Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and ensemble refinement against SAXS data: combining MD simulations with Bayesian inference or with the maximum entropy principle

Small-angle X-ray scattering (SAXS) is a powerful method for tracking conformational transitions of proteins or soft-matter complexes in solution. However, the interpretation of the experimental data is challenged by the low spatial resolution and the low information content of the data, which lead to a high risk of overinterpreting the data. Here, we illustrate how SAXS data can be integrated into all-atom molecular dynamics (MD) simulation to derive atomic structures or heterogeneous ensembles that are compatible with the data. Besides providing atomistic insight, the MD simulation adds physico-chemical information, as encoded in the MD force fields, which greatly reduces the risk of overinterpretation. We present an introduction into the theory of SAXS-driven MD simulations as implemented in GROMACS-SWAXS, a modified version of the GROMACS simulation software. We discuss SAXS-driven parallel-replica ensemble refinement with commitment to the maximum entropy principle as well as a Bayesian formulation of SAXS-driven structure refinement. Practical considerations for running and interpreting the simulations are presented. The methods are freely available via GitLab at https://gitlab.com/cbjh/gromacs-swaxs.
Design of a minimal di-nickel hydrogenase peptide

The most ancient processes for energy production in the evolution of life involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13 amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe]-hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase (ACS), two ancient, extant proteins central to metabolism. These experimental results clearly demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth. One Sentence Summary Small metal-binding peptides were the likely precursors of modern enzymes.
Larger and more dentated hippocampal structure is associated with better memory in the oldest-old

Episodic memory is widely recognized as a critically important aspect of cognition that is often impacted by cognitive and brain aging. Prior work has shown that episodic memory is related to the presence of teeth-like folds on the dentate gyrus, called dentation. We hypothesized that episodic memory performance relates to overall hippocampal structure (i.e., dentation and volume) in an oldest-old cohort. We used data from the McKnight Brain Aging Registry, which consisted of cognitively healthy 85+-year-old adults. We conducted a canonical correlation analysis on 111 participants between a set of episodic memory tests and a set of characterizations of hippocampal structure. The analysis yielded a strong canonical correlation between episodic memory and hippocampal structure (r = 0.491, p = <0.001). The results suggest there is a connection between hippocampal morphology and function in the oldest-old. Our findings suggest that dentation may play an important role in relation to the individual differences observed in episodic memory performance among the oldest old and that hippocampal structure supports healthy cognitive aging. Highlights We characterized hippocampal dentation in a healthy oldest-old sample. Hippocampal structure is related to episodic memory in healthy oldest-old adults. Memory functioning is related to both hippocampal volume and dentation.
Acquired resistance to anti-PD1 therapy in patients with NSCLC reveals changes in T cell phenotypes and MET amplification

The treatment of non-small cell lung cancer (NSCLC) patients with immune checkpoint inhibitors has prolonged their survival dramatically. However, some patients develop resistance after initial response. Here, we used imaging mass cytometry and whole exome and RNA sequencing to analyze matching tumor samples from a cohort of NSCLC patients who initially responded to immune checkpoint inhibitor therapy and later developed acquired resistance. We detected two patterns of resistance: One group of patients had reduced numbers of tumor-infiltrating CD8+ T cells and reduced expression of PD-L1 after development of resistance, whereas the other group showed high CD8+ T cell infiltration and high expression of PD-L1 and markedly elevated expression of other immune-inhibitory molecules. In two cases, we detected downregulation of type I and II IFN pathways after resistance developed, which could lead to an impaired anti-tumor immune response. This study adds to our knowledge of the mechanisms that cause resistance to immunotherapy in NSCLC patients.
Abstinence-Dependent Effects of Long-Access Cocaine Self-Administration on Nucleus Accumbens Astrocytes Are Observed in Male, But Not Female, Rats

Abstract Accumulating evidence indicates significant consequences for astrocytes associated with drug abuse. For example, reductions in structural features and synaptic colocalization of male rat nucleus accumbens (NAc) astrocytes are observed following short-access (ShA; 2 h/d) self-administration and extinction from cocaine, methamphetamine, and heroin. However, it is unknown whether these observations extend to other rodent models of drug abuse, how enduring these effects may be, and whether similar effects are observed in female rats. Here, we assess the effects of long-access (LgA; 6 h/d) cocaine self-administration and abstinence on NAc astrocytes separately in male and female rats, employing a commonly used behavioral approach to investigate the incubation of cocaine craving. NAc astrocytes from male rats exhibit extensive (∼40%) reductions in surface area, volume, and postsynaptic colocalization 45 d but not 24 h after the last self-administration session. In contrast, no effect of self-administration and abstinence was observed in astrocytes from female rats. Moreover, no effect of LgA self-administration and abstinence was observed on NAc GLT-1 expression in female rats, an effect that has been well described in males. These results indicate striking and sexually dimorphic effects of abstinence subsequent to LgA self-administration on astrocytes. Taken together, these results indicate a pivotal role of prolonged abstinence in the effects of cocaine self-administration on NAc astrocytes, and extend a growing body of evidence regarding sex differences in the cellular consequences of drug self-administration in the brain.
The isoforms of pyruvate kinase act as nutrient sensors for the β-cell K ATP channel

The authors have declared that no conflict of interest exists. SUMMARY Pyruvate kinase (PK) and the phosphoenolpyruvate (PEP) cycle play key roles in nutrient-stimulated K ATP channel closure and insulin secretion. To identify the PK isoforms involved, we generated mice lacking β-cell PKm1, PKm2, and mitochondrial PEP carboxykinase (PCK2) that generates mitochondrial PEP. Glucose metabolism generates both glycolytic and mitochondrially-derived PEP, which triggers K ATP closure through local PKm1 and PKm2 signaling at the plasma membrane. Amino acids, which generate mitochondrial PEP without producing glycolytic fructose 1,6-bisphosphate to allosterically activate PKm2, signal through PKm1 to raise ATP/ADP, close K ATP channels, and stimulate insulin secretion. Raising cytosolic ATP/ADP with amino acids is insufficient to close K ATP channels in the absence of PK activity or PCK2, indicating that K ATP channels are regulated by mitochondrially-derived PEP that provides ATP via plasma membrane-associated PK, but not via mitochondrially-derived ATP. Following membrane depolarization, the PEP cycle is also involved in an “off-switch” that facilitates K ATP channel reopening and Ca 2+ extrusion, as shown by PK activation experiments and β-cell PCK2 deletion that prolonged Ca 2+ oscillations and increased insulin secretion. In conclusion, the differential response of PKm1 and PKm2 to the glycolytic and mitochondrial sources of PEP influences the β-cell nutrient response, and controls the oscillatory cycle regulating insulin secretion.
Global disparity of research allocation and the Aichi biodiversity conservation targets

Tracking progress towards global biodiversity conservation targets requires appropriate allocation of research and monitoring efforts. We conducted a global review of camera trap research on mammals as a proxy for biodiversity research and monitoring over the last two decades. We assessed how 3395 research locations from 2324 studies tracked priority regions for attaining the 2020 Aichi Biodiversity Targets. We used a geospatial distribution modelling approach to predict the spatial allocation of biodiversity research and to identify its key drivers. We show that conservation research in the past two decades has often failed to target areas important for conservation, and that 76.8% of the global research allocation can be attributed to country income, biome, mammal richness and accessibility. We predicted lowest probabilities of research allocation in low income countries. The Amazon and Congo Forest basins — two highly biodiverse ecosystems facing unprecedented human alteration — received inadequate research attention. Even in the most researched regions, an average of 51.4% of the research locations were outside the top 20% most important areas for the global biodiversity Aichi Targets. To support biodiversity conservation targets, policy and practice, more research and monitoring is required in regions with high importance for conservation.
An adaptive filtering framework for non-specific and inefficient reactions in multiplex digital PCR based on sigmoidal trends

Real-time digital PCR (qdPCR) coupled with artificial intelligence has shown the potential of unlocking scientific breakthroughs, particularly in the field of molecular diagnostics for infectious diseases. One of the most promising applications is the use of machine learning (ML) methods to enable single fluorescent channel PCR multiplex by extracting target-specific kinetic and thermodynamic information contained in amplification curves. However, the robustness of such methods can be affected by the presence of undesired amplification events and nonideal reaction conditions. Therefore, here we proposed a novel framework to filter non-specific and low efficient reactions from qdPCR data using outlier detection algorithms purely based on sigmoidal trends of amplification curves. As a proof-of-concept, this framework is implemented to improve the classification performance of the recently reported ML-based Amplification Curve Analysis (ACA), using available data from a previous publication where the ACA method was used to screen carbapenemase-producing organisms in clinical isolates. Furthermore, we developed a novel strategy, named Adaptive Mapping Filter (AMF), to consider the variability of positive counts in digital PCR. Over 152,000 amplification events were analyzed. For the positive reactions, filtered and unfiltered amplification curves were evaluated by comparing against melting peak distribution, proving that abnormalities (filtered out data) are linked to shifted melting distribution or decreased PCR efficiency. The ACA was applied to compare classification accuracies before and after AMF, showing an improved sensitivity of 1.18% for inliers and 20% for outliers (p-value < 0.0001). This work explores the correlation between kinetics of amplification curves and thermodynamics of melting curves and it demonstrates that filtering out non-specific or low efficient reactions can significantly improve the classification accuracy for cutting edge multiplexing methodologies.
Hypothalamic gene network dysfunction is associated with cognitive decline and body weight loss in Alzheimer’s disease mice

Recent studies, both clinical and experimental, indicate that many neurodegenerative disorders including Alzheimer’s disease (AD) often display coexisting metabolic dysfunctions, which may exacerbate neurological symptoms. The hypothalamus is a brain region highly involved in maintaining metabolic and other homeostatic processes and is known to be involved in the etiology of AD, although the role of hypothalamic dysfunction in the onset, progression, and severity of AD is poorly understood. In this study, we demonstrate that our new model of genetic diversity in AD, the AD-BXDs, exhibits non-cognitive symptoms consistent with hypothalamic dysfunction and examined hypothalamic bulk RNA sequencing data in the AD-BXD panel to investigate how the AD transgene impacts gene expression profiles in the hypothalamus. Mostly notably, we identified strong neuroinflammatory signatures from the hypothalamus in the AD-BXDs as early as six months of age. A functionally unknown WGCNA module showed correlation to female body weight and contextual fear acquisition. Eigengene expression of microglial/macrophagic modules and their hub gene expressions were correlated to cognitive phenotypes. From these analyses, we nominated Plek and Laptm5 as new targets to attenuate neuroinflammation in AD.
Dynamic rewiring of electrophysiological brain networks during learning

Human learning is an active and complex process. However, the brain mechanisms underlying human skill learning and the effect of learning on the communication between brain regions, at different frequency bands, are still largely unknown. Here, we tracked changes in large-scale electrophysiological networks over a 6-week training period during which participants practiced a series of motor sequences during 30 home training sessions. Our findings showed that brain networks become more flexible with learning in all the frequency bands from theta to gamma ranges. We found consistent increase of flexibility in the prefrontal and limbic areas in the theta and alpha band, and over somatomotor and visual areas in the alpha band. Specific to the beta rhythm, we revealed that higher flexibility of prefrontal regions during the early stage of learning strongly correlated with better performance measured during home training sessions. Our findings provide novel evidence that prolonged motor skill practice results in higher, frequency-specific, temporal variability in brain network structure. AUTHOR SUMMARY We investigated the large-scale organization of electrophysiological brain networks of a cohort of 30 participants practicing a series of motor sequences during 6 weeks of training. With learning, we observed a progressive modulation of the dynamics of prefrontal and limbic regions from theta to alpha frequencies, and of centro-parietal and occipital regions within visuomotor networks in the alpha band. In addition, higher prefrontal regional flexibility during early practice correlated with learning occurring during the 6 weeks of training. This provides novel evidence of a frequency-specific reorganization of brain networks with prolonged motor skill learning and an important neural basis for non-invasive research into the role of cortical functional interactions in (visuo)motor learning.
Humans have distinct repertoires of IgA1

The most abundant immunoglobulin present in the human body is IgA1. It has the highest concentrations at the mucosal lining and in biofluids such as milk and is the second most abundant class of antibodies in serum. We assessed the structural diversity and clonal repertoire of IgA1-containing molecular assemblies longitudinally in human serum and milk from three donors using a mass spectrometry-based approach. IgA-containing molecules purified from serum or milk were assessed by the release and subsequent analysis of their Fab fragments. Our data revealed that serum IgA1 consists of two distinct structural populations, namely monomeric IgA1 (∼ 80%) and dimeric joining (J-) chain coupled IgA1 (∼ 20%). Also, we confirmed that IgA1 in milk is present solely as secretory (S)IgA, consisting of two (∼ 50%), three (∼ 33%) or four (∼ 17%) IgA1 molecules assembled with a J-chain and secretory component (SC). Interestingly, the serum and milk IgA1-Fab repertoires were distinct between monomeric, and J-chain coupled dimeric IgA1. The serum dimeric J-chain coupled IgA1 repertoire contained several abundant clones also observed in the milk IgA1 repertoire. The latter repertoire had little to no overlap with the serum monomeric IgA1 repertoire. This suggests that human IgA1s have (at least) two distinct origins; one of these produces dimeric J-chain coupled IgA1 molecules, shared in human serum and milk, and another produces monomeric IgA1 ending up exclusively in serum.
Intrinsically photosensitive retinal ganglion cells evade temporal filtering to encode environmental light intensity

The retina encodes environmental light intensity to drive innate physiological responses. The synaptic basis of such coding remains obscure. Intrinsically photosensitive retinal ganglion cells (ipRGCs) are the only retinal output neurons stably encoding intensity. They do so even without their melanopsin photopigment, so specializations in their synaptic drive from bipolar cells (BCs) must also contribute. Here, we shed new light on mechanisms responsible for this unique intensity-coding drive. By ultrastructural reconstruction, we show that specific BC types and unusual ribbon synapses carry photoreceptor signals to ipRGCs. By glutamate imaging and electrophysiology, we show that their light responses are unusually persistent. Still, we find that virtually all BCs encode intensity. Intensity coding becomes restricted to ipRGCs primarily because other RGCs filter out steady-state intensity signals postsynaptically. Thus, neural “pinholes” in global, persistent neural “masking” allow intensity signals to be encoded by ipRGCs and sent to specific centers of the visual brain.
HiFENS: High-throughput FISH detection of endogenous pre-mRNA splicing isoforms

Splicing factors play an essential role in regulation of alternative pre-mRNA splicing. While much progress has been made in delineating the mechanisms of the splicing machinery, the identity of signal transduction pathways and upstream factors that regulate splicing factor activity is less well understood. A major challenge in the discovery of upstream regulatory factors of pre-mRNA splicing is the scarcity of functional genomics screening methods to monitor splicing outcomes of endogenous genes. Here, we have developed HiFENS (High throughput FISH Detection of ENdogenous Splicing Isoforms), a high-throughput imaging assay based on hybridization chain reaction (HCR) and used HiFENS to screen for cellular factors that regulate alternative splicing of endogenous genes. We demonstrate optimized detection with high specificity of endogenous splicing isoforms and multiplexing of probes for accurate detection of splicing outcomes with single cell resolution. As proof-of-principle, we perform an RNAi screen of 702 human kinases and identify potential candidate upstream splicing regulators of the FGFR2 gene. HiFENS should be a useful tool for the unbiased delineation of cellular pathways involved in alternative splicing regulation.
Variation in subcortical anatomy: relating interspecies differences, heritability, and brain-behavior relationships

There has been an immense research focus on the topic of cortical reorganization in human evolution, but much less is known regarding the reorganization of subcortical circuits which are intimate working partners of the cortex. Here, by combining advanced image analysis techniques with comparative neuroimaging data, we systematically map organizational differences in striatal, pallidal and thalamic anatomy between humans and chimpanzees. We relate interspecies differences, a proxy for evolutionary changes, to genetics and behavioral correlates. We show that highly heritable morphological measures are significantly expanded across species, in contrast to previous findings in the cortex. The identified morphological-cognitive latent variables were associated with striatal expansion, and affective latent variables were associated with more evolutionarily-conserved areas in the thalamus and globus pallidus. These findings provide new insight into the architecture of these subcortical hubs and can provide greater information on the role of these structures in health and illness.
The development of logical root cause analysis in manufacturing process for mitigation loss and waste

This paper aims to develop an approach for identifying root causes of loss and waste in manufacturing process by reducing human judgments. The newly development of root cause analysis is the Logical Root Cause Analysis (LRCA) which has two elements as the Input, Material, Process, Product and Output Chart (IMPPO) and the Cause of Symptom Identification Method (CSIM). IMPPO is applied for characterizing manufacturing process while the other is for identifying the origin of root cause and symptom. Both methods have been tested with the industrial case. It is found that the root cause analysis (RCA) activity is achieved while human judgment isrequired less than the existing approach.
CHD-associated enhancers shape human cardiomyocyte lineage commitment

Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We perform a single-cell CRISPRi screen to assess the endogenous roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHD). We identify 16 enhancers whose repression leads to deficient differentiation of human cardiomyocytes (CMs). A focused CRISPRi validation screen shows that repression of TBX5 enhancers delays the transcriptional switch from mid- to late-stage CM states. Endogenous genetic deletions of two TBX5 enhancers phenocopy epigenetic perturbations. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients. HIGHLIGHTS Single-cell enhancer perturbation screens during human cardiomyocyte differentiation. Perturbation of CHD-linked enhancers/genes causes deficient CM differentiation. Repression or knockout of TBX5 enhancers delays transition from mid to late CM states. Deficient differentiation coincides with reduced expression of known cardiac genes.