Miracle-dz/UniFAR-FTUs huggingface dataset:
The ribonucleoprotein-mediated CRISPR–Cas9 system induces recurrent Aire gene mutations in contrast to the nickase expression vector in murine in vitro or in vivo models

Although in vitro mTEC cultures can help determine the role of the autoimmune regulator (Aire) gene, the mechanisms of Aire mutations were identified using Aire mutant mice. Nevertheless, long-term cultures of mTECs from mice are difficult to establish. To overcome this, we used a CRISPR–Cas9 system to edit Aire in a murine mTEC line in vitro and mouse embryos. Two ribonucleoprotein (RNP) complexes were designed to separately target Aire exons 6 and 8. NHEJ-derived indels or HDR-derived mutations were obtained. Recurrent NHEJ-derived mutations were observed among editions, one in exon 6 (del 3554G) and the other in exon 8 (del 5676_5677TG), i.e., the exon 6 mutation was kept in an mTEC clone edited in vitro and in vivo in a mouse, and the exon 8 mutation was kept in mTECs in vitro. None of the mutations obtained with the nickase system were recurrent, indicating the participation of the RNP complex.
Causal role of the frontal eye field in attention-induced ocular dominance plasticity

Previous research has found that prolonged eye-based attention can bias ocular dominance. If one eye long-termly views a regular movie meanwhile the opposite eye views a backward movie of the same episode, perceptual ocular dominance will shift towards the eye previously viewing the backward movie. Yet it remains unclear whether the role of eye-based attention in this phenomenon is causal or not. To address this issue, the present study relied on both the functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) techniques. We found robust activation of the frontal eye field (FEF) and intraparietal sulcus (IPS) when participants were watching the dichoptic movie while focusing their attention on the regular movie. Interestingly, we found a robust effect of attention-induced ocular dominance shift when the cortical function of vertex or IPS was transiently inhibited by continuous theta burst stimulation (cTBS), yet the effect was significantly attenuated to a negligible extent when cTBS was delivered to FEF. A control experiment verified that the attenuation of ocular dominance shift after inhibitory stimulation of FEF was not due to any impact of the cTBS on the binocular rivalry measurement of ocular dominance. These findings suggest that the fronto-parietal attentional network is involved in controlling eye-based attention in the “dichoptic-backward-movie” adaptation paradigm, and in this network, FEF plays a crucial causal role in generating the attention-induced ocular dominance shift.
Genomic sequence context differs between germline and somatic structural variants allowing for their differentiation in tumor samples without paired normals

There is currently no method to distinguish between germline and somatic structural variants (SVs) in tumor samples that lack a matched normal sample. In this study, we analyzed several features of germline and somatic SVs from a cohort of 974 patients from The Cancer Genome Atlas (TCGA). We identified a total of 21 features that differed significantly between germline and somatic SVs. Several of the germline SV features were associated with each other, as were several of the somatic SV features. We also found that these associations differed between the germline and somatic classes, for example, we found that somatic inversions were more likely to be longer events than their germline counterparts. Using these features we trained a support vector machine (SVM) classifier on 555,849 TCGA SVs to computationally distinguish germline from somatic SVs in the absence of a matched normal. This classifier had an ROC curve AUC of 0.984 when tested on an independent test set of 277,925 TCGA SVs. In this dataset, we achieved a positive predictive value (PPV) of 0.81 for an SV called somatic by the classifier being truly somatic. We further tested the classifier on a separate set of 7,623 SVs from pediatric high-grade gliomas (pHGG). In this non-TCGA cohort, our classifier achieved a PPV of 0.828, showing robust performance across datasets.
Manganese homeostasis modulates fungal virulence and stress tolerance in Candida albicans

Due to the scarcity of transition metals within the human host, fungal pathogens have evolved sophisticated mechanisms to uptake and utilize these micronutrients at the infection interface. While considerable attention was turned to iron and copper acquisition mechanisms and their importance in fungal fitness, less was done regarding either the role of manganese (Mn) in infectious processes or the cellular mechanism by which fungal cells achieve their Mn- homeostasis. Here, we undertook transcriptional profiling in the pathogenic fungus Candida albicans experiencing both Mn starvation and excess to capture biological processes that are modulated by this metal. We uncovered that Mn scarcity influences diverse processes associated with fungal fitness including invasion of host cells and antifungal sensitivity. We show that Mn levels influence the abundance of iron and zinc emphasizing the complex crosstalk between metals. Deletion of SMF12, a member of Mn Nramp transporters confirmed its contribution to Mn uptake. smf12 was unable to form hyphae and damage host cells and exhibited sensitivity to azoles. We found that the unfolded protein response (UPR), likely activated by decreased glycosylation under Mn limitation, was required to restore growth when cells were shifted from a Mn-starved to a Mn-repleted medium. RNA-seq profiling of cells exposed to Mn excess revealed that UPR was also activated. Furthermore, the UPR signaling axis Ire1-Hac1 was required to bypass Mn toxicity. Collectively, this study underscores the importance of Mn homeostasis in fungal virulence, and comprehensively provides a portrait of biological functions that are modulated by Mn in a fungal pathogen.
Simulated geomagnetic reversals and preferred virtual geomagnetic pole paths

SUMMARY The question of whether virtual geomagnetic poles (VGPs) recorded during reversals and excursions show a longitudinal preference is a controversial one amongst palaeomagnetists. One possible mechanism for such VGP clustering is the heterogeneity of heat flux at the core–mantle boundary (CMB). We use 3-D convection-driven numerical dynamo models with imposed non-uniform CMB heat flow that show stochastic reversals of the dipole field. We calculate transitional VGPs for a large number of token sites at the Earth's surface. In a model with a simple heat flux variation given by a Y22 harmonic, the VGP density maps for individual reversals differ substantially from each other, but the VGPs have a tendency to fall around a longitude of high heat flow. The mean VGP density for many reversals and excursions shows a statistically significant correlation with the heat flow. In a model with an imposed heat flux pattern derived from seismic tomography we find maxima of the mean VGP density at American and East Asian longitudes, roughly consistent with the VGP paths seen in several palaeomagnetic studies. We find that low-latitude regions of high heat flow are centres of magnetic activity where intense magnetic flux bundles are generated. They contribute to the equatorial dipole component and bias its orientation in longitude. During reversals the equatorial dipole part is not necessarily dominant at the Earth's surface, but is strong enough to explain the longitudinal preference of VGPs as seen from different sites.
Lipid discovery enabled by sequence statistics and machine learning

Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that Streptococcus agalactiae MprF synthesizes lysyl-phosphatidylglycerol (Lys-PG) from anionic PG, and a novel cationic lipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), from neutral glycolipid Glc-DAG. This unexpected result prompted us to investigate whether Lys-Glc-DAG occurs in other MprF-containing bacteria, and whether other novel MprF products exist. Here, we studied protein sequence features determining MprF substrate specificity. First, pairwise analyses identified several streptococcal MprFs synthesizing Lys-Glc-DAG. Second, a restricted Boltzmann machine-guided approach led us to discover an entirely new substrate for MprF in Enterococcus, diglucosyl-diacylglycerol (Glc2-DAG), and an expanded set of organisms that modify glycolipid substrates using MprF. Overall, we combined the wealth of available sequence data with machine learning to model evolutionary constraints on MprF sequences across the bacterial domain, thereby identifying a novel cationic lipid.
Proteomic Analysis Reveals a PLK1-Dependent G2/M Degradation Program and Links PKA-AKAP2 to Cell Cycle Control

Targeted protein degradation by the ubiquitin-proteasome system is an essential mechanism regulating cellular division. The kinase PLK1 coordinates protein degradation at the G2/M phase of the cell cycle by promoting the binding of substrates to the E3 ubiquitin ligase SCFβTrCP. However, the magnitude to which PLK1 shapes the mitotic proteome has not been characterized. Combining deep, quantitative proteomics with pharmacologic PLK1 inhibition (PLK1i), we identified more than 200 proteins whose abundances were increased by PLK1i at G2/M. We validate many new PLK1-regulated proteins, including several substrates of the cell cycle E3 SCFCyclin F, demonstrating that PLK1 promotes proteolysis through at least two distinct SCF-family E3 ligases. Further, we found that the protein kinase A anchoring protein AKAP2 is cell cycle regulated and that its mitotic degradation is dependent on the PLK1/βTrCP-signaling axis. Interactome analysis revealed that the strongest interactors of AKAP2 function in signaling networks regulating proliferation, including MAPK, AKT, and Hippo. Altogether, our data demonstrate that PLK1 coordinates a widespread program of protein breakdown at G2/M. We propose that dynamic proteolytic changes mediated by PLK1 integrate proliferative signals with the core cell cycle machinery during cell division. This has potential implications in malignancies where PLK1 is aberrantly regulated.
Effects of hippocampal noninvasive theta-burst stimulation on consolidation of associative memory in healthy older adults

Stimulation of deep brain areas can offer benefits against cognitive impairments associated with aging. So far, this was only possible via invasive methods accompanied by risks. Grossman et al. proposed a new noninvasive stimulation technique, transcranial temporal interference electric stimulation (tTIS), which can be steered to target and modulate activity of deep brain structures. Memory capacity depends on subcortical structures such as the hippocampus, hence, modulation of hippocampal activity could benefit declining cognitive functions. The current study investigates whether theta-burst patterned tTIS targeting the hippocampus influences performance of associative memory in older adults. We found that theta-burst patterned tTIS, but not the control stimulation, improved recollection time in a follow-up 24h after the stimulation, suggesting that theta-burst patterned tTIS can influence the efficiency of longer-term encoding. This outcome indicates that tTIS may provide a new noninvasive deep brain stimulation method to modulate senescent memory processes.
Engineered dsRNA-protein nanoparticles for effective long-distance transport, delivery and gene silencing in plants

Long-distance transport of exogenous biologically active RNA molecules in higher plants has not been reported. Here, we report that cationized bovine serum albumin (cBSA) avidly binds double-stranded beta-glucuronidase RNA (dsGUS RNA) to form nucleic acid-protein nanocomplexes. Using tobacco and poplar plants, we have shown effective uptake and long-distance transport of cBSA/dsGUS RNA nanocomplexes from basal ends of leaf petioles to leaf blades as well as from basal ends of shoots to their apexes and apical leaves. We have further demonstrated that the cBSA/dsGUS RNA nanocomplexes are highly effective in silencing both conditionally inducible DR5-GUS gene and constitutively active 35S-GUS gene in leaf, shoot and shoot meristem tissues. This cBSA/dsRNA delivery technology may provide a convenient, fast, and inexpensive tool for characterizing gene functions in plants, and potentially for in planta gene-editing.
ViCEKb: Vitiligo-linked Chemical Exposome Knowledgebase

Vitiligo is a complex disease wherein the environmental factors, in conjuction with the underlying genetic predispositions, trigger the autoimmune destruction of melanocytes, ultimately leading to depigmented patches on the skin. Apart from being susceptible to other autoimmune disorders, the affected patients may face social stigmatization leading to a decreased quality in life. While genetic factors have been extensively studied, the knowledge on environmental triggers remains sparse and less understood. Therefore, a comprehensive understanding of the environemental triggers will not only explain the complex etiology of the disease, it will also enable the prioritization of potential toxic chemicals in human chemcical exposome. Towards this, we present the first comprehensive knowledgbase of vitiligo triggering chemicals compiled from published literature namely, Vitiligo-linked Chemical Exposome Knowledgbase (ViCEKb). ViCEKb involved an extensive and systematic manual effort in curation of published literature and subsequent compilation of 113 unique chemical triggers of vitiligo. ViCEKb standardises various chemical information, and categorizes the chemicals based on their evidences and sources of exposure. Importantly, ViCEKb contains a wide range of metrics necessary for different toxicological evaluations. Moreover, our extensive cheminformatics-based analysis of the ViCEKb chemical space highlighted its diversity and uniqueness in comparison to other skin specific chemical regulatory lists. We also observed that ViCEKb chemicals are present in various consumer products and are not regulated. Additionally, a transcriptomics based analysis of ViCEKb chemical perturbations in skin cell samples highlighted the commonality in their linked biological processes. Overall, we present the first comprehensive effort in compilation and exploration of various chemical triggers of vitiligo. We believe such a resource will enable in deciphering the complex etiology of vitiligo and aid in the characterization of human chemical exposome. ViCEKb is freely available for academic research at: https://cb.imsc. res.in/vicekb.
Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma

CIC-DUX4 is a rare and understudied transcription factor fusion oncoprotein. CIC-DUX4 co-opts native gene targets to drive a lethal form of human sarcoma. The molecular underpinnings that lead to oncogenic reprograming and CIC-DUX4 sarcomagenesis remain largely undefined. Through an integrative ChIP and RNA-Seq analysis using patient-derived CIC-DUX4 cells, we define CIC-DUX4 mediated chromatin states and function. We show that CIC-DUX4 primarily localizes to proximal and distal cis-regulatory elements where it associates with active histone marks. Our findings nominate key signaling pathways and molecular targets that enable CIC-DUX4 to mediate tumor cell survival. Collectively, our data demonstrate how the CIC-DUX4 fusion oncoprotein impacts chromatin state and transcriptional responses to drive an oncogenic program in undifferentiated sarcoma. Significance CIC-DUX4 sarcoma is a rare and lethal sarcoma that affects children, adolescent young adults, and adults. CIC-DUX4 sarcoma is associated with rapid metastatic dissemination and relative insensitivity to chemotherapy. There are no current standard-of-care therapies for CIC-DUX4 sarcoma leading to universally poor outcomes for patients. Through a deep mechanistic understanding of how the CIC-DUX4 fusion oncoprotein reprograms chromatin state and function, we aim to improve outcomes for CIC-DUX4 patients.
CHRONO participates in multi-modal repression of circadian transcriptional complexes

The mammalian protein CHRONO is a rhythmically expressed repressor of the circadian transcriptional activator complex CLOCK:BMAL1, and was proposed to be a novel component of the circadian clock. However, lack of specific mechanistic understanding of the activity and function of CHRONO meant that its role within the circadian machinery was opaque. Here we fill this knowledge gap, confirming an evolutionarily conserved minimal repressive domain (MRD) of CHRONO that interacts with specific regions in the BMAL1 C-terminal transactivation domain (TAD) to repress CLOCK:BMAL1 activity. Notably, this binding region overlaps with the binding site for the repressor CRY and coactivators CBP/p300, with CHRONO capable of competing with both of these classical regulators of BMAL1 for TAD binding, highlighting CHRONO as a direct regulator of BMAL1 function. Additionally, we investigate the interaction between CHRONO and the major circadian repressor, PERIOD2 (PER2). We show that CHRONO reduces PER2 stability through interaction between the CHRONO C-terminus and the Casein Kinase 1 (CK1)-binding domain of PER2. This results in competition between CHRONO and CK1 for binding at this site on PER2, with CHRONO binding inhibiting CK1 phosphorylation of PER2 at the stabilising S662 residue. Taken together, these data show a more substantive and complex role for CHRONO in molecular circadian timekeeping than previously posited, suggesting that CHRONO acts to fine-tune cellular timekeeping by modulating multiple protein-protein interactions that are critical for maintenance of circadian rhythmicity.
Modeling 3‐D density distribution in the mantle from inversion of geoid anomalies: Application to the Yellowstone Province

We developed a three‐dimensional scheme to invert geoid anomalies aiming to map density variations in the mantle. Using an ellipsoidal‐Earth approximation, the model space is represented by tesseroids. To assess the quality of the density models, the resolution and covariance matrices were computed. From a synthetic geoid anomaly caused by a plume tail with Gaussian noise added, the inversion code was able to recover a plausible solution about the density contrast and geometry when it is compared to the synthetic model. To test the inversion algorithm in a natural case study, geoid anomalies from the Yellowstone Province (YP) were inverted. From the Earth Gravitational Model 2008 expanded up to degree 2160, lower crust‐ and mantle‐related negative geoid anomalies with amplitude of approximately 70 m were obtained after removing long‐wavelength components (>5400 km) and crustal effects. We estimated three density models for the YP. The first model, the EDM‐1 (estimated density model), uses a starting model with density contrast equal to 0. The other two models, the EDM‐2 and EDM‐3, use an initial density derived from two S‐velocity models for the western United States, the Dynamic North America Models of S Waves by Obrebsky et al. (2011) and the Northwestern United States Teleseismic Tomography of S Waves (NWUS11‐S) by James et al. (2011). In these three models, a lower and an upper bound for the density solution was also imposed as a priori information. Regardless of the initial constraints, the inversion of the residual geoid indicates that the lower crust and the upper mantle of the YP have a predominantly negative density contrast (~ −50 kg/m3) relative to the surrounding mantle. This solution reveals that the density contrast extends at least to 660 km depth. Regional correlation analysis between the EDM‐1 and NWUS11‐S indicates an anticorrelation (coefficient of ~ −0.7) at 400 km depth. Our study suggests that the mantle density derived from the inversion of geoid could be integrated with seismic velocity models to image mantle anomalous features beyond the depth limit of investigation achieved combining gravity and seismic tomography. ©2013. American Geophysical Union. All Rights Reserved.
REL deregulation stands as a primary hit for AID-imprinted B-cells along the germinal center competition

In diffuse large B-cell lymphomas (DLBCLs), gains and amplifications of the 2p15-16 region, which always encompass the REL gene, are mostly restricted to the germinal center (GC) B- cell DLBCL subtype (GCB-DLBCL) for which c-Rel is the pivotal Rel/NF-κB subunit. While REL is also known to play a key role in the GC reaction, its contribution to GCB-DLBCL transformation is still unclear. To understand the role of REL in the very first steps of GCB transformation, i.e when B-cells with deregulated REL are competing with other B-cells during chronic antigenic stimulation, we have created a dual-color mouse that allows to induce REL in a limited pool of AID- imprinted B-cells after immunization and to differentially stain AID-imprinted B-cells cells that overexpress REL or not. Our results demonstrate that dysregulation of REL at the GC B-cell stage promotes GC B-cell expansion and favors both class-switch recombination and plasma cell differentiation. Additionally, although REL overexpression was neutral on post-GC memory B-cell differentiation, it did confer a long-term competitive advantage allowing for GC persistence and continuous recirculation of REL-overexpressing B-cells. Functionally, REL enhanced the protection against apoptosis in the early steps of GCB differentiation. REL- overexpressing B-cells can my occasionally transform into in an aggressive B-cell tumor. Highlighting the role of repeated immune responses, our results confirm the role of REL in the germinal center reaction and provide evidence supporting the fact that genetic deregulation of c-Rel expression is most likely a primary event in the aggressive transformation of GC B-cells. Key points - REL provides a long-term competitive advantage allowing for GC B-cell persistence and continuous recirculation of AID-imprinted B-cells - AID-imprinted B-cells overexpressing REL can occasionally transform into aggressive B-cell lymphomas Explanation of the novelty By showing in a new dual-color mouse model that dysregulation of REL in a very limited pool of AID-imprinted B-cells confers a strong long-term competitive advantage in the context of repeated immune responses and may occasionally lead to transformation into an aggressive B- cell lymphoma, we provide for the first time experimental evidence supporting the fact that that REL is most likely a primary event in the aggressive transformation of germinal center B-cells.
A long trilobite-trackway, Cruziana semiplicata Salter, from the Upper Cambrian of the Holy Cross Mts

A long trilobite-trackway, Cruziana semiplicata Salter, found in the Upper Cambrian depoits, of Wielka Wiśniowka in the Holy Cross Mts, is studied and compared both to previously known specimens from the same ichnotope, as well as to Salter's type-locality forms from North Wales. The trilobites mode of life, their behaviour when settling on the sea bottom and the resulting ichnoassemblage characterized by a dominance of Cruziana semiplicata and Rusophycus polonicus forms, were closely comparable in both Polish and Welsh environments.