Miracle-dz/UniFAR-FTUs huggingface dataset:
Ndel1 modulates dynein activation in two distinct ways

Dynein is the primary minus-end-directed microtubule motor [1]. To achieve activation, dynein binds to the dynactin complex and an adaptor to form the “activated dynein complex” [2, 3]. The protein Lis1 aids activation by binding to dynein and promoting its association with dynactin and adaptor [4, 5]. Ndel1 and its orthologue Nde1 are dynein and Lis1 binding proteins that help control where dynein localizes within the cell [6]. Cell-based assays suggest that Ndel1/Nde1 also work with Lis1 to promote dynein activation, although the underlying mechanism is unclear [6]. Using purified proteins and quantitative binding assays, we found that Ndel1’s C-terminal region contributes to binding to dynein and negatively regulates binding to Lis1. Using single-molecule imaging and protein biochemistry, we observed that Ndel1 inhibits dynein activation in two distinct ways. First, Ndel1 disfavors the formation of the activated dynein complex. We found that phosphomimetic mutations in Ndel1’s C-terminal domain increase its ability to inhibit dynein-dynactin-adaptor complex formation. Second, we observed that Ndel1 interacts with dynein and Lis1 simultaneously and sequesters Lis1 away from its dynein binding site. In doing this, Ndel1 prevents Lis1-mediated dynein activation. Our work suggests that in vitro, Ndel1 is a negative regulator of dynein activation, which contrasts with cellular studies where Ndel1 promotes dynein activity. To reconcile our findings with previous work, we posit that Ndel1 functions to scaffold dynein and Lis1 together while keeping dynein in an inhibited state. We speculate that Ndel1 release can be triggered in cellular settings to allow for timed dynein activation.
Rescue of Normal Excitability in LGI1-Deficient Epileptic Neurons

Leucine-rich glioma inactivated 1 (LGI1) is a glycoprotein secreted by neurons, the deletion of which leads to autosomal dominant lateral temporal lobe epilepsy. We previously showed that LGI1 deficiency in a mouse model (i.e., knock-out for LGI1 or KO-Lgi1) decreased Kv1.1 channel density at the axon initial segment (AIS) and at presynaptic terminals, thus enhancing both intrinsic excitability and glutamate release. However, it is not known whether normal excitability can be restored in epileptic neurons. Here, we show that the selective expression of LGI1 in KO-Lgi1 neurons from mice of both sexes, using single-cell electroporation, reduces intrinsic excitability and restores both the Kv1.1-mediated D-type current and Kv1.1 channels at the AIS. In addition, we show that the homeostatic-like shortening of the AIS length observed in KO-Lgi1 neurons is prevented in neurons electroporated with the Lgi1 gene. Furthermore, we reveal a spatial gradient of intrinsic excitability that is centered on the electroporated neuron. We conclude that expression of LGI1 restores normal excitability through functional Kv1 channels at the AIS. SIGNIFICANCE STATEMENT The lack of leucine-rich glioma inactivated 1 (LGI1) protein induces severe epileptic seizures that leads to death. Enhanced intrinsic and synaptic excitation in KO-Lgi1 mice is because of the decrease in Kv1.1 channels in CA3 neurons. However, the conditions to restore normal excitability profile in epileptic neurons remain to be defined. We show here that the expression of LGI1 in KO-Lgi1 neurons in single neurons reduces intrinsic excitability, and restores both the Kv1.1-mediated D-type current and Kv1.1 channels at the axon initial segment (AIS). Furthermore, the homeostatic shortening of the AIS length observed in KO-Lgi1 neurons is prevented in neurons in which the Lgi1 gene has been rescued. We conclude that LGI1 constitutes a critical factor to restore normal excitability in epileptic neurons.
PI(3,5)P2 Controls the Signaling Activity of Class I PI3K

3’-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Generation of 3’-phosphoinositides are driven by three families of phosphoinositide 3-kinases (PI3K) but the mechanisms underlying their regulation and cross-talk are not fully understood. Among 3’-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) remains the least understood species in terms of its spatiotemporal dynamics and physiological function due to the lack of specific probes. By means of spatiotemporally resolved in situ quantitative imaging of PI(3,5)P2 using a newly developed ratiometric PI(3,5)P2 sensor we demonstrate that a special pool of PI(3,5)P2 is generated on lysosomes and late endosomes in response to growth factor stimulation. This PI(3,5)P2 pool, the formation of which is mediated by Class II PI3KC2β and PIKFyve, plays a crucial role in terminating the activity of growth factor-stimulated Class I PI3K, one of the most frequently mutated proteins in cancer, via specific interaction with its regulatory p85 subunit. Cancer-causing mutations of Class I PI3K inhibit the p85-PI(3,5)P2 interaction and thereby induce sustained activation of Class I PI3K. Our results unravel a hitherto unknown tight regulatory interplay between Class I and II PI3Ks mediated by PI(3,5)P2, which may be important for controlling the strength of PI3K-mediated growth factor signaling. These results also suggest a new therapeutic possibility of treating cancer patients with p85 mutations.
A fundamental law underlying predictive remapping

Predictive remapping (R) — the ability of cells in retinotopic brain structures to transiently exhibit spatiotemporal shifts beyond the spatial extent of their classical anatomical receptive fields — has been proposed as a primary mechanism that stabilizes an organism’s percept of the visual world around the time of a saccadic eye movement. Despite the well-documented effects of R, a biologically plausible mathematical abstraction that specifies a fundamental law and the functional architecture that actively mediates this ubiquitous phenomenon does not exist. I introduce the Newtonian model of R, where each modular component of R manifests as three temporally overlapping forces - a centripetal , convergent and translational force , that perturb retinotopic cells from their equilibrium extent. The resultant and transient influences of these forces gives rise to a neuronal force field that governs the spatiotemporal dynamics of R. This neuronal force field fundamentally obeys an inverse-distance law, akin to Newton’s law of universal gravitation [1] and activates retinotopic elastic fields (elφs). I posit that elφs are transient functional structures that are self-generated by a visual system during active vision and approximate the sloppiness (or degrees of spatial freedom) within which receptive fields are allowed to shift while ensuring that retinotopic organization does not collapse. The predictions of the proposed general model are borne out by the spatiotemporal changes in sensitivity to probe stimuli in human subjects around the time of a saccadic eye movement and qualitatively match neural signatures associated with predictive shifts in the receptive fields of cells in premotor and higher-order retinotopic brain structures.
The infectious salmon anemia virus esterase prunes erythrocyte surfaces in infected Atlantic salmon and exposes terminal sialic acids to lectin recognition

Many sialic acid-binding viruses express a receptor-destroying enzyme (RDE) that removes the virus-targeted receptor and limits viral interactions with the host cell surface. Despite a growing appreciation of how the viral RDE promotes viral fitness, little is known about its direct effects on the host. Infectious salmon anaemia virus (ISAV) attaches to 4-O-acetylated sialic acids on the surface of Atlantic salmon epithelial, endothelial, and red blood cells. ISAV receptor binding and destruction are effectuated by the same surface molecule, the haemagglutinin esterase (HE). We recently discovered a global loss of vascular 4-O-acetylated sialic acids in ISAV-infected fish. The loss correlated with the expression of viral proteins, giving rise to the hypothesis that it was mediated by the HE. Here, we report that the capacity to bind new ISAV particles is also progressively lost from circulating erythrocytes in infected fish. Furthermore, salmon erythrocytes exposed to ISAV ex vivo lost their capacity to bind new ISAV particles. The loss of ISAV binding was not associated with receptor saturation. Moreover, upon loss of the ISAV receptor, erythrocyte surfaces became more available to the lectin wheat germ agglutinin, suggesting a potential to alter interactions with endogenous lectins of similar specificity. The pruning of erythrocyte surfaces was inhibited by an antibody that prevented ISAV attachment. Furthermore, recombinant HE, but not an esterase-silenced mutant, was sufficient to induce the observed surface modulation. Our results directly link the ISAV-induced erythrocyte modulation to the hydrolytic activity of the HE and show that the observed effects are not mediated by endogenous esterases. Our findings are the first to directly link a viral esterase to extensive host cell surface modulation in infected individuals. This raises the question of how common the phenomenon is among sialic acid-binding viruses. It is also relevant to ask if the altered sialic acid landscape of the affected cells influences host biological functions with relevance to viral disease.
Selective recruitment: Evidence for task-dependent gating of inputs to the cerebellum

fMRI studies have documented cerebellar activity across a wide array of tasks. However, the functional contribution of the cerebellum within these task domains remains unclear because cerebellar activity is often studied in isolation. This is problematic, as cerebellar fMRI activity may simply reflect the transmission of neocortical activity through fixed connections. Here we present a new approach that addresses this problem. Rather than focus on task-dependent activity changes in the cerebellum alone, we ask if neocortical inputs to the cerebellum are gated in a task-dependent manner. We hypothesize that input is upregulated when the cerebellum functionally contributes to a task. We first validated this approach using a finger movement task, where the integrity of the cerebellum has been shown to be essential for the coordination of rapid alternating movements but not for force generation. While both neocortical and cerebellar activity increased with increasing speed and force, the speed-related changes in the cerebellum were larger than predicted by an optimized cortico-cerebellar connectivity model. We then applied the same approach in a cognitive domain, assessing how the cerebellum supports working memory. Enhanced gating was associated with the encoding of items in working memory, but not with the manipulation or retrieval of the items. Focusing on task-dependent gating of neocortical inputs to the cerebellum offers a promising approach for using fMRI to understand the specific contributions of the cerebellum to cognitive function.
Exposure to oxacillin subinhibitory concentrations and in vitro induction of resistance expression in heteroresistant and non-heteroresistant oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA)

Resistance expression can occur as a consequence of irrational use of antibiotics, since this implies dissemination of subinhibitory concentration (sub-MICs) in different environments and generates a selective pressure. The study aimed to evaluate the in vitro influence of selective pressure on antibiotic resistance expression in two oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA), through exposure to oxacillin sub-MICs. One heteroresistant OS-MRSA strain and a non-heteroresistant strain, both isolated from nasal colonization were exposed to two-fold serial dilutions of oxacillin (0,125 a 256 μg/mL) during seven consecutive days. Disc diffusion test was used to determine the susceptibility to several antibiotics and population analysis profile (PAP) was used to evaluate the expression of oxacillin resistance before and after antibiotic exposure. Susceptibility to non-β-lactam antibiotics was not altered but changes in phenotypic expression of penicillin and oxacillin resistance were observed. Both OS-MRSA strains began to express homoresistance (oxacillin MIC = 256 μg/mL) and had no penicillin zone inhibition after induction, different from that was observed before oxacillin exposure, which suggested increased in β-lactamase production. In vitro selective pressure with oxacillin stimulated β-lactamase production and led phenotypic expression of oxacillin resistance in heteroresistant and non-heteroresistant OS-MRSA, which became homoresistant. This reinforces the impact that irrational use of antibiotics has on individuals colonized by S. aureus and on the population, emphasizing that the emergence and spread of resistance to antibiotics represent a process of evolution in response to selective antimicrobial pressure.
Wingless signaling promotes lipid mobilization through signal-induced transcriptional repression

Conserved Wnt/Wingless signaling plays pivotal roles in regulating normal development and energy metabolism in metazoans, and aberrant activation of Wnt signaling drives the pathogenesis of many diseases including cancer. However, the role of Wnt signaling in regulating cellular lipid homeostasis, particularly lipid mobilization, remains poorly understood. Here we show that canonical Wg signaling inhibits lipid accumulation in Drosophila larval adipocytes by stimulating lipid catabolism while simultaneously inhibiting lipogenesis. Using a combination of RNA-sequencing and CUT&RUN assays, we identified a battery of Wg target genes encoding key factors required for lipogenesis (such as FASN1 and AcCoS), lipolysis (such as lipid droplet-associated proteins Lsd-1 and Lsd-2), and fatty acid β-oxidation in the mitochondria and peroxisome (e.g., CPT1 and CRAT), most of which are directly repressed by active Wg signaling. Furthermore, lipid accumulation defects caused by active Wg signaling are rescued by either ectopically expressing Lsd-1 and Lsd-2 or depleting the transcriptional repressor Aef1, whose binding motif was identified in 52% of Wg signaling-repressed genes. These findings suggest that active Wg signaling reduces intracellular lipid accumulation by inhibiting lipogenesis and fatty acid β-oxidation and by promoting lipolysis and lipid mobilization, and Wg signaling-induced transcriptional repression play a prominent role in these converging mechanisms.
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins

Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexible k-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic HMM. In making the latter, we also wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotated Drosophila genomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.
Functional connectivity between the amygdala and prefrontal cortex underlies processing of emotion ambiguity

Processing facial expressions of emotion draws on a distributed brain network. In particular, judging ambiguous facial emotions involves coordination between multiple brain areas. Here, we applied multimodal functional connectivity analysis to achieve network-level understanding of the neural mechanisms underlying perceptual ambiguity in facial expressions. We found directional effective connectivity between the amygdala, dorsomedial prefrontal cortex (dmPFC), and ventromedial PFC, supporting both bottom-up affective processes for ambiguity representation/perception and top-down cognitive processes for ambiguity resolution/decision. Direct recordings from the human neurosurgical patients showed that the responses of amygdala and dmPFC neurons were modulated by the level of emotion ambiguity, and amygdala neurons responded earlier than dmPFC neurons, reflecting the bottom-up process for ambiguity processing. We further found parietal-frontal coherence and delta-alpha cross-frequency coupling involved in encoding emotion ambiguity. We replicated the EEG coherence result using independent experiments and further showed modulation of the coherence. EEG source connectivity revealed that the dmPFC top-down regulated the activities in other brain regions. Lastly, we showed altered behavioral responses in neuropsychiatric patients who may have dysfunctions in amygdala-PFC functional connectivity. Together, using multimodal experimental and analytical approaches, we have delineated a neural network that underlies processing of emotion ambiguity. Significance Statement A large number of different brain regions participate in emotion processing. However, it remains elusive how these brain regions interact and coordinate with each other and collectively encode emotions, especially when the task requires orchestration between different brain areas. In this study, we employed multimodal approaches that well complemented each other to comprehensively study the neural mechanisms of emotion ambiguity. Our results provided a systematic understanding of the amygdala-PFC network underlying emotion ambiguity with fMRI-based connectivity, EEG coordination of cortical regions, synchronization of brain rhythms, directed information flow of the source signals, and latency of single-neuron responses. Our results further shed light on neuropsychiatric patients who have abnormal amygdala-PFC connectivity.
Single and double ionization of atomic oxygen by electron impact

A pulsed crossed beam technique incorporating time-of-flight spectroscopy (previously developed in this laboratory) has been used to study the single and double ionization of ground-state oxygen atoms produced by an iridium tube furnace source. Relative cross sections sigma 1 and sigma 2 for single and double ionization have been determined in the respective energy ranges 14.1-2000 eV and 90-2000 eV which are wider than any previous measurements. These values have been normalized by reference to the absolute values of sigma 1 previously measured by Brook et al at energies (50-997 eV) where the possible influence of an unknown admixture of long-lived excited atoms in their experiment should be small. However at energies below about 25 eV our values of al become much smaller than the values of Brook at al. Above 40 eV, the present ratios sigma 2/ sigma 1 are in satisfactory agreement with other measurements which extend to 400 eV. Our values of al have been compared with selected theoretical predictions. Some evidence of structure in the energy dependence of sigma 1 in the region of the cross section maximum is consistent with predicted contributions from inner-shell 2s ionization and from autoionization in addition to outer 2p electron removal.
Four-Dimensional Variational Assimilation of Total Column Water Vapor in Rainy Areas

Abstract This paper studies the impact of assimilating rain-derived information in the European Centre for Medium-Range Weather Forecasts (ECMWF) four-dimensional variational (4DVAR) system. The approach is based on a one-dimensional variational (1DVAR) method. First, model temperature and humidity profiles are adjusted by assimilating observed surface rain rates in 1DVAR. Second, 1DVAR total column water vapor (TCWV) estimates are assimilated in 4DVAR. Observations used are Tropical Rainfall Measuring Mission (TRMM) surface rain-rate estimates from the TRMM Microwave Imager. Two assimilation experiments making use of 1DVAR TCWV were run for a 15-day period. The “Rain-1” experiment only assimilates 1DVAR retrievals where the observed rain rate is nonzero while the “Rain-2” experiment assimilates all 1DVAR TCWV estimates. The period selected includes Hurricane Bonnie, which was well sampled by TRMM (late August 1998). Results show a positive impact on the humidity analysis of assimilating 1DVAR TCWV in 4DV.
A new mouse model of ATR-X syndrome carrying a common patient mutation exhibits neurological and morphological defects

ATRX is a chromatin remodelling ATPase that is involved in transcriptional regulation, DNA damage repair and heterochromatin maintenance. It has been widely studied for its role in ALT-positive cancers, but its role in neurological function remains elusive. Hypomorphic mutations in the X-linked ATRX gene cause a rare form of intellectual disability combined with alpha-thalassemia called ATR-X syndrome in hemizygous males. Patients also have facial dysmorphism, microcephaly, musculoskeletal defects and genital abnormalities. Since complete deletion of ATRX in mice results in early embryonic lethality, the field has largely relied on conditional knockout models to assess the role of ATRX in multiple tissues. Given that null alleles are not found in patients, a more patient-relevant model was needed. Here, we have produced and characterised the first patient mutation knock-in model of ATR-X syndrome, carrying the most common patient mutation, R246C. This is one of a cluster of missense mutations located in the chromatin interaction domain that disrupts its function. The knock-in mice recapitulate several aspects of the patient disorder, including craniofacial defects, microcephaly and impaired neurological function. They provide a powerful model for understanding the molecular mechanisms underlying ATR-X syndrome and for testing potential therapeutic strategies.
Individual Differences in Delay Discounting are Associated with Dorsal Prefrontal Cortex Connectivity in Youth

Delay discounting is a measure of impulsive choice relevant in adolescence as it predicts many real-life outcomes, including substance use disorders, obesity, and academic achievement. However, the functional networks underlying individual differences in delay discounting during youth remain incompletely described. Here we investigate the association between multivariate patterns of functional connectivity and individual differences in impulsive choice in a large sample of youth. A total of 293 youth (9-23 years) completed a delay discounting task and underwent resting-state fMRI at 3T. A connectome-wide analysis using multivariate distance-based matrix regression was used to examine whole-brain relationships between delay discounting and functional connectivity was then performed. These analyses revealed that individual differences in delay discounting were associated with patterns of connectivity emanating from the left dorsal prefrontal cortex, a hub of the default mode network. Delay discounting was associated with greater functional connectivity between the dorsal prefrontal cortex and other parts of the default mode network, and reduced connectivity with regions in the dorsal and ventral attention networks. These results suggest that delay discounting in youth is associated with individual differences in relationships both within the default mode network and between the default mode and networks involved in attentional and cognitive control.