Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly.

X-linked Dystonia-Parkinsonism (XDP) is a Mendelian neurodegenerative disease that is endemic to the Philippines and is associated with a founder haplotype. We integrated multiple genome and transcriptome assembly technologies to narrow the causal mutation to the TAF1 locus, which included a SINE-VNTR-Alu (SVA) retrotransposition into intron 32 of the gene. Transcriptome analyses identified decreased expression of the canonical cTAF1 transcript among XDP probands, and de novo assembly across multiple pluripotent stem-cell-derived neuronal lineages discovered aberrant TAF1 transcription that involved alternative splicing and intron retention (IR) in proximity to the SVA that was anti-correlated with overall TAF1 expression. CRISPR/Cas9 excision of the SVA rescued this XDP-specific transcriptional signature and normalized TAF1 expression in probands. These data suggest an SVA-mediated aberrant transcriptional mechanism associated with XDP and may provide a roadmap for layered technologies and integrated assembly-based analyses for other unsolved Mendelian disorders.

Regulation of macrophage IFNγ-stimulated gene expression by the transcriptional coregulator CITED1.

Macrophages serve as a first line of defense against microbial pathogens. Exposure to interferon-γ (IFNγ) increases interferon-stimulated gene (ISG) expression in these cells, resulting in enhanced antimicrobial and proinflammatory activity. Although this response must be sufficiently vigorous to ensure the successful clearance of pathogens, it must also be carefully regulated to prevent tissue damage. This is controlled in part by CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxyl-terminal domain 2 (CITED2), a transcriptional coregulator that limits ISG expression by inhibiting STAT1 and IRF1. Here, we show that the closely related Cited1 is an ISG, which is expressed in a STAT1-dependent manner, and that IFNγ stimulates the nuclear accumulation of CITED1 protein. In contrast to CITED2, ectopic CITED1 enhanced the expression of a subset of ISGs, including Ccl2, Ifit3b, Isg15 and Oas2. This effect was reversed in a Cited1-null cell line produced by CRISPR-based genomic editing. Collectively, these data show that CITED1 maintains proinflammatory gene expression during periods of prolonged IFNγ exposure and suggest that there is an antagonistic relationship between CITED proteins in the regulation of macrophage inflammatory function. This article has an associated First Person interview with the first author of the paper.

Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics.

Many cellular processes are governed by protein-protein interactions that require tight spatial and temporal regulation. Accordingly, it is necessary to understand the dynamics of these interactions to fully comprehend and elucidate cellular processes and pathological disease states. To map de novo protein-protein interactions with time resolution at an organelle-wide scale, we developed a quantitative mass spectrometry method, time-resolved interactome profiling (TRIP). We apply TRIP to elucidate aberrant protein interaction dynamics that lead to the protein misfolding disease congenital hypothyroidism. We deconvolute altered temporal interactions of the thyroid hormone precursor thyroglobulin with pathways implicated in hypothyroidism pathophysiology, such as Hsp70-/90-assisted folding, disulfide/redox processing, and N-glycosylation. Functional siRNA screening identified VCP and TEX264 as key protein degradation components whose inhibition selectively rescues mutant prohormone secretion. Ultimately, our results provide novel insight into the temporal coordination of protein homeostasis, and our TRIP method should find broad applications in investigating protein-folding diseases and cellular processes.

Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation.

The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.

Negative mood induction in children: An examination across mood, physiological, and cognitive variables.

Experimental mood induction procedures are commonly used in studies of children's emotions, although research on their effectiveness is lacking. Studies that support their effectiveness report sample-level changes in self-reported affect from pre- to post-induction, and a subset of children who do not self-report expected changes in affect (i.e., "nonresponders"). Given children's limited abilities to self-report their emotions, it is critical to know whether these paradigms also shift physiological and social-cognitive indices of emotion. We hypothesized increases in physiological reactivity and accuracy for discerning facial expressions of negative emotions from pre- to post-induction and smaller increases for nonresponders, Children (N = 80; 7- to 12-year-olds) completed a facial emotion recognition task and had an electrocardiogram recorded to index high-frequency heart rate variability (HF-HRV) before and after a mood induction procedure. The mood induction involved watching a 3-min sad film clip while attending to their feelings. In the sample overall, from pre- to post-mood induction, children self-reported significantly sadder affect, displayed significant increases in HF-HRV, and displayed significant increases in accuracy of recognizing facial emotion expressions congruent with the mood induced. One quarter (25%) of the sample did not self-report expected increases in sad affect. Contrary to expectations, responders and nonresponders did not differ in mood-induced changes in physiological reactivity or emotion recognition accuracy. These findings support that mood inductions are efficacious in shifting not only children's self-reported affect but also underlying physiological and social-cognitive processes. Furthermore, they are an effective methodology for research questions related to underlying processes even in self-reported nonresponders.

Mild Cognitive Impairment Subtype Performance in Comparison to Healthy Older Controls on the NIH Toolbox and Cogstate.

BACKGROUND: Early detection is necessary for the treatment of dementia. Computerized testing has become more widely used in clinical trials; however, it is unclear how sensitive these measures are to early signs of neurodegeneration. We investigated the use of the NIH Toolbox-Cognition (NIHTB-CB) and Cogstate-Brief computerized neuropsychological batteries in the identification of mild cognitive impairment (MCI) versus healthy older adults [healthy control (HC)] and amnestic (aMCI) versus nonamnestic MCI (naMCI). Exploratory analyses include investigating potential racial differences. METHODS: Two hundred six older adults were diagnosed as aMCI (n = 58), naMCI (n = 15), or cognitively healthy (HC; n = 133). RESULTS: The NIH Toolbox-CB subtests of Flanker, Picture Sequence Memory, and Picture Vocabulary significantly differentiated MCI from HC. Further, subtests from both computerized batteries differentiated patients with aMCI from those with naMCI. Although the main effect of race differences was noted on tests and in diagnostic groups was significant, there were no significant race-by-test interactions. CONCLUSIONS: Computer-based subtests vary in their ability to help distinguish MCI subtypes, though these tests provide less expensive and easier-to-administer clinical screeners to help identify patients early who may qualify for more comprehensive evaluations. Further work is needed, however, to refine computerized tests to achieve better precision in distinguishing impairment subtypes.

Wild chimpanzees exhibit humanlike aging of glucocorticoid regulation.

Cortisol, a key product of the stress response, has critical influences on degenerative aging in humans. In turn, cortisol production is affected by senescence of the hypothalamic-pituitary-adrenal (HPA) axis, leading to progressive dysregulation and increased cortisol exposure. These processes have been studied extensively in industrialized settings, but few comparative data are available from humans and closely related species living in natural environments, where stressors are very different. Here, we examine age-related changes in urinary cortisol in a 20-y longitudinal study of wild chimpanzees (n = 59 adults) in the Kanyawara community of Kibale National Park, Uganda. We tested for three key features of HPA aging identified in many human studies: increased average levels, a blunted diurnal rhythm, and enhanced response to stressors. Using linear mixed models, we found that aging was associated with a blunting of the diurnal rhythm and a significant linear increase in cortisol, even after controlling for changes in dominance rank. These effects did not differ by sex. Aging did not increase sensitivity to energetic stress or social status. Female chimpanzees experienced their highest levels of cortisol during cycling (versus lactation), and this effect increased with age. Male chimpanzees experienced their highest levels when exposed to sexually attractive females, but this effect was diminished by age. Our results indicate that chimpanzees share some key features of HPA aging with humans. These findings suggest that impairments of HPA regulation are intrinsic to the aging process in hominids and are side effects neither of extended human life span nor of atypical environments.

Signatures of emotional face processing measured by event-related potentials in 7-month-old infants.

The ability to distinguish facial emotions emerges in infancy. Although this ability has been shown to emerge between 5 and 7 months of age, the literature is less clear regarding the extent to which neural correlates of perception and attention play a role in processing of specific emotions. This study's main goal was to examine this question among infants. To this end, we presented angry, fearful, and happy faces to 7-month-old infants (N = 107, 51% female) while recording event-related brain potentials. The perceptual N290 component showed a heightened response for fearful and happy relative to angry faces. Attentional processing, indexed by the P400, showed some evidence of a heightened response for fearful relative to happy and angry faces. We did not observe robust differences by emotion in the negative central (Nc) component, although trends were consistent with previous work suggesting a heightened response to negatively valenced expressions. Results suggest that perceptual (N290) and attentional (P400) processing is sensitive to emotions in faces, but these processes do not provide evidence for a fear-specific bias across components.

Resolving the full spectrum of human genome variation using Linked-Reads.

Large-scale population analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short-read whole-genome sequencing. However, these short-read approaches fail to give a complete picture of a genome. They struggle to identify structural events, cannot access repetitive regions, and fail to resolve the human genome into haplotypes. Here, we describe an approach that retains long range information while maintaining the advantages of short reads. Starting from ∼1 ng of high molecular weight DNA, we produce barcoded short-read libraries. Novel informatic approaches allow for the barcoded short reads to be associated with their original long molecules producing a novel data type known as "Linked-Reads". This approach allows for simultaneous detection of small and large variants from a single library. In this manuscript, we show the advantages of Linked-Reads over standard short-read approaches for reference-based analysis. Linked-Reads allow mapping to 38 Mb of sequence not accessible to short reads, adding sequence in 423 difficult-to-sequence genes including disease-relevant genes STRC, SMN1, and SMN2 Both Linked-Read whole-genome and whole-exome sequencing identify complex structural variations, including balanced events and single exon deletions and duplications. Further, Linked-Reads extend the region of high-confidence calls by 68.9 Mb. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.

HD-tDCS as a neurorehabilitation technique for a case of post-anoxic leukoencephalopathy.

Post-anoxic leukoencephalopathy is a rare event that causes global demyelination secondary to anoxic injury. Given the nature and extent of the damage, cognitive and functional deficits are typically chronic even after standard therapies. Here, we describe a novel treatment approach that used high definition transcranial direct-current stimulation (HD-tDCS) with a 62-year-old male who was 5 years post-anoxic leukoencephalopathy secondary to an accidental drug overdose. HD-tDCS was administered over the left lateral prefrontal cortex across 29 daily sessions at 2 mA (20 min/session) in order to address dysexecutive behaviors. Results demonstrated improved delayed memory and trends for improved visuospatial and semantic fluency performance as well as improved insight and daily functioning, all of which returned to baseline by the end of a 10 week no-contact follow up period. Resting state fMRI connectivity results mirrored these changes by showing increased dorsal attention and cingulo-opercular but reduced ventral attention network connectivity after session 29, all of which returned to baseline at follow-up. These findings suggest HD-tDCS may benefit functioning even following serious and pervasive anoxic injury. Findings also suggest the need for continued HD-tDCS for maintenance purposes, though future work is needed to identify optimal dose-response information.

The Antidepressant Duloxetine Inhibits Platelet Function and Protects against Thrombosis.

While cardiovascular disease (CVD) is the leading cause of death, major depressive disorder (MDD) is the primary cause of disability, affecting more than 300 million people worldwide. Interestingly, there is evidence that CVD is more prevalent in people with MDD. It is well established that neurotransmitters, namely serotonin and norepinephrine, are involved in the biochemical mechanisms of MDD, and consequently, drugs targeting serotonin-norepinephrine reuptake, such as duloxetine, are commonly prescribed for MDD. In this connection, serotonin and norepinephrine are also known to play critical roles in primary hemostasis. Based on these considerations, we investigated if duloxetine can be repurposed as an antiplatelet medication. Our results-using human and/or mouse platelets show that duloxetine dose-dependently inhibited agonist-induced platelet aggregation, compared to the vehicle control. Furthermore, it also blocked agonist-induced dense and α-granule secretion, integrin αIIbß3 activation, phosphatidylserine expression, and clot retraction. Moreover duloxetine-treated mice had a significantly prolonged occlusion time. Finally, duloxetine was also found to impair hemostasis. Collectively, our data indicate that the antidepressant duloxetine, which is a serotonin-norepinephrine antagonist, exerts antiplatelet and thromboprotective effects and inhibits hemostasis. Consequently, duloxetine, or a rationally designed derivative, presents potential benefits in the context of CVD, including that associated with MDD.

Prosocial Video Game Content, Empathy and Cognitive Ability in a Large Sample of Youth.

Whether playing video games with prosocial content has an influence on empathy among players remains contentious in the research literature. Some evidence suggests playing cooperatively with other gamers enhances empathy, but data have not conclusively linked prosocial content with empathy. Further, mechanisms of this potential relationship are unclear, and little work has been conducted on how cognitive skills, such as fluid reasoning, may mediate this relationship. The current study examines these relationships with a large sample of 3034 youth (27.2% female, Mage = 11.2; range 8-17 at time 1) in Singapore. Data were considered longitudinally across two years in three waves. Ultimately, no evidence emerged that prosocial content in video games had any impact on empathy related outcomes, nor was fluid reasoning a mediator variable for any relationship. However, variables such as social competence and depression and anxiety symptoms were highly related to empathy measures. This evidence adds to the growing debate in the field that video games may not dramatically alter, whether positively or negatively, the development of emotional and behavioral outcomes for youth.

Exposure to prenatal maternal distress and infant white matter neurodevelopment.

The prenatal period represents a critical time for brain growth and development. These rapid neurological advances render the fetus susceptible to various influences with life-long implications for mental health. Maternal distress signals are a dominant early life influence, contributing to birth outcomes and risk for offspring psychopathology. This prospective longitudinal study evaluated the association between prenatal maternal distress and infant white matter microstructure. Participants included a racially and socioeconomically diverse sample of 85 mother-infant dyads. Prenatal distress was assessed at 17 and 29 weeks' gestational age (GA). Infant structural data were collected via diffusion tensor imaging at 42-45 weeks' postconceptional age. Findings demonstrated that higher prenatal maternal distress at 29 weeks' GA was associated with increased fractional anisotropy (b = .283, t(64) = 2.319, p = .024) and with increased axial diffusivity (b = .254, t(64) = 2.067, p = .043) within the right anterior cingulate white matter tract. No other significant associations were found with prenatal distress exposure and tract fractional anisotropy or axial diffusivity at 29 weeks' GA, nor earlier in gestation.

Children's recognition of happy, sad, and angry facial expressions across emotive intensities.

Sharing emotional experiences is a key task that requires accurate recognition of peers' emotions during middle childhood. Existing research suggests that children are proficient at discerning emotion from facial expressions during middle childhood, but this research has focused on recognition of adults' intense emotional expressions. In this study, facial emotion recognition for children's happy, sad, and angry expressions across low, medium, and high intensities was measured in a sample of 7- to 10-year-old children (N = 80; 53% female) to quantify overall accurate recognition as well as inaccuracies, including identifying an emotion as present when it is not (false alarms) and failing to identify an emotion when present (miss rate). Children's recognition accuracy for low-threshold happiness, sadness, and anger was quite poor but improved in a cubic fashion as expression intensity increased, with dramatic improvements across medium-intensity expressions, and little further improvement across high-intensity expressions. A positivity bias was evident; children were more accurate at recognizing happiness than at recognizing sadness and anger, rarely failed to identify happiness when present, and tended to mislabel expressions as happy rather than as angry or sad. Children were generally better at recognizing anger compared with sadness but were more accurate at recognizing subtle sadness compared with anger, which appeared to be due to children missing subtle anger when present. The findings are discussed with regard to the functionality of others' happiness for signaling positive socializing opportunities, anger for signaling threatening interactions, and sadness for prompting prosocial action and with regard to how children's facial emotion recognition may affect general socioemotional development.

Contextual Data in IPUMS DHS: Physical and Social Environment Variables linked to the Demographic and Health Surveys.

The Demographic and Health Surveys (DHS) are the most important source of comparative information on the health of women and young children in low- and middle-income countries and are well-suited for studies of the relationship between environmental factors and health. However, barriers have limited the use of the DHS for these purposes. IPUMS DHS, an online data dissemination tool, overcomes these barriers, simplifying comparative analyses with DHS. IPUMS DHS recently incorporated environmental variables that can easily be attached to individual or household records, facilitating the use of DHS data for the study of population and environment issues. We provide a brief introduction to IPUMS DHS, describe the current and anticipated environmental variables and how to use them, and provide an example of the novel research possibilities facilitated by this latest IPUMS DHS development. IPUMS-DHS is available free online at dhs.ipums.org.

Tranexamic acid and traumatic brain injuries.

The CRASH-3 trial examined the use of tranexamic acid (TXA) in patients with intracranial bleeding secondary to traumatic brain injury. The trial demonstrated that TXA, an antifibrinolytic medication, reduces mortality in patients with mild to moderate head injuries. However, because of the trial's multiple limitations, TXA cannot yet be called the gold standard.

Seed dispersal by dispersing juvenile animals: a source of functional connectivity in fragmented landscapes.

Juvenile animals generally disperse from their birthplace to their future breeding territories. In fragmented landscapes, habitat-specialist species must disperse through the anthropogenic matrix where remnant habitats are embedded. Here, we test the hypothesis that dispersing juvenile frugivores leave a footprint in the form of seed deposition through the matrix of fragmented landscapes. We focused on the Sardinian warbler ( Sylvia melanocephala), a resident frugivorous passerine. We used data from field sampling of bird-dispersed seeds in the forest and matrix of a fragmented landscape, subsequent disperser identification through DNA-barcoding analysis, and data from a national bird-ringing programme. Seed dispersal by Sardinian warblers was confined to the forest most of the year, but warblers contributed a peak of seed-dispersal events in the matrix between July and October, mainly attributable to dispersing juveniles. Our study uniquely connects animal and plant dispersal, demonstrating that juveniles of habitat-specialist frugivores can provide mobile-link functions transiently, but in a seasonally predictable way.

Does Prenatal Maternal Distress Contribute to Sex Differences in Child Psychopathology?

PURPOSE OF REVIEW: Prenatal maternal psychological distress is an established risk factor for the development of psychopathology in offspring. The purpose of this review is to evaluate whether sex differences in fetal responses to maternal distress contribute to sex differences in subsequent psychopathology. RECENT FINDINGS: Male and female fetuses respond differently to stress signals. We review recent evidence that demonstrates a sex-specific pattern of association between prenatal maternal distress and pathways associated with risk for psychopathology including offspring hypothalamic pituitary adrenocortical (HPA) axis regulation, brain development, and negative emotionality. Prenatal maternal distress exerts sex-specific consequences on the fetus. These differences may contribute to the well-established sex differences in psychopathology and in particular to greater female vulnerability to develop internalizing problems.

Early somatic mosaicism is a rare cause of long-QT syndrome.

Somatic mosaicism, the occurrence and propagation of genetic variation in cell lineages after fertilization, is increasingly recognized to play a causal role in a variety of human diseases. We investigated the case of life-threatening arrhythmia in a 10-day-old infant with long QT syndrome (LQTS). Rapid genome sequencing suggested a variant in the sodium channel NaV1.5 encoded by SCN5A, NM_000335:c.5284G > T predicting p.(V1762L), but read depth was insufficient to be diagnostic. Exome sequencing of the trio confirmed read ratios inconsistent with Mendelian inheritance only in the proband. Genotyping of single circulating leukocytes demonstrated the mutation in the genomes of 8% of patient cells, and RNA sequencing of cardiac tissue from the infant confirmed the expression of the mutant allele at mosaic ratios. Heterologous expression of the mutant channel revealed significantly delayed sodium current with a dominant negative effect. To investigate the mechanism by which mosaicism might cause arrhythmia, we built a finite element simulation model incorporating Purkinje fiber activation. This model confirmed the pathogenic consequences of cardiac cellular mosaicism and, under the presenting conditions of this case, recapitulated 2:1 AV block and arrhythmia. To investigate the extent to which mosaicism might explain undiagnosed arrhythmia, we studied 7,500 affected probands undergoing commercial gene-panel testing. Four individuals with pathogenic variants arising from early somatic mutation events were found. Here we establish cardiac mosaicism as a causal mechanism for LQTS and present methods by which the general phenomenon, likely to be relevant for all genetic diseases, can be detected through single-cell analysis and next-generation sequencing.

Unequal distribution of the mating type (MAT) locus idiomorphs in dermatophyte species.

The mating type (MAT) locus is the key regulator of sexual reproduction in fungi. In the dermatophytes and other Ascomycetes this genomic region exists in two distinct forms (idiomorphs) and their balanced presence is a precondition for successful mating in heterothallic fungi. But the MAT locus not only drives sexual reproduction, it has also been shown to influence pathogenicity, virulence, and/or morphological changes in pathogenic fungi of the genera Candida, Histoplasma, and Cryptococcus. In order to find out whether there are similar trends in dermatophytes, we investigated the MAT locus of 19 anthropophilic and zoophilic species via Sanger sequencing and primer walking. We identified for the first time the MAT locus idiomorphs of the dermatophyte species Microsporum audouinii (MAT1-2), M. ferrugineum (MAT1-2), Trichophyton schoenleinii (MAT1-2), T. bullosum (MAT1-1), T. quinckeanum (MAT1-1), T. concentricum (MAT1-1), T. eriotrephon (MAT1-1), and T. erinacei (MAT1-2). In addition, we determined the MAT locus sequence for dermatophyte species whose mating type idiomorphs had been described on the basis of results of classical confrontation experiments (e.g. M. canis, MAT1-2) and we confirmed recently published molecular data (e.g. T. rubrum, MAT1-2). Our results corroborate that MAT locus idiomorphs are unequally distributed in the majority of the analyzed species and the ability to mate with a partner of the opposite sex is limited to a few zoophilic species. Clonal spreads are identified that are connected to one of the idiomorphs and a higher virulence and/or a higher transmission rate to humans (T. benhamiae and T. mentagrophytes). For the imbalanced idiomorph distribution pattern we hypothesize that either: (I) one of the mating type idiomorphs may be extinct due to clonal reproduction (e.g., T. rubrum and M. canis), (II) mating partners of one species adapted to different hosts followed by speciation in the new niche (e.g., T. equinum and T. tonsurans) or (III) unisexual reproduction is the next evolutionary stage of propagation in dermatophytes which involves the extinction of one mating idiomorph.