Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic sequence characteristics and the empiric accuracy of short-read sequencing

Background Short-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias, reduce the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. For the clonal pathogen Mycobacterium tuberculosis (Mtb), researchers frequently exclude 10.7% of the genome believed to be repetitive and prone to erroneous variant calls. To benchmark short-read variant calling, we used 36 diverse clinical Mtb isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically study the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias, and GC content. å Results Reference based Illumina variant calling had a recall ≥89.0% and precision ≥98.5% across parameters evaluated. The best balance between precision and recall was achieved by tuning the mapping quality (MQ) threshold, i.e. confidence of the read mapping (recall 85.8%, precision 99.1% at MQ ≥ 40). Masking repetitive sequence content is an alternative conservative approach to variant calling that maintains high precision (recall 70.2%, precision 99.6% at MQ≥40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52 of the 168 PE/PPE genes (34.5%). We present a refined list of low confidence regions and examine the largest sources of variant calling error. Conclusions Our improved approach to variant calling has broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems, and more generally for WGS applications in other organisms.
Engineering paralog-specific PSD-95 synthetic binders as potent and minimally invasive imaging probes

Despite the constant advances in fluorescence imaging techniques, monitoring endogenous proteins still constitutes a major challenge in particular when considering dynamics studies or super-resolution imaging. We have recently evolved specific protein-based binders for PSD-95, the main postsynaptic scaffold proteins at excitatory synapses. Since the synthetic binders recognize epitopes not directly involved in the target protein activity, we consider them here as tools to develop endogenous PSD-95 imaging probes. After confirming their lack of impact on PSD-95 function, we validated their use as intrabody fluorescent probes. We further engineered the probes and demonstrated their usefulness in different super-resolution imaging modalities (STED, PALM and DNA-PAINT) in both live and fixed neurons. Finally, we exploited the binders to enrich at the synapse genetically encoded calcium reporters. Overall, we demonstrate that these evolved binders constitute a robust and efficient platform to selectively target and monitor endogenous PSD-95 using various fluorescence imaging techniques.
Feedback-related potentials and oscillations during trial and error learning in Parkinson’s disease

Electrophysiological markers of performance monitoring are thought to reflect functioning of dedicated neural networks and neuromodulatory systems. Whether and how these markers are altered in neurological diseases and whether they can reflect particular cognitive deficits remains to be confirmed. Here we first tested whether the frontal medial feedback-related potential, evoked during a trial and error learning task, is changed in early Parkinson’s disease patients compared to control subjects. The potential was not changed in amplitude and discriminated negative and positive feedback as in controls. Feedback-related markers in Parkinson’s patients also appeared in time-frequency analyses, unaltered in theta (3-7 Hz) band but reduced in beta (20-30 Hz) oscillations for positive feedback. Beta oscillations power appeared to be dramatically globally reduced during the task. Overall, our results show that Beta oscillation markers of performance monitoring captured by EEG are selectively altered in Parkinson’s disease patients, and that they are accompanied by changes in task-related oscillatory dynamics. Significance Statement Frontal neural activity evoked by outcomes reveal the functioning of neural systems devoted to flexible behaviours. Modulations of such activity in Parkinson’s disease (PD) patients could reflect specific alterations of neural systems and cognitive processing. The goal is to evaluate whether such activity can serve as markers of the disease. Here, using EEG and a trial and error learning protocol, we show that mid-frontal midline performance feedback-related potentials for different types of feedback were similar in controls and early diagnosed PD patients. However, task-related oscillations revealed alterations in the beta range accompanied by more global beta activity alteration in PD compared to controls subjects. This study provides data relevant to the search for non-motor biomarkers in early stages of PD.
Genetic regulation of homeostatic immune architecture in the lungs of Collaborative Cross mice

Variation in immune homeostasis, immune system stability, in organ systems such as the lungs is likely to shape the host response to infection at these exposed tissues. We evaluated immune homeostasis in immune cell populations in the lungs of the Collaborative Cross (CC) mouse genetic reference population. We found vast heritable variation in leukocyte populations with the frequency of many of these cell types showing distinct patterns relative to classic inbred strains C57BL/6J and BALB/cJ. We identified 28 quantitative trait loci (QTL) associated with variation in baseline lung immune cell populations, including several loci that broadly regulate the abundance of immune populations from distinct developmental lineages, and found that many of these loci have predictive value for influenza disease outcomes, demonstrating that genetic determinants of homeostatic immunity in the lungs regulate susceptibility to virus-induced disease. All told, we highlight the need to assess diverse mouse strains in understanding immune homeostasis and resulting immune responses.
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Significance Primer-dependent transcription initiation—the use of RNA primers as initiating entities in transcription initiation—yields RNA products having a 5′-hydroxyl. Here, we show that primer-dependent initiation in vivo in Escherichia coli involves predominantly dinucleotide primers, involves any of the 16 possible dinucleotide primers, and depends on promoter sequences in, upstream, and downstream of the primer binding site. Crystal structures explain the structural basis of sequence dependence at the promoter position immediately upstream of the primer binding site, namely, interchain base stacking between the promoter template-strand nucleotide and primer 5′ nucleotide. Taken together, our findings provide a mechanistic and structural description of primer-dependent initiation in E. coli. Chemical modifications of RNA 5′-ends enable “epitranscriptomic” regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5′-end. In Escherichia coli cells, RNAs with a 5′-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, “primer-dependent initiation. ” Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5′-ends generated by primer-dependent initiation for ∼410 (∼1,000,000) promoter sequences in E. coli. The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS−2NTSS−1NTSSWTSS+1, where TSS is the transcription start site, NTSS−1NTSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS−2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS−2) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded E. coli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.
Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid acquisition are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or expression level. Here we show — using a combination of experimental evolution, reverse genetics, and transcriptomics — that fitness costs of two divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid acquisition. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by upregulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained upregulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer due to their propensity for amelioration by single compensatory mutations, explaining why plasmids are so common in bacterial genomes.
VHL ligand binding increases intracellular level of VHL

The von–Hippel Lindau (VHL) protein is a tumour suppressor protein frequently mutated in the VHL disease, which functions as substrate recognition subunit of a Cul2 E3 ubiquitin ligase (CRL2VHL). CRL2VHL plays an important role in oxygen sensing, by binding and targeting Hypoxia Inducible Factor-alpha subunits (HIF-alpha) for ubiquitination and degradation. VHL is also commonly hijacked by heterobifunctional degrader molecules known as proteolysis-targeting chimeras (PROTACs). In previous work we reported the structure-based design and functional characterisation of VHL inhibitors (VH032 and VH298) that induce the HIF response in cells. Here, we use unbiased quantitative mass spectrometry to identify the proteomic changes elicited by the VHL inhibitor and compare this to hypoxia or broad-spectrum prolyl-hydroxylase domain (PHD) enzyme inhibitor IOX2. Our results demonstrate the VHL inhibitor selectively activates the HIF response that is also present in the hypoxia- and IOX2-induced proteomic changes. Interestingly, VHL inhibitors were found to selectively upregulate a single protein, which is VHL itself. Our analysis revealed that this occurs via protein stabilisation of VHL isoforms and not via changes in transcript levels. Increased VHL levels upon VH298 treatment resulted in turn to reduced levels of HIF-1α protein. Our results demonstrate the high specificity of VHL inhibitors and suggest that use of these inhibitors would not produce overtly side effects due to prolonged HIF stabilisation. They also exemplify the concept that small-molecule binding induced protein stabilisation can increase protein levels inside cells.
Differential variation of NSCs in root branch orders of Fraxinus mandshurica Rupr. seedlings across different drought intensities and soil substrates

Non-structural carbohydrates (NSCs) facilitate plants adapt to drought stress, could characterize trees growth and survival ability and buffer against external disturbances. Previous studies have focused on the distribution and dynamics of NSCs among different plant organs under drought conditions. However, discussion about the NSC levels of fine roots in different root branch order were little, especially the relationship between fine root trait variation and NSCs content. The aim of the study is to shed light into the synergistic variation of fine root traits and NSC content in different root branch order under different drought and soil substrate conditions. 2-year-old Fraxinus mandshurica Rupr. potted seedlings were planted in three different soil substrates (humus, loam and sandy-loam soil) and conducted to four drought intensities (CK, mild drought, moderate drought and severe drought) for two months. With the increase of drought intensity, the biomass of fine roots decreased significantly. Under the same drought intensity, seedlings in sandy-loam soil have higher root biomass, and the coefficient of variation of fifth-order roots (37.4%, 44.5% and 53.0% in humus, loam and sandy loam, respectively) is higher than that of lower-order roots. With the increase of drought intensity, the specific root length (SRL) and average diameter (AD) of all five orders increased and decreased, respectively. The fine roots in humus soil had higher soluble sugar content and lower starch content. Also, the soluble sugar and starch content of fine roots showed decreasing and increasing tendency respectively. Soluble sugar and starch explain the highest degree of total variation of fine root traits, that is 32.0% and 32.1% respectively. With ascending root order, the explanation of the variation of root traits by starch decreased (only 6.8% for fifth-order roots). The response of different root branch order fine root morphological traits of F. mandshurica seedlings to resource fluctuations ensures that plants maintain and constructure the root development by an economical way to obtain more resources.
Intrinsic mechanisms in the gating of resurgent Na+ currents

The resurgent component of the voltage-gated sodium current (INaR) is a depolarizing conductance, revealed on membrane hyperpolarizations following brief depolarizing voltage steps, which has been shown to contribute to regulating the firing properties of numerous neuronal cell types throughout the central and peripheral nervous systems. Although mediated by the same voltage-gated sodium (Nav) channels that underlie the transient and persistent Nav current components, the gating mechanisms that contribute to the generation of INaR remain unclear. Here, we characterized Nav currents in mouse cerebellar Purkinje neurons, and used tailored voltage-clamp protocols to define how the voltage and the duration of the initial membrane depolarization affect the amplitudes and kinetics of INaR. Using the acquired voltage-clamp data, we developed a novel Markov kinetic state model with parallel (fast and slow) inactivation pathways and, we show that this model reproduces the properties of the resurgent, as well as the transient and persistent, Nav currents recorded in (mouse) cerebellar Purkinje neurons. Based on the acquired experimental data and the simulations, we propose that resurgent Na+ influx occurs as a result of fast inactivating Nav channels transitioning into an open/conducting state on membrane hyperpolarization, and that the decay of INaR reflects the slow accumulation of recovered/opened Nav channels into a second, alternative and more slowly populated, inactivated state. Additional simulations reveal that extrinsic factors that affect the kinetics of fast or slow Nav channel inactivation and/or impact the relative distribution of Nav channels in the fast- and slow-inactivated states, such as the accessory Navβ4 channel subunit, can modulate the amplitude of INaR. SUMMARY The resurgent component of the voltage-gated sodium current (INaR) is revealed on membrane hyperpolarizations following brief depolarizing voltage steps that activate the rapidly activating and inactivating, transient Nav current (INaT). To probe the mechanisms contributing to the generation and properties of INaR, we combined whole-cell voltage-clamp recordings from mouse cerebellar Purkinje neurons with computational modeling to develop a novel, blocking particle-independent, model for the gating of INaR that involves two parallel inactivation pathways, and we show that this model recapitulates the detailed biophysical properties of INaR measured in mouse cerebellar Purkinje neurons.
PsiNorm: a scalable normalization for single-cell RNA-seq data

Single-cell RNA sequencing (scRNA-seq) enables transcriptome-wide gene expression measurements at single-cell resolution providing a comprehensive view of the compositions and dynamics of tissue and organism development. The evolution of scRNA-seq protocols has led to a dramatic increase of cells throughput, exacerbating many of the computational and statistical issues that previously arose for bulk sequencing. In particular, with scRNA-seq data all the analyses steps, including normalization, have become computationally intensive, both in terms of memory usage and computational time. In this perspective, new accurate methods able to scale efficiently are desirable. Here we propose PsiNorm, a between-sample normalization method based on the power-law Pareto distribution parameter estimate. Here we show that the Pareto distribution well resembles scRNA-seq data, independently of sequencing depths and technology. Motivated by this result, we implement PsiNorm, a simple and highly scalable normalization method. We benchmark PsiNorm with other seven methods in terms of cluster identification, concordance and computational resources required. We demonstrate that PsiNorm is among the top performing methods showing a good trade-off between accuracy and scalability. Moreover PsiNorm does not need a reference, a characteristic that makes it useful in supervised classification settings, in which new out-of-sample data need to be normalized. PsiNorm is available as an R package available at https://github.com/MatteoBlla/PsiNorm
Human Fronto-Striatal Connectivity is Organized into Discrete Functional Subnetworks

The striatum is interconnected with the cerebral cortex via multiple recurrent loops that play a major role in many neuropsychiatric conditions. Primate cortico-striatal connections can be precisely mapped using invasive tract-tracing. However, noninvasive human research has not mapped these connections with anatomical precision, limited by the practice of averaging neuroimaging data across individuals. Here we utilized highly-sampled resting-state functional connectivity MRI for individually-specific precision functional mapping of cortico-striatal connections. We identified ten discrete, individual-specific subnetworks linking cortex—predominately frontal cortex—to striatum. These subnetworks included previously unknown striatal connections to the human language network. The discrete subnetworks formed a stepped rostral-caudal gradient progressing from nucleus accumbens to posterior putamen; this organization was strongest for projections from medial frontal cortex. The stepped gradient organization fit patterns of fronto-striatal connections better than a smooth, continuous gradient. Thus, precision subnetworks identify detailed, individual-specific stepped gradients of cortico-striatal connectivity that include human-specific language networks.
Anuran Heart Metamorphosis: Anatomical Support for Pulmonary Blood Separation in the Early Aquatic Phase

Background In both larval and adult anurans, blood separation and respiratory physiology have remained an enigma. While various blood separation mechanisms have been proposed, the same structure is seen as playing a key role: the conus arteriosus. However, previous findings on its internal structure are contradictory, depending on the specifics of the 2D imaging methods used by different authors. To resolve this problem, we used high-resolution X-ray microtomography of whole Bufo bufo specimens to acquire the first detailed 3D descriptions of this complex structure through metamorphosis. Results In early tadpoles two small valvular openings develop at the ventricular-conal junction, providing two paths separated by the septum coni and continuing into the aortic arches. Thus, structures to support segregated pulmonary circulation are fully developed well before the lungs appear. The external gills undergo partial resorption and retreat asymmetrically into a gill chamber formed by a hyoidal cover, leaving only a single opening on the left side, the opercular spout. Conclusions The timing of events in Bufo circulatory development does not track the changing modes of respiration used by the developing tadpole. In particular, a system capable of double circulation carries only oxygen-depleted blood for a significant portion of the tadpole stage.
Rapid appetitive transitions are sculpted by amygdala to accumbens pathways

Foraging, pursuit, and predation rapidly transition into behavioral quiescence during reward capture and consumption. While appetitive-consummatory dissociations are embedded at both psychological and neural levels, the mechanisms controlling switches or transitions between appetitive seeking and consummatory behaviors remain poorly understood. Here we identify the BLA→AcbSh pathway as critical to these transitions by showing that this pathway inhibits the appetitive seeking response in the presence of consummatory demands. Using an appetitive cue-discrimination task in male rats, we show that reward delivery is a significant driver of seeking inhibition and that a BLA→AcbSh pathway mediates this inhibition. This role in suppressing seeking responses during periods of consumption was not due to a general suppression of behavior because responding to other cues during the same test was unaffected. Moreover, it was specific to the BLA→AcbSh pathway, because the contribution of the BLA→AcbC pathway to appetitive switching was distinct and modest. State-dependent silencing of BLA→AcbSh revealed that the modulation of seeking before and after reward delivery are co-dependent. Finally, we found that BLA terminals in AcbSh have functional connectivity to LH-projecting AcbSh neurons, thereby identifying a BLA→AcbSh→LH pathway as a putative route for the rapid regulation of appetitive behaviors. Taken together, these findings suggest that the BLA→AcbSh pathway is a core component of an appetitive switching system, recruited under conditions requiring rapid or dynamic shifts in appetitive behavior, and that this pathway enables these shifts by actively inhibiting seeking. Significance statement Foraging, pursuit, and predation quickly transition into behavioral quiescence during reward capture and consumption. These transitions are critical for flexible and responsive sequences of behavior. Here we show that behavioral transitions are actively controlled at the limbic-striatal interface. We identify reward receipt as a proximal trigger for transition between reward seeking and taking, we identify active inhibition as the functional operation of this transition, and we identify the basolateral amygdala→accumbens shell pathway as critical to this functional operation.