molecular arrangement of the MksBEFG complex. Importantly, we identified MksG as a novel nuclease that degrades plasmid DNA and is, thus, the executing part of the system. The crystal structure of MksG revealed a dimeric assembly through its DUF2220 C-terminal domains. This domain is homologous to the TOPRIM domain of the topoisomerase II family of enzymes and contains the corresponding divalent ion binding site that is essential for DNA cleavage in topoisomerases, explaining the in vitro nuclease activity of MksG. We further show that the MksBEF subunits exhibit an ATPase cycle similar to MukBEF in vitro and we reason that this reaction cycle, in combination with the nuclease activity provided by MksG, allows for processive degradation of invading plasmids. Super-resolution localization microscopy revealed that the Mks system is spatially regulated via to the polar scaffold protein DivIVA. Introduction of plasmids increases the diffusion rate and alters the localization of MksG, indicating an activation of the system in vivo.