Miracle-dz/UniFAR-FTUs huggingface dataset:
Paradoxical Associations Between Familial Affective Responsiveness, Stress, and Amygdala Reactivity

Studies of early life extremes such as trauma, abuse, and neglect highlight the critical importance of quality caregiving in the development of brain circuits supporting emotional behavior and mental health. The impact of normative variability in caregiving on such biobehavioral processes, however, is poorly understood. Here, we provide initial evidence that even subtle variability in normative caregiving shapes threat-related brain function and, potentially, associated psychopathology in adolescence. Specifically, we report that greater familial affective responsiveness is associated with heightened amygdala reactivity to interpersonal threat, particularly in adolescents having experienced relatively low recent stress. These findings extend the literature on the effects of caregiving extremes on brain function to subtle, normative variability, but suggest that presumably protective factors may be associated with increased risk-related amygdala reactivity. We consider these paradoxical associations with regard to studies of basic associative threat learning and further consider their relevance for understanding potential effects of caregiving on psychological development.
graphsim: An R package for simulating gene expression data from graph structures of biological pathways

Transcriptomic analysis is used to capture the molecular state of a cell or sample in many biological and medical applications. In addition to identifying alterations in activity at the level of individual genes, understanding changes in the gene networks that regulate fundamental biological mechanisms is also an important objective of molecular analysis. As a result, databases that describe biological pathways are increasingly uesad to assist with the interpretation of results from large-scale genomics studies. Incorporating information from biological pathways and gene regulatory networks into a genomic data analysis is a popular strategy, and there are many methods that provide this functionality for gene expression data. When developing or comparing such methods, it is important to gain an accurate assessment of their performance. Simulation-based validation studies are frequently used for this. This necessitates the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This procedure has been released as the graphsim R package on CRAN and GitHub (https://github.com/TomKellyGenetics/graphsim) and is compatible with any graph structure that can be described using the igraph package. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression.
The transcription and export complex THO/TREX contributes to transcription termination in plants

Transcription termination has important regulatory functions, impacting mRNA stability, localization and translation potential. Failure to appropriately terminate transcription can also lead to read-through transcription and the synthesis of antisense RNAs which can have profound impact on gene expression. The Transcription-Export (THO/TREX) protein complex plays an important role in coupling transcription with splicing and export of mRNA. However, little is known about the role of the THO/TREX complex in the control of transcription termination. In this work, we show that two proteins of the THO/TREX complex, namely TREX COMPONENT 1 (TEX1 or THO3) and HYPER RECOMBINATION1 (HPR1 or THO1) contribute to the correct transcription termination at several loci in Arabidopsis thaliana. We first demonstrate this by showing defective termination in tex1 and hpr1 mutants at the nopaline synthase (NOS) terminator present in a T-DNA inserted between exon 1 and 3 of the PHO1 locus in the pho1-7 mutant. Read-through transcription beyond the NOS terminator and splicing-out of the T-DNA resulted in the generation of a near full-length PHO1 mRNA (minus exon 2) in the tex1 pho1-7 and hpr1 pho1-7 double mutants, with enhanced production of a truncated PHO1 protein that retained phosphate export activity. Consequently, the strong reduction of shoot growth associated with the severe phosphate deficiency of the pho1-7 mutant was alleviated in the tex1 pho1-7 and hpr1 pho1-7 double mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants leads to 3’UTR extensions in several plant genes. These results demonstrate that THO/TREX complex contributes to the regulation of transcription termination. Author summary Production of messenger RNAs (mRNAs) involves numerous steps including initiation of transcription, elongation, splicing, termination, as well as export out of the nucleus. All these steps are highly coordinated and failure in any steps has a profound impact on the level and identity of mRNAs produced. The THO/TREX protein complex is associated with nascent RNAs and contributes to several mRNA biogenesis steps, including splicing and export. However, the contribution of the THO/TREX complex to mRNA termination was poorly defined. We have identified a role for two components of the THO/TREX complex, namely the proteins TEX1 and HPR1, in the control of transcription termination in the plant Arabidopsis thaliana. We show that the tex1 and hpr1 mutants have defects in terminating mRNA at the nopaline synthase (NOS) terminator found in T-DNA insertion mutants leading to the transcriptional read-through pass the NOS terminator. We also show that tex1 and hpr1 mutants have defects in mRNA termination at several endogenous genes, leading to the production of 3’UTR extensions. Together, these results highlight a role for the THO/TREX complex in mRNA termination.
Queuing models of gene expression: Analytical distributions and beyond

Activation of a gene is a multistep biochemical process, involving recruitments of transcription factors and histone kinases as well as modification of histones. Many of these intermediate reaction steps would have been unspecified by experiments. Therefore, classical two-state models of gene expression established based on the memoryless (or Markovian) assumption would not well describe the reality in gene expression. In fact, recent experimental data have indicated that the inactive phases of gene promoters are differently distributed, showing strong memory. Here, we use a non-exponential waiting-time distribution to model the complex activation process of a gene, and analyze a queuing model of stochastic transcription. We successfully derive the analytical expression for the mRNA distribution, which provides insight into the effect of molecular memory created by complex activating events on the mRNA expression. We find that the reduction in the waiting-time noise may result in the increase in the mRNA noise, contrary to the previous conclusion. Based on the derived distribution, we also develop a method to infer the waiting-time distribution from a known mRNA distribution. Data analysis on a realistic example verifies the validity of this method. SIGNIFICANCE Activation of a gene is a complex biochemical process and involve several intermediate reaction steps, many of which have been unspecified by experiments. Stochastic models of gene expression that were previously established based on the constant reaction rates would not well reflect the reality in gene expression. To this end, we study a queuing model of stochastic transcription which assume that the reaction waiting time follows a general distribution and derive the analytical expression for mRNA distribution. Our results provide insight into the role of molecular memory in fine-tuning the gene expression noise, and can be used to infer the underlying molecular mechanism.
IL8 Drives an Elaborate Signal Transduction Process for CD38 to Produce NAADP from NAAD and NADP+ in Endolysosomes to Effect Cell Migration

Nicotinic acid adenine dinucleotide phosphate (NAADP) is an obligate driver of calcium signaling whose formation from other metabolites of nicotinamide adenine dinucleotide (NAD+) has remained elusive. In vitro, CD38-mediated NAADP synthesis requires an acidic pH and a nonphysiological concentration of nicotinic acid (NA). We discovered that the type II membrane form of CD38 catalyzes synthesis of NAADP by exchanging the nicotinamide moiety of nicotinamide adenine dinucleotide phosphate (NADP+) for the NA group of nicotinic acid adenine dinucleotide (NAAD) inside endolysosomes of interleukin 8 (IL8)-treated lymphokine-activated killer cells. Upon IL8 stimulation, cytosolic NADP+ is transported to acidified endolysosomes via connexin 43 via cAMP-EPAC-RAP1-PP2A signaling. Luminal CD38 then performs a base exchange reaction with the donor NA group deriving from NAAD, produced by newly described endolysosomal activities of NA phosphoribosyltransferase and NMN adenyltransferase 3. Thus, the membrane organization of endolysosomal CD38, a signal-mediated transport system for NADP+ and luminal NAD+ biosynthetic enzymes integrate signals from a chemokine and cAMP to specify the spatiotemporal mobilization of calcium to drive cell migration.
From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners

Microbial interactions are major determinants in shaping microbiome structure and function. Although fungi are found across diverse microbiomes, the mechanisms through which fungi interact with other species remain largely uncharacterized. In this work, we explore the diversity of ways in which fungi can impact bacteria by characterizing interaction mechanisms across 16 different bacterial-fungal pairs, involving 8 different fungi and 2 bacteria (Escherichia coli and Pseudomonas psychrophila). Using random barcode transposon-site sequencing (RB-TnSeq), we identified a large number of bacterial genes and pathways important in fungal interaction contexts. Within each interaction, fungal partners elicit both antagonistic and beneficial effects. Using a panel of phylogenetically diverse fungi allowed us to identify interactions that were conserved across all species. Our data show that all fungi modulate the availability of iron and biotin, suggesting that these may represent conserved bacterial-fungal interactions. Several fungi also appear to produce previously uncharacterized antibiotic compounds. Generating a mutant in a master regulator of fungal secondary metabolite production showed that fungal metabolites are key shapers of bacterial fitness profiles during interactions. This work demonstrates a diversity of mechanisms through which fungi are able to interact with bacterial species. In addition to many species-specific effects, there appear to be conserved interaction mechanisms which may be important across microbiomes.
Neuron Type-Specific Translatomes in Spinal Cords of Naïve and Neuropathic Mice

The spinal dorsal horn harbors a sophisticated and heterogeneous network of excitatory and inhibitory neurons that process peripheral signals encoding different sensory modalities. Although it has long been recognized that this network is crucial both for the separation and the integration of sensory signals of different modalities, the molecular identity of the underlying neurons and signaling mechanisms are still only partially understood. Here, we have used the translating ribosome affinity purification (TRAP) technique to map the translatomes of excitatory glutamatergic (VGLUT2+) and inhibitory GABA and/or glycinergic (VGAT+ or Gad67+) neurons of the mouse spinal cord. Our analyses demonstrate that inhibitory and excitatory neurons are primarily set apart by the expression of genes encoding transcription factors or genes related to the production, release or re-uptake of their principal neurotransmitters (glutamate, GABA or glycine). Subsequent gene ontology (GO) term analyses revealed that neuropeptide signaling-related GO terms were highly enriched in the excitatory population. Eleven neuropeptide genes displayed largely non-overlapping expression patterns closely adhering to the laminar and hence also functional organization of the spinal cord grey matter, suggesting that they may serve as major determinants of modality-specific processing. Since this modality-specific processing of sensory input is severely compromised in chronic, especially neuropathic, pain, we also investigated whether peripheral nerve damage changes the neuron typespecific translatome. In summary, our results suggest that neuropeptides contribute to modalityspecific sensory processing in the spinal cord but also indicate that altered sensory encoding in neuropathic pain states occurs independent of major translatome changes in the spinal neurons.
Development of a new class of liver receptor homolog-1 (LRH-1) agonists by photoredox conjugate addition

LRH-1 is a nuclear receptor that regulates lipid metabolism and homeostasis, making it an attractive target for the treatment of diabetes and non-alcoholic fatty liver disease. Building on recent structural information about ligand binding from our labs, we have designed a series of new LRH-1 agonists that further engage LRH-1 through added polar interactions. While the current synthetic approach to this scaffold has, in large part, allowed for decoration of the agonist core, significant variation of the bridgehead substituent is mechanistically precluded. We have developed a new synthetic approach to overcome this limitation, identified that bridgehead substitution is necessary for LRH-1 activation, and described an alternative class of bridgehead substituents for effective LRH-1 agonist development. We determined the crystal structure of LRH-1 bound to a bridgehead-modified compound, revealing a promising opportunity to target novel regions of the ligand-binding pocket to alter LRH-1 target gene expression.
2.8 Å resolution cryo-EM structure of human parechovirus 3 in complex with Fab from a neutralizing antibody

Human parechovirus 3 (HPeV3) infection is associated with sepsis in neonates characterized by significant immune activation and subsequent tissue damage. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and lack of a vaccine or specific antiviral therapy. Towards the latter, we present a 2.8 Å-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody AT12-015 using cryo-EM and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally at high-resolution, it was possible to model a stretch of RNA inside the virion and from this identify the key features that drive and stabilize protein-RNA association during assembly. Importance HPeV3 is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, which despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Towards this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high-resolution it was possible to precisely define the epitope that when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interaction, viral pathogenesis mechanisms, and for finding potential cures for infection and disease.
Cytoplasmic incompatibility between Old and New World populations of a tramp ant

As we enter the Anthropocene, the evolutionary dynamics of species will change drastically, and as yet unpredictably, due to human activity. Already today, increases in global human traffic have resulted in the rapid spread of species to new areas, leading to the formation of geographically isolated populations. These go on to evolve in allopatry, which can lead to reproductive isolation, and potentially, the formation of new species. Surprisingly, little is known about such eco-evolutionary processes in ants, even though numerous invasive ant species are globally distributed in geographically isolated populations. Here, we describe the first case of cytoplasmic incompatibility (CI) between populations of a cosmotropic distributed tramp ant with Asian roots, Cardiocondyla obscurior, which has acquired a novel Wolbachia strain in the New World. Our study uncovers the first symbiont-induced mechanism of reproductive isolation in ants, providing a novel perspective on the biology of globally distributed ants.
Nanopore-based genome assembly and the evolutionary genomics of basmati rice

The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved. To address these gaps, we used long-read nanopore sequencing and assembled the genomes of two circum-basmati rice varieties, Basmati 334 and Dom Sufid.We generated two high-quality, chromosome-level reference genomes that represented the 12 chromosomes of Oryza. The assemblies showed a contig N50 of 6.32Mb and 10.53Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies we characterized structural variations segregating across circum-basmati genomes. We discovered repeat expansions not observed in japonica—the rice group most closely related to circum- basmati—as well as presence/absence variants of over 20Mb, one of which was a circum- basmati-specific deletion of a gene regulating awn length. We further detected strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow had its greatest effect on chromosome 10, causing both structural variation and single nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties showed three major geographically structured genetic groups: (1) Bhutan/Nepal group, (2) India/Bangladesh/Myanmar group, and (3) Iran/Pakistan group.Availability of high-quality reference genomes from nanopore sequencing allowed functional and evolutionary genomic analyses, providing genome-wide evidence for gene flow between circum-aus and circum-basmati, the nature of circum-basmati structural variation, and the presence/absence of genes in this important and iconic rice variety group.
TCF7L2 is a terminal selector that regulates postmitotic differentiation programs and excitability patterns in the thalamus

The thalamus and habenula integrate sensory information, adaptive task control, and reward processing. Their postmitotic differentiation and establishment of their electrophysiological properties are not well understood. The present study investigated the role of the thalamo-habenular-specific transcription factor TCF7L2 in molecular and functional development of this region. In Tcf7l2 knockout embryos, expression of the postmitotic pan-thalamic and pan-habenular selectors Gbx2 and Pou4f1, respectively, was not maintained, and cell adhesion and axon guidance genes were downregulated. Neurons adopted proper neurotransmitter fate, but they did not segregate to form separate nuclei and did not grow axons toward their targets, and their afferent connections were disorganised. When Tcf7l2 was knocked out postnatally, thalamus-specific voltage-gated ion channel genes were not induced, and burst and tonic spiking in thalamic neurons was strongly reduced. These findings indicate that TCF7L2 functions as a master and versatile terminal selector in the thalamo-habenular region to regulate the morphological differentiation and molecular divergence of cells during embryogenesis and the establishment of postnatal thalamic intrinsic excitability. These results provide new insights into regulatory principles of neuronal terminal differentiation in vertebrates.
From a biological template model to gait assistance with an exosuit

The invention of soft wearable assistive devices, known as exosuits, introduced a new aspect in assisting unimpaired subjects. In this study, we designed and developed an exosuit with compliant biarticular thigh actuators called BATEX. Unlike the conventional method of using rigid actuators in exosuits, the BATEX is made of serial elastic actuators (SEA) resembling artificial muscles. This bioinspired design is complemented by the novel control concept of using the ground reaction force to adjust the artificial muscles’ stiffness in the stance phase. By locking the motors in the swing phase, the SEAs will be simplified to passive biarticular springs, which is sufficient for leg swinging. The key concept in our design and control approach is to synthesize human locomotion to develop an assistive device instead of copying human motor control outputs. Analyzing human walking assistance using experiment-based OpenSim simulations demonstrates the advantages of the proposed design and control of BATEX, such as 9.4% reduction in metabolic cost during normal walking condition. This metabolic reduction increases to 10.4% when the subjects carry a 38 kg load. The adaptability of our proposed model-based control to such an unknown condition outperforms the assistance level of the model-free optimal controller. Moreover, increasing the assistive system’s efficiency by adjusting the actuator compliance with the force feedback supports our previous findings on the LOPES II exoskeleton.
Coral accurately bridges paired-end RNA-seq reads alignment

Motivation The established high-throughput RNA-seq technologies usually produce paired-end reads. A challenging problem is therefore to computationally infer the alignment of entire fragments given the alignment of the two mate ends. Solving this problem essentially provide longer RNA-seq reads, and hence benefits downstream RNA-seq analysis. Results We introduce Coral, a new tool that can accurately bridge paired-end RNA-seq reads. The core of Coral is a novel optimization formulation that can capture the most reliable bridging path while also filter out false paths. An efficient dynamic programming algorithm is designed to calculate the top N optimum. Coral implements a consensus approach to select the best solution among the N candidates by taking into account the distribution of fragment length. Coral is modular, can be easily incorporated into existing RNA-seq analysis pipeline. We show that Coral can improve transcript assembly by a large margin: on average over 2377 RNA-seq samples from GTEx, the improvement (measured with adjusted precision) is 7.5% and 11.2% when Coral is incorporated with StringTie and Scallop, respectively. Availability Coral is open-source, freely available at GitHub (https://github.com/Shao-Group/coral) and Bioconda. Scripts, datasets and documentations that can reproduce all experimental results in this paper are available at https://github.com/Shao-Group/coraltest.