nils-herrmann/clean_scirepeval huggingface dataset:
Ribosome biogenesis is a downstream effector of the oncogenic U2AF1-S34F mutation
Venue: PLoS biology

U2 Small Nuclear RNA Auxiliary Factor 1 (U2AF1) forms a heterodimeric complex with U2AF2 that is primarily responsible for 3ʹ splice site selection. U2AF1 mutations have been identified in most cancers but are prevalent in Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML), and the most common mutation is a missense substitution of serine-34 to phenylalanine (S34F). The U2AF heterodimer also has a noncanonical function as a translational regulator. Here, we report that the U2AF1-S34F mutation results in specific misregulation of the translation initiation and ribosome biogenesis machinery. The net result is an increase in mRNA translation at the single-cell level. Among the translationally up-regulated targets of U2AF1-S34F is Nucleophosmin 1 (NPM1), which is a major driver of myeloid malignancy. Depletion of NPM1 impairs the viability of the U2AF1-S34F mutant cells and causes ribosomal RNA (rRNA) processing defects, thus indicating an unanticipated synthetic interaction between U2AF1, NPM1, and ribosome biogenesis. Our results establish a unique molecular phenotype for the U2AF1 mutation that recapitulates translational misregulation in myeloid disease.
Many, but not all, lineage-specific genes can be explained by homology detection failure
Venue: PLoS biology

Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study.
Integrating when and what information in the left parietal lobe allows language rule generalization
Venue: PLoS biology

A crucial aspect when learning a language is discovering the rules that govern how words are combined in order to convey meanings. Because rules are characterized by sequential co-occurrences between elements (e.g., “These cupcakes are unbelievable”), tracking the statistical relationships between these elements is fundamental. However, purely bottom-up statistical learning alone cannot fully account for the ability to create abstract rule representations that can be generalized, a paramount requirement of linguistic rules. Here, we provide evidence that, after the statistical relations between words have been extracted, the engagement of goal-directed attention is key to enable rule generalization. Incidental learning performance during a rule-learning task on an artificial language revealed a progressive shift from statistical learning to goal-directed attention. In addition, and consistent with the recruitment of attention, functional MRI (fMRI) analyses of late learning stages showed left parietal activity within a broad bilateral dorsal frontoparietal network. Critically, repetitive transcranial magnetic stimulation (rTMS) on participants’ peak of activation within the left parietal cortex impaired their ability to generalize learned rules to a structurally analogous new language. No stimulation or rTMS on a nonrelevant brain region did not have the same interfering effect on generalization. Performance on an additional attentional task showed that this rTMS on the parietal site hindered participants’ ability to integrate “what” (stimulus identity) and “when” (stimulus timing) information about an expected target. The present findings suggest that learning rules from speech is a two-stage process: following statistical learning, goal-directed attention—involving left parietal regions—integrates “what” and “when” stimulus information to facilitate rapid rule generalization.
Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Venue: PLoS biology

Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo–electron microscopy structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which may act as an architectural co-factor to stabilize a protein–protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation.
Multiple systems in macaques for tracking prediction errors and other types of surprise
Venue: PLoS biology

Animals learn from the past to make predictions. These predictions are adjusted after prediction errors, i.e., after surprising events. Generally, most reward prediction errors models learn the average expected amount of reward. However, here we demonstrate the existence of distinct mechanisms for detecting other types of surprising events. Six macaques learned to respond to visual stimuli to receive varying amounts of juice rewards. Most trials ended with the delivery of either 1 or 3 juice drops so that animals learned to expect 2 juice drops on average even though instances of precisely 2 drops were rare. To encourage learning, we also included sessions during which the ratio between 1 and 3 drops changed. Additionally, in all sessions, the stimulus sometimes appeared in an unexpected location. Thus, 3 types of surprising events could occur: reward amount surprise (i.e., a scalar reward prediction error), rare reward surprise, and visuospatial surprise. Importantly, we can dissociate scalar reward prediction errors—rewards that deviated from the average reward amount expected—and rare reward events—rewards that accorded with the average reward expectation but that rarely occurred. We linked each type of surprise to a distinct pattern of neural activity using functional magnetic resonance imaging. Activity in the vicinity of the dopaminergic midbrain only reflected surprise about the amount of reward. Lateral prefrontal cortex had a more general role in detecting surprising events. Posterior lateral orbitofrontal cortex specifically detected rare reward events regardless of whether they followed average reward amount expectations, but only in learnable reward environments.
Expanding conservation culturomics and iEcology from terrestrial to aquatic realms
Venue: PLoS biology

The ongoing digital revolution in the age of big data is opening new research opportunities. Culturomics and iEcology, two emerging research areas based on the analysis of online data resources, can provide novel scientific insights and inform conservation and management efforts. To date, culturomics and iEcology have been applied primarily in the terrestrial realm. Here, we advocate for expanding such applications to the aquatic realm by providing a brief overview of these new approaches and outlining key areas in which culturomics and iEcology are likely to have the highest impact, including the management of protected areas; fisheries; flagship species identification; detection and distribution of threatened, rare, and alien species; assessment of ecosystem status and anthropogenic impacts; and social impact assessment. When deployed in the right context with awareness of potential biases, culturomics and iEcology are ripe for rapid development as low-cost research approaches based on data available from digital sources, with increasingly diverse applications for aquatic ecosystems.
Modeling flexible behavior in childhood to adulthood shows age-dependent learning mechanisms and less optimal learning in autism in each age group
Venue: PLoS biology

Flexible behavior is critical for everyday decision-making and has been implicated in restricted, repetitive behaviors (RRB) in autism spectrum disorder (ASD). However, how flexible behavior changes developmentally in ASD remains largely unknown. Here, we used a developmental approach and examined flexible behavior on a probabilistic reversal learning task in 572 children, adolescents, and adults (ASD N = 321; typical development [TD] N = 251). Using computational modeling, we quantified latent variables that index mechanisms underlying perseveration and feedback sensitivity. We then assessed these variables in relation to diagnosis, developmental stage, core autism symptomatology, and associated psychiatric symptoms. Autistic individuals showed on average more perseveration and less feedback sensitivity than TD individuals, and, across cases and controls, older age groups showed more feedback sensitivity than younger age groups. Computational modeling revealed that dominant learning mechanisms underpinning flexible behavior differed across developmental stages and reduced flexible behavior in ASD was driven by less optimal learning on average within each age group. In autistic children, perseverative errors were positively related to anxiety symptoms, and in autistic adults, perseveration (indexed by both task errors and model parameter estimates) was positively related to RRB. These findings provide novel insights into reduced flexible behavior in relation to clinical symptoms in ASD.
Sequence heterochrony led to a gain of functionality in an immature stage of the central complex: A fly–beetle insight
Venue: PLoS biology

Animal behavior is guided by the brain. Therefore, adaptations of brain structure and function are essential for animal survival, and each species differs in such adaptations. The brain of one individual may even differ between life stages, for instance, as adaptation to the divergent needs of larval and adult life of holometabolous insects. All such differences emerge during development, but the cellular mechanisms behind the diversification of brains between taxa and life stages remain enigmatic. In this study, we investigated holometabolous insects in which larvae differ dramatically from the adult in both behavior and morphology. As a consequence, the central complex, mainly responsible for spatial orientation, is conserved between species at the adult stage but differs between larvae and adults of one species as well as between larvae of different taxa. We used genome editing and established transgenic lines to visualize cells expressing the conserved transcription factor retinal homeobox, thereby marking homologous genetic neural lineages in both the fly Drosophila melanogaster and the beetle Tribolium castaneum. This approach allowed us for the first time to compare the development of homologous neural cells between taxa from embryo to the adult. We found complex heterochronic changes including shifts of developmental events between embryonic and pupal stages. Further, we provide, to our knowledge, the first example of sequence heterochrony in brain development, where certain developmental steps changed their position within the ontogenetic progression. We show that through this sequence heterochrony, an immature developmental stage of the central complex gains functionality in Tribolium larvae.
Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae
Venue: PLoS biology

Predicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important human pathogen, and the pneumococcal conjugate vaccines (PCVs), which target only a fraction of the strains in the population. Here, we use the frequencies of accessory genes to predict changes in the pneumococcal population after vaccination, hypothesizing that these frequencies reflect negative frequency-dependent selection (NFDS) on the gene products. We find that the standardized predicted fitness of a strain, estimated by an NFDS-based model at the time the vaccine is introduced, enables us to predict whether the strain increases or decreases in prevalence following vaccination. Further, we are able to forecast the equilibrium post-vaccine population composition and assess the invasion capacity of emerging lineages. Overall, we provide a method for predicting the impact of an intervention on pneumococcal populations with potential application to other bacterial pathogens in which NFDS is a driving force.
Entraining neurons via noninvasive electric stimulation improves cognition
Venue: PLoS biology

Transcranial Alternating Current Stimulation (tACS) is a method that injects rhythmic currents into the human brain via electrodes attached to the scalp of a participant. This technique allows researchers to control naturally occurring brain rhythms and study their causal relevance for cognition. Recent findings, however, cast doubts on the effectiveness of tACS to stimulate the brain and its mode of action. Two new studies by Vieira and colleagues and Marchesotti and colleagues reported in the current issue report promising new results in showing that tACS can entrain single neuron activity and improve reading abilities in dyslexic individuals.
Neural speech restoration at the cocktail party: Auditory cortex recovers masked speech of both attended and ignored speakers
Venue: PLoS biology

Humans are remarkably skilled at listening to one speaker out of an acoustic mixture of several speech sources. Two speakers are easily segregated, even without binaural cues, but the neural mechanisms underlying this ability are not well understood. One possibility is that early cortical processing performs a spectrotemporal decomposition of the acoustic mixture, allowing the attended speech to be reconstructed via optimally weighted recombinations that discount spectrotemporal regions where sources heavily overlap. Using human magnetoencephalography (MEG) responses to a 2-talker mixture, we show evidence for an alternative possibility, in which early, active segregation occurs even for strongly spectrotemporally overlapping regions. Early (approximately 70-millisecond) responses to nonoverlapping spectrotemporal features are seen for both talkers. When competing talkers’ spectrotemporal features mask each other, the individual representations persist, but they occur with an approximately 20-millisecond delay. This suggests that the auditory cortex recovers acoustic features that are masked in the mixture, even if they occurred in the ignored speech. The existence of such noise-robust cortical representations, of features present in attended as well as ignored speech, suggests an active cortical stream segregation process, which could explain a range of behavioral effects of ignored background speech.
Neurobiological origins of individual differences in mathematical ability
Venue: PLoS biology

Mathematical ability is heritable and related to several genes expressing proteins in the brain. It is unknown, however, which intermediate neural phenotypes could explain how these genes relate to mathematical ability. Here, we examined genetic effects on cerebral cortical volume of 3–6-year-old children without mathematical training to predict mathematical ability in school at 7–9 years of age. To this end, we followed an exploration sample (n = 101) and an independent replication sample (n = 77). We found that ROBO1, a gene known to regulate prenatal growth of cerebral cortical layers, is associated with the volume of the right parietal cortex, a key region for quantity representation. Individual volume differences in this region predicted up to a fifth of the behavioral variance in mathematical ability. Our findings indicate that a fundamental genetic component of the quantity processing system is rooted in the early development of the parietal cortex.
Gradient of tactile properties in the rat whisker pad
Venue: PLoS biology

The array of vibrissae on a rat’s face is the first stage in a high-resolution tactile sensing system. Progressing from rostral to caudal in any vibrissae row results in an increase in whisker length and thickness. This may, in turn, provide a systematic map of separate tactile channels governed by the mechanical properties of the whiskers. To examine whether this map is expressed in a location-dependent transformation of tactile signals into whisker vibrations and neuronal responses, we monitored whiskers’ movements across various surfaces and edges. We found a robust rostral-caudal (R-C) gradient of tactile information transmission in which rostral shorter vibrissae displayed a higher sensitivity and bigger differences in response to different textures, whereas longer caudal vibrissae were less sensitive. This gradient is evident in several dynamic properties of vibrissae trajectories. As rodents sample the environment with multiple vibrissae, we found that combining tactile signals from multiple vibrissae resulted in an increased sensitivity and bigger differences in response to the different textures. Nonetheless, we found that texture identity is not represented spatially across the whisker pad. Based on the responses of first-order sensory neurons, we found that they adhere to the tactile information conveyed by the vibrissae. That is, neurons innervating rostral vibrissae were better suited for texture discrimination, whereas neurons innervating caudal vibrissae were more suited for edge detection. These results suggest that the whisker array in rodents forms a sensory structure in which different facets of tactile information are transmitted through location-dependent gradient of vibrissae on the rat’s face.
Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio
Venue: PLoS biology

Externally deposited eggs begin development with an immense cytoplasm and a single overwhelmed nucleus. Rapid mitotic cycles restore normality as the ratio of nuclei to cytoplasm (N/C) increases. A threshold N/C has been widely proposed to activate zygotic genome transcription and onset of morphogenesis at the mid-blastula transition (MBT). To test whether a threshold N/C is required for these events, we blocked N/C increase by down-regulating cyclin/Cdk1 to arrest early cell cycles in Drosophila. Embryos that were arrested two cell cycles prior to the normal MBT activated widespread transcription of the zygotic genome including genes previously described as N/C dependent. Zygotic transcription of these genes largely retained features of their regulation in space and time. Furthermore, zygotically regulated post-MBT events such as cellularization and gastrulation movements occurred in these cell cycle–arrested embryos. These results are not compatible with models suggesting that these MBT events are directly coupled to N/C. Cyclin/Cdk1 activity normally declines in tight association with increasing N/C and is regulated by N/C. By experimentally promoting the decrease in cyclin/Cdk1, we uncoupled MBT from N/C increase, arguing that N/C-guided down-regulation of cyclin/Cdk1 is sufficient for genome activation and MBT.
Expression of concern: A chaperonin subunit with unique structures is essential for folding of a specific substrate
Venue: PLoS biology

Concerns were raised about discontinuities in the lower regions of lanes 1 and 5 in Fig 2B, which suggest that rectangular portions of the image were spliced or otherwise altered. The corresponding author provided the underlying gel image for Fig 2B (S1 File). Coomassie Brilliant Blue staining in the areas of concern was not as strong in the raw image as in the figure, supporting that the image was selectively enhanced or otherwise manipulated in these areas. This is in violation of community standards and PLOS Biology’s requirements for image data reporting, which require that any adjustments must be applied consistently to the entire image. The underlying data provided by the authors support the overall results presented in Fig 2B, although the PLOS Biology Editors remain concerned about the integrity with which the data were reported in the published article.
Visual detection is locked to the internal dynamics of cortico-motor control
Venue: PLoS biology

Movements overtly sample sensory information, making sensory analysis an active-sensing process. In this study, we show that visual information sampling is not just locked to the (overt) movement dynamics but to the internal (covert) dynamics of cortico-motor control. We asked human participants to perform continuous isometric contraction while detecting unrelated and unpredictable near-threshold visual stimuli. The motor output (force) shows zero-lag coherence with brain activity (recorded via electroencephalography) in the beta-band, as previously reported. In contrast, cortical rhythms in the alpha-band systematically forerun the motor output by 200 milliseconds. Importantly, visual detection is facilitated when cortico-motor alpha (not beta) synchronization is enhanced immediately before stimulus onset, namely, at the optimal phase relationship for sensorimotor communication. These findings demonstrate an ongoing coupling between visual sampling and motor control, suggesting the operation of an internal and alpha-cycling visuomotor loop.
A novel function for CDK2 activity at meiotic crossover sites
Venue: PLoS biology

Genetic diversity in offspring is induced by meiotic recombination, which is initiated between homologs at >200 sites originating from meiotic double-strand breaks (DSBs). Of this initial pool, only 1–2 DSBs per homolog pair will be designated to form meiotic crossovers (COs), where reciprocal genetic exchange occurs between parental chromosomes. Cyclin-dependent kinase 2 (CDK2) is known to localize to so-called “late recombination nodules” (LRNs) marking incipient CO sites. However, the role of CDK2 kinase activity in the process of CO formation remains uncertain. Here, we describe the phenotype of 2 Cdk2 point mutants with elevated or decreased activity, respectively. Elevated CDK2 activity was associated with increased numbers of LRN-associated proteins, including CDK2 itself and the MutL homolog 1 (MLH1) component of the MutLγ complex, but did not lead to increased numbers of COs. In contrast, reduced CDK2 activity leads to the complete absence of CO formation during meiotic prophase I. Our data suggest an important role for CDK2 in regulating MLH1 focus numbers and that the activity of this kinase is a key regulatory factor in the formation of meiotic COs.