Miracle-dz/UniFAR-FTUs huggingface dataset:
Dually localized proteins found in both the apicoplast and mitochondrion utilize the Golgi-dependent pathway for apicoplast targeting in Toxoplasma gondii

Like other apicomplexan parasites, Toxoplasma gondii harbours a four-membraned endosymbiotic organelle - the apicoplast. Apicoplast proteins are nuclear-encoded and trafficked to the organelle through the endoplasmic reticulum (ER). From the ER to the apicoplast, two distinct protein trafficking pathways can be used. One such pathway is the cell’s secretory pathway involving the Golgi, while the other is a unique Golgi-independent pathway. Using different experimental approaches, many apicoplast proteins have been shown to utilize the Golgi-independent pathway, while a handful of reports show that a few proteins use the Golgi-dependent pathway. This has led to an emphasis towards the unique Golgi-independent pathway when apicoplast protein trafficking is discussed in the literature. Additionally, the molecular features that drive proteins to each pathway are not known. In this report, we systematically test eight apicoplast proteins, using a C-terminal HDEL sequence to assess the role of the Golgi in their transport. We demonstrate that dually localised proteins of the apicoplast and mitochondrion (TgSOD2, TgTPx1/2 and TgACN) are trafficked through the Golgi while proteins localised exclusively to the apicoplast are trafficked independent of the Golgi. Mutants of the dually localised proteins that localised exclusively to the apicoplast also showed trafficking through the Golgi. Phylogenetic analysis of TgSOD2, TgTPx1/2 and TgACN suggested that the evolutionary origins of TgSOD2, TgTPx1/2 lie in the mitochondrion while TgACN appears to have originated from the apicoplast. Collectively, with these results, for the first time, we establish that the driver of the Golgi-dependent trafficking route to the apicoplast is the dual localisation of the protein to the apicoplast and the mitochondrion.
The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen

Containing fungal diseases often depends on the application of fungicidal compounds. Fungicides can rapidly lose effectiveness due to the rise of resistant individuals in populations. However, the lack of knowledge about resistance mutations beyond known target genes challenges investigations into pathways to resistance. We used whole-genome sequencing data and association mapping to reveal the multilocus genetic architecture of fungicide resistance in a global panel of 159 isolates of Parastagonospora nodorum, an important fungal pathogen of wheat. We found significant differences in azole resistance among global field populations. The populations evolved distinctive combinations of resistance alleles which can interact synergistically. We identified 34 significantly associated SNPs located in close proximity to genes associated with fungicide resistance in other fungi, including an MFS transporter. Using fungal colony growth rates and melanin production at different temperatures as fitness proxies, we found no evidence that resistance was constrained by genetic trade-offs. Our study demonstrates how genome-wide association studies of a global collection of pathogen strains can recapitulate the emergence of fungicide resistance. The distinct complement of resistance mutations found among populations illustrates how the evolutionary trajectory of fungicide adaptation can be complex and challenging to predict.
Brain structures associated with reading and their abnormalities in dyslexia: a whole-brain analysis

Developmental dyslexia (DD) is a highly prevalent neurodevelopmental disorder, which often has a devastating influence on the individual’s academic achievement and career. Research on the neural origins of DD has continued for half a century, yielding, however, inconsistent results. The current study was set out to determine abnormalities of grey and white matter volumes in adults with DD and to shed light on neural architectures associated with reading and related skills. To this end, we conducted a whole-brain voxel based morphometry following current recommendations on analysis approaches, coupled with rigorous neuropsychological testing, to characterize the associations between neuroanatomy and skills vital for reading in DD. We found decreased volumes of grey matter in DD, comprising a left-hemispheric network including superior temporal and inferior frontal gyri, insula, the limbic system, and basal ganglia, and white matter, including the right middle temporal gyrus and hippocampus, as well as the right precuneus. These results are both consistent with the most robust previous findings on cortical abnormalities in DD and yield novel insight to the role of subcortical structures in DD, scarcely studied so far. Crucially, areas with decreased grey matter in DD overlapped with brain areas associated with technical reading skills. This supports the conclusion that the grey matter regions that we identified to have a low volume in DD are associated with the core areas vital for reading.
Differential alphavirus defective RNA diversity between intracellular and encapsidated compartments is driven by subgenomic recombination events

Alphaviruses are positive-sense RNA arboviruses that can cause either a chronic arthritis or a potentially lethal encephalitis. Like other RNA viruses, alphaviruses produce truncated, defective genomes featuring large deletions during replication. Defective RNAs (D-RNAs) have primarily been isolated from virions after high-multiplicity of infection passaging. Here, we aimed to characterize both intracellular and packaged viral D-RNA populations during early passage infections under the hypothesis that D-RNAs arise de novo intracellularly that may not be packaged and thus have remained undetected. To this end, we generated NGS libraries using RNA derived from passage 1 (P1) stock chikungunya virus (CHIKV) 181/clone 25, intracellular virus, and encapsidated P2 virus and analyzed samples for D-RNA expression, followed by diversity and differential expression analyses. We found that the diversity of D-RNA species is significantly higher for intracellular D-RNA populations than encapsidated and specific populations of D-RNAs are differentially expressed between intracellular and encapsidated compartments. Importantly, these trends were likewise observed in a murine model of CHIKV 15561 infection, as well as in vitro studies using related Mayaro, Sindbis, and Aura viruses. Additionally, we identified a novel subtype of subgenomic D-RNA that are conserved across arthritogenic alphaviruses. D-RNAs specific to intracellular populations were defined by recombination events specifically in the subgenomic region, which was confirmed by direct RNA nanopore sequencing of intracellular CHIKV RNAs. Together, these studies show that only a portion of D-RNAs generated intracellularly are packaged and D-RNAs readily arise de novo in the absence of transmitted template. IMPORTANCE Our understanding of viral defective RNAs (D-RNAs), or truncated viral genomes, comes largely from passaging studies in tissue culture under artificial conditions and/or packaged viral RNAs. Here, we show that specific populations of alphavirus D-RNAs arise de novo and that they are not packaged into virions, thus imposing a transmission bottleneck and impeding their prior detection. This raises important questions about the roles of D-RNAs, both in nature and in tissue culture, during viral infection and whether their influence is constrained by packaging requirements. Further, during the course of these studies, we found a novel type of alphavirus D-RNA that is enriched intracellularly; dubbed subgenomic D-RNAs (sgD-RNAs), they are defined by deletion boundaries between capsid/E3 and E1/3’UTR regions and are common to chikungunya, Mayaro, Sindbis, and Aura viruses. These sgD-RNAs are enriched intracellularly and do not appear to be selectively packaged, and additionally may exist as subgenome-derived transcripts.
TMEM184B promotes pruriceptive neuron specification to allow itch sensitivity

Nociceptive and pruriceptive neurons in the dorsal root ganglia (DRG) convey sensations of pain and itch to the spinal cord, respectively. One subtype of mature DRG neurons, marked by Somatostatin (Sst) expression, is responsible for sensing mediators of acute itch and atopic dermatitis, including the cytokine IL-31. How itch-sensitive (pruriceptive) neurons are specified is unclear. Here we show that Tmem184b, a gene with roles in axon degeneration and nerve terminal maintenance, is required for the expression of a large cohort of itch receptors, including those for IL-31, Leukotriene C4, and Histamine. Mice lacking Tmem184b fail to respond to IL-31, but maintain normal responses to pain and mechanical force, indicating a specific behavioral defect in pruriception. Lineage-tracing studies using Sst-driven Cre recombinase show a loss of pruriceptive neurons in Tmem184b-mutant mice, suggesting a defect in neuron subtype specification. We identify an early failure of proper Wnt-dependent transcriptional signatures and signaling components in Tmem184b mutant mice that can explain the improper DRG neuronal subtype specification. Lentiviral re-expression of Tmem184b in mutant embryonic neurons restores Wnt signatures, whereas re-expression of Tmem184b in adult DRG fails to restore itch responses. Together, these data demonstrate that Tmem184b promotes adult somatosensation through developmental Wnt signaling and specification of pruriceptive neurons. Our data illuminate a new key regulatory step in the processes controlling the establishment of diversity in the somatosensory system.
TMS alters multivoxel patterns in the absence of overall activity changes

Transcranial magnetic stimulation (TMS) has become one of the major tools for establishing the causal role of specific brain regions in perceptual, motor, and cognitive processes. Nevertheless, a persistent limitation of the technique is the lack of clarity regarding its precise effects on neural dynamics. Here, we examined the effects of TMS intensity and frequency on concurrently recorded blood-oxygen level-dependent (BOLD) signals at the site of stimulation in dorsolateral prefrontal cortex. In Experiment 1, we delivered a series of pulses at high (100% of motor threshold) or low (50% of motor threshold) intensity, whereas in Experiment 2, we always used high intensity but delivered stimulation at four different frequencies (5, 8.33, 12.5, and 25 Hz). We found that the TMS intensity and frequency could be reliably decoded using multivariate analysis techniques even though TMS had no effect on overall BOLD activity at the site of stimulation in either experiment. These results provide important insight into the mechanisms through which TMS influences neural activity.
Dynamic inhibition of sensory responses mediated by an olfactory corticofugal system

Processing of sensory information is substantially modulated by centrifugal projections from higher cortical areas, yet their behavioral relevance and underlying neural mechanisms remain unclear in most cases. The anterior olfactory nucleus (AON) is part of the olfactory cortex and its extensive connections to lower and higher brain centers put it in a prime position to modulate early sensory information in the olfactory system. Here, we show that optogenetic activation of AON neurons in awake animals was not perceived as an odorant equivalent cue. However, AON activation during odorant presentation reliably suppressed odor responses. This AON mediated effect was fast and constant across odors and concentrations. Likewise, activation of glutamatergic AON projections to the olfactory bulb (OB) transiently inhibited the excitability of mitral/tufted cells (MTCs) that relay olfactory input to cortex. Single-unit MTC recordings revealed that optogenetic activation of glutamatergic AON terminals in the OB transiently decreased sensory-evoked MTC spiking, regardless of the strength or polarity of the sensory response. These findings suggest that glutamatergic AON projections to the OB suppress early olfactory processing by inhibiting OB output neurons and that the AON can dynamically gate sensory throughput to the cortex. Significance Statement The anterior olfactory nucleus (AON) as an olfactory information processing area sends extensive projections to lower and higher brain centers but the behavioral consequences of its activation have been scarcely investigated. Using behavioral tests in combination with optogenetic manipulation we show that in contrast to what has been suggested previously, the AON does not seem to form odor percepts but instead suppresses odor responses across odorants and concentrations. Furthermore, this study shows that glutamatergic cortical projections to the olfactory bulb suppress olfactory processing by inhibiting output neurons, pointing to a potential mechanisms by which the olfactory cortex can actively and dynamically gate sensory throughput to higher brain centers. Highlights AON stimulation suppresses odor responses across odorants and concentrations AON activation is not perceived as an odorant equivalent cue The AON dynamically shapes olfactory bulb output on a fast timescale AON input to the olfactory bulb strongly suppresses mitral/tufted cells firing
Complex naturalistic stimuli capture attention automatically when maintained in working memory

Recent studies suggest that a stimulus actively maintained in working memory (WM) automatically captures visual attention when subsequently perceived. However, such a WM guidance effect has been so far observed only for stimuli defined by simple features, such as colour or orientation. Here we investigated whether the effect occurs also for naturalistic stimuli, whose identity is defined by multiple features and relations among them, specifically for faces and houses. The experiment comprised two conditions: a WM condition and a mere exposure condition. Subjects (N = 28) either memorized or merely saw a template stimulus, and then performed several dot-probe trials, in which pairs of stimuli were presented laterally as distractors (memorized or seen on the one side, control stimulus on the other) and followed by a target dot. We found that response times were faster when targets followed a memorized stimulus than when they followed a control one, and that the memory-matching stimuli evoked the N2pc ERP component. Further, in an exploratory analysis we found electrophysiological evidence for an early (100-200 ms post stimulus) prioritization specific to the memorized faces. Importantly, neither the RT, nor the electrophysiological effects were observed in the mere exposure condition. In conclusion, showing an attention capture by complex stimuli maintained in WM contributes to identifying the mechanism of WM-based attentional selection and provides novel evidence that complex stimuli can, in principle, guide attention automatically. Finally, we interpret the early prioritization of the memorized faces as evidence supporting the sensory recruitment theory of WM.
APOBEC3C Tandem Domain Proteins Create Super Restriction Factors against HIV-1

As a part of the innate immune system, humans encode proteins that inhibit viruses such as HIV-1. These broadly acting antiviral proteins do not protect humans from viral infections because viruses encode proteins that antagonize the host antiviral proteins to evade the innate immune system. One such example of a host antiviral protein is APOBEC3C (A3C), which weakly inhibits HIV-1. Here, we show that we can improve the antiviral activity of A3C by duplicating the DNA sequence to create a synthetic tandem domain and, furthermore, that the proteins thus generated are relatively resistant to the viral antagonist Vif. Together, these data give insights about how nature has evolved a defense against viral pathogens such as HIV. ABSTRACT Humans encode proteins, called restriction factors, that inhibit replication of viruses such as HIV-1. The members of one family of antiviral proteins, apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; shortened here to A3), act by deaminating cytidines to uridines during the reverse transcription reaction of HIV-1. The A3 locus encodes seven genes, named A3A to A3H. These genes have either one or two cytidine deaminase domains, and several of these A3s potently restrict HIV-1. A3C, which has only a single cytidine deaminase domain, however, inhibits HIV-1 only very weakly. We tested novel double domain protein combinations by genetically linking two A3C genes to make a synthetic tandem domain protein. This protein created a “super restriction factor” that had more potent antiviral activity than the native A3C protein, which correlated with increased packaging into virions. Furthermore, disabling one of the active sites of the synthetic tandem domain protein resulted in an even greater increase in the antiviral activity—recapitulating a similar evolution seen in A3F and A3G (double domain A3s that use only a single catalytically active deaminase domain). These A3C tandem domain proteins do not have an increase in mutational activity but instead inhibit formation of reverse transcription products, which correlates with their ability to form large higher-order complexes in cells. Finally, the A3C-A3C super restriction factor largely escaped antagonism by the HIV-1 viral protein Vif. IMPORTANCE As a part of the innate immune system, humans encode proteins that inhibit viruses such as HIV-1. These broadly acting antiviral proteins do not protect humans from viral infections because viruses encode proteins that antagonize the host antiviral proteins to evade the innate immune system. One such example of a host antiviral protein is APOBEC3C (A3C), which weakly inhibits HIV-1. Here, we show that we can improve the antiviral activity of A3C by duplicating the DNA sequence to create a synthetic tandem domain and, furthermore, that the proteins thus generated are relatively resistant to the viral antagonist Vif. Together, these data give insights about how nature has evolved a defense against viral pathogens such as HIV.
Quantifying myelin content in brain tissue using color Spatial Light Interference Microscopy (cSLIM)

Deficient myelination of the brain is associated with neurodevelopmental delays, particularly in high-risk infants, such as those born small in relation to their gestational age (SGA). New methods are needed to further study this condition. Here, we employ Color Spatial Light Interference Microscopy (cSLIM), which uses a brightfield objective and RGB camera to generate pathlength-maps with nanoscale sensitivity in conjunction with a regular brightfield image. Using tissue sections stained with Luxol Fast Blue, the myelin structures were segmented from a brightfield image. Using a binary mask, those portions were quantitatively analyzed in the corresponding phase maps. We first used the CLARITY method to remove tissue lipids and validate the sensitivity of cSLIM to lipid content. We then applied cSLIM to brain histology slices. These specimens are from a previous MRI study, which demonstrated that appropriate for gestational age (AGA) piglets have increased internal capsule myelination (ICM) compared to small for gestational age (SGA) piglets and that a hydrolyzed fat diet improved ICM in both. The identity of samples was blinded until after statistical analyses.
SWI/SNF antagonizes SIR heterochromatin to promote transcription of genes expressed during mitotic exit in Saccharomyces cerevisiae

Heterochromatin is a repressive, specialized chromatin structure that is central to eukaryotic transcriptional regulation and genome stability. In the budding yeast, Saccharomyces cerevisiae, heterochromatin formation requires Sir2p, Sir3p, and Sir4p, and these Sir proteins create specialized chromatin structures at telomeres and silent mating type loci. Previously, we reported that the SWI/SNF chromatin remodeling enzyme can evict Sir3 from chromatin fibers in vitro, though whether this activity contributes to the role of SWI/SNF as a transcriptional activator at euchromatic loci is unknown. Here, we characterize genetic interactions between the SIR genes (SIR2, SIR3, and SIR4) and genes encoding subunits of the chromatin remodelers SWI/SNF and INO80C, as well genes encoding the histone deacetylases Hst3 and Hst4. We find that loss of SIR genes partially rescues the growth defects of swi2, ino80, and hst3/hst4 mutants during replication stress conditions. Interestingly, partial suppression of swi2, ino80, and hst3 hst4 mutant phenotypes is due to the pseudo-diploid state of sir mutants, but a significant portion is due to more direct functional interactions. Consistent with this view, transcriptional profiling of strains lacking Swi2 or Sir3 identifies a set of genes whose expression in the M/G1 phase of the cell cycle requires SWI/SNF to antagonize the repressive impact of Sir3.
Circulating Epigenetic Biomarkers in Malignant Pleural Mesothelioma: State of the Art and critical Evaluation

Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer, which originates from the mesothelial cells of the pleura and is associated with asbestos exposure. In light of its aggressive nature, late diagnosis and dismal prognosis, there is an urgent need for identification of biomarkers in easily accessible samples (such as blood) for early diagnosis of MPM. In the last 10 years, epigenetic markers, such as DNA methylation and microRNAs (miRNAs), have gained popularity as possible early diagnostic and prognostic biomarkers in cancer research. The aim of this review is to provide a critical analysis of the current evidences on circulating epigenetic biomarkers for MPM and on their translational potential to the clinical practice for early diagnosis and for prognosis.
Cybervictimization and Cyberbullying: The Role of Socio-Emotional Skills

Social and emotional competences are considered to have a crucial role in cyberbullying as, e.g., difficulties concerning emotion regulation and empathy can characterize both cyberbullies and cybervictims. Although, the dynamics of socio-emotional processes underlying cyberbullying are still open for research, as e.g., there are contradicting results concerning the role of empathy in cybervictimization. Thus, the aim of our study was to explore the specific maladaptive emotion regulation strategies characterizing cybervictims and to clarify the role of empathy in cybervictimization. Furthermore, another goal was to explore whether moral disengagement characterizes cyberbullies in absence of empathic and adaptive emotion regulation skills. 524 students (214 males, aged 12–19 years) participated in our research. We used self-report questionnaires to measure cyberbullying perpetration and cybervictimization, adaptive and maladaptive emotion regulation strategies, moral disengagement, affective, cognitive empathy, and intention to comfort. Our main findings show that cyberbullying is associated with difficulties in socio-emotional competences. Cyberbullies and bully-victims demonstrate less empathic responsiveness and display higher moral disengagement than noncyberbullies. On the other hand cybervictims tend to use both adaptive and maladaptive emotion regulation strategies to cope with their negative emotions. In addition, cybervictims have higher cognitive and affective empathy than cyberbullies and bully-victims. Our findings confirm and extend the research on the relationship among socio-emotional skills and cyberbullying as well as cybervictimization. Moreover, our results have important implications for prevention programs targeting emotion regulation and empathy.