bluuebunny/crossref_metadata_2025 huggingface dataset:
High Throughput Sequencing For Plant Virus Detection and Discovery
Authors: Villamor D. E. V. , Ho T. , Al Rwahnih M. , Martin R. R. , Tzanetakis I. E.
Published: February 2019

Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists’ utility in their research.
A case for environmental statistics of early-life effects
Authors: Frankenhuis Willem E. , Nettle Daniel , Dall Sasha R. X.
Published: February 2019

There is enduring debate over the question of which early-life effects are adaptive and which ones are not. Mathematical modelling shows that early-life effects can be adaptive in environments that have particular statistical properties, such as reliable cues to current conditions and high autocorrelation of environmental states. However, few empirical studies have measured these properties, leading to an impasse. Progress, therefore, depends on research that quantifies cue reliability and autocorrelation of environmental parameters in real environments. These statistics may be different for social and non-social aspects of the environment. In this paper, we summarize evolutionary models of early-life effects. Then, we discuss empirical data on environmental statistics from a range of disciplines. We highlight cases where data on environmental statistics have been used to test competing explanations of early-life effects. We conclude by providing guidelines for new data collection and reflections on future directions.

This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine'.
The evolution of early-life effects on social behaviour—why should social adversity carry over to the future?
Authors: Kuijper Bram , Johnstone Rufus A.
Published: February 2019

Numerous studies have shown that social adversity in early life can have long-lasting consequences for social behaviour in adulthood, consequences that may in turn be propagated to future generations. Given these intergenerational effects, it is puzzling why natural selection might favour such sensitivity to an individual’s early social environment. To address this question, we model the evolution of social sensitivity in the development of helping behaviours, showing that natural selection indeed favours individuals whose tendency to help others is dependent on early-life social experience. In organisms with non-overlapping generations, we find that natural selection can favour positive social feedbacks, in which individuals who received more help in early life are also more likely to help others in adulthood, while individuals who received no early-life help develop low tendencies to help others later in life. This positive social sensitivity is favoured because of an intergenerational relatedness feedback: patches with many helpers tend to be more productive, leading to higher relatedness within the local group, which in turn favours higher levels of help in the next generation. In organisms with overlapping generations, this positive feedback is less likely to occur, and those who received more help may instead be less likely to help others (negative social feedback). We conclude that early-life social influences can lead to strong between-individual differences in helping behaviour, which can take different forms dependent on the life history in question.

This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.
Revisiting mechanisms and functions of prenatal hormone-mediated maternal effects using avian species as a model
Authors: Groothuis Ton G. G. , Hsu Bin-Yan , Kumar Neeraj , Tschirren Barbara
Published: February 2019

Maternal effects can adaptively modulate offspring developmental trajectories in variable but predictable environments. Hormone synthesis is sensitive to environmental factors, and maternal hormones are thus a powerful mechanism to transfer environmental cues to the next generation. Birds have become a key model for the study of hormone-mediated maternal effects because the embryo develops outside the mother's body, facilitating the measurement and manipulation of prenatal hormone exposure. At the same time, birds are excellent models for the integration of both proximate and ultimate approaches, which is key to a better understanding of the evolution of hormone-mediated maternal effects. Over the past two decades, a surge of studies on hormone-mediated maternal effects has revealed an increasing number of discrepancies. In this review, we discuss the role of the environment, genetic factors and social interactions in causing these discrepancies and provide a framework to resolve them. We also explore the largely neglected role of the embryo in modulating the maternal signal, as well as costs and benefits of hormone transfer and expression for the different family members. We conclude by highlighting fruitful avenues for future research that have opened up thanks to new theoretical insights and technical advances in the field.

This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.
Early-life manipulation of cortisol and its receptor alters stress axis programming and social competence
Authors: Reyes-Contreras Maria , Glauser Gaétan , Rennison Diana J. , Taborsky Barbara
Published: February 2019

In many vertebrate species, early social experience generates long-term effects on later life social behaviour. These effects are accompanied by persistent modifications in the expression of genes implicated in the stress axis. It is unknown, however, whether stress axis programming can affect the development of social competence, and if so, by which mechanism(s). Here, we used pharmacological manipulations to persistently reprogramme the hypothalamic–pituitary–interrenal axis of juvenile cooperatively breeding cichlids,
Neolamprologus pulcher.
During the first two months of life, juveniles were repeatedly treated with cortisol, mifepristone or control treatments. Three months after the last manipulation, we tested for treatment effects on (i) social competence, (ii) the expression of genes coding for corticotropin-releasing factor (
crf
), glucocorticoid receptor (
gr1
) and mineralocorticoid receptor (
mr
) in the telencephalon and hypothalamus and (iii) cortisol levels. Social competence in a social challenge was reduced in cortisol-treated juveniles, which is in accordance with previous work applying early-life manipulations using different social experiences. During early life, both cortisol and mifepristone treatments induced a persistent downregulation of
crf
and upregulation of
mr
in the telencephalon. We suggest that these persistent changes in stress gene expression may represent an effective physiological mechanism for coping with stress.

This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.
Preterm birth in evolutionary context: a predictive adaptive response?
Authors: Williams Thomas C. , Drake Amanda J.
Published: February 2019

Preterm birth is a significant public health problem worldwide, leading to substantial mortality in the newborn period, and a considerable burden of complications longer term, for affected infants and their carers. The fact that it is so common, and rates vary between different populations, raising the question of whether in some circumstances it might be an adaptive trait. In this review, we outline some of the evolutionary explanations put forward for preterm birth. We specifically address the hypothesis of the predictive adaptive response, setting it in the context of the Developmental Origins of Health and Disease, and explore the predictions that this hypothesis makes for the potential causes and consequences of preterm birth. We describe how preterm birth can be triggered by a range of adverse environmental factors, including nutrition, stress and relative socioeconomic status. Examining the literature for any associated longer-term phenotypic changes, we find no strong evidence for a marked temporal shift in the reproductive life-history trajectory, but more persuasive evidence for a re-programming of the cardiovascular and endocrine system, and a range of effects on neurodevelopment. Distinguishing between preterm birth as a predictive, rather than immediate adaptive response will depend on the demonstration of a positive effect of these alterations in developmental trajectories on reproductive fitness.

This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine'.
Molecular subtyping and prognostic assessment based on tumor mutation burden in patients with lung adenocarcinomas
Authors: Wang Changzheng , Li Fuqiang , Xie Guoyun , Qiao Sitan , Shi Xulian , Deng Jianlian , Liang Han , Lin Cong , Zhao Xin , Wu Kui , Zhang Xiuqing
Published: February 2019

Tumor mutation burden (TMB) is a potential biomarker for response to immunotherapy. The subset of patients with TMB has not been well characterized in lung adenocarcinomas. Here we performed molecular subtyping based on TMB and compared the features of different subtypes including clinical features, somatic driver genes and mutational signatures. We found that patients with lower tumor mutation burden had a longer disease-free survival, while higher tumor mutation burden is associated with smoking and aging. Analysis of somatic driver genes and mutational signatures demonstrates a significant association between somaticRYR2mutations and the subtype with higher mutation burden. Overall, our study identified two molecular subtypes based on TMB and described the corresponding difference in their clinical and genomic levels.
BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions
Authors: Menzel Peter , Meyer Irmtraud M
Published: February 2019

Circular RNAs (circRNAs) are a class of RNA transcripts that originate from non-canonical splicing events and are characterized by a backsplice junction connecting the 3’ splice site to an upstream 5’ splice site. Here, we present the program BIQ for indexing and querying transcriptome sequencing datasets for backsplice junctions. BIQ can be used for instantaneously querying all indexed transcriptomes for occurrence and abundance of reads overlapping the backsplice junction of a particular circular RNA, which can help in the functional characterization of known and novel circular RNAs. BIQ is free software and available at https://github.com/pmenzel/biq.
Bacterial transformation buffers environmental fluctuations through the reversible integration of mobile genetic elements
Authors: Carvalho Gabriel , Fouchet David , Danesh Gonché , Godeux Anne-Sophie , Laaberki Maria-Halima , Pontier Dominique , Charpentier Xavier , Venner Samuel
Published: February 2019

Horizontal gene transfer (HGT) is known to promote the spread of genes in bacterial communities, which is of primary importance to human health when these genes provide resistance to antibiotics. Among the main HGT mechanisms, natural transformation stands out as being widespread and encoded by the bacterial core genome. From an evolutionary perspective, transformation is often viewed as a mean to generate genetic diversity and mixing within bacterial populations. However, another recent paradigm proposes that its main evolutionary function would be to cure bacterial genomes from their parasitic mobile genetic elements (MGEs). Here, we propose to combine these two seemingly opposing points of view because MGEs, although costly for bacterial cells, can carry functions that are point-in-time beneficial to bacteria under stressful conditions (e.g. antibiotic resistance genes under antibiotic exposure). Using computational modeling, we show that, in stochastic environments (unpredictable stress exposure), an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes but costly for the replication of host cells. By ensuring such reversible genetic diversification (acquisition then removal of MGEs), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, which would explain its striking conservation.
Gtf2i and Gtf2ird1 mutation are not sufficient to reproduce mouse phenotypes caused by the Williams Syndrome critical region
Authors: Kopp Nathan , McCullough Katherine , Maloney Susan E. , Dougherty Joseph D.
Published: February 2019

Williams syndrome is a neurodevelopmental disorder caused by a 1.5-1.8Mbp deletion on chromosome 7q11.23, affecting the copy number of 26-28 genes. Phenotypes of Williams syndrome include cardiovascular problems, craniofacial dysmorphology, deficits in visual spatial cognition, and a characteristic hypersocial personality. There are still no genes in the region that have been consistently linked to the cognitive and behavioral phenotypes, although human studies and mouse models have led to the current hypothesis that the general transcription factor 2 I family of genes, GTF2I and GTF2IRD1, are responsible. Here we test the hypothesis that these two transcription factors are sufficient to reproduce the phenotypes that are caused by deletion of the Williams syndrome critical region (WSCR). We compare a new mouse model with loss of function mutations in both Gtf2i and Gtf2ird1 to an established mouse model lacking the complete WSCR. We show that the complete deletion model has deficits across several behavioral domains including social communication, motor functioning, and conditioned fear that are not explained by loss of function mutations in Gtf2i and Gtf2ird1. Furthermore, transcriptome profiling of the hippocampus shows changes in synaptic genes in the complete deletion model that are not seen in the double mutants. Thus, we have thoroughly defined a set of molecular and behavioral consequences of complete WSCR deletion, and shown that other genes or combinations of genes are necessary to produce these phenotypic effects.
Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean
Authors: Bayer Barbara , Hansman Roberta L. , Bittner Meriel J. , Noriega-Ortega Beatriz E. , Niggemann Jutta , Dittmar Thorsten , Herndl Gerhard J.
Published: February 2019

Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20-40% of the ocean’s prokaryotic plankton and thus play an important role in global nitrogen cycle. However, it remains enigmatic to what extent these chemolithoautotrophic archaea are releasing dissolved organic matter (DOM). A combination of targeted and untargeted metabolomics was used to characterise the exometabolomes of three model AOA strains of theNitrosopumilusgenus. Furthermore, we compared the composition of intra- and extracellular dissolved free amino acids (DFAA). Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivity, dominated by nitrogen-containing compounds. A significant fraction of the released DOM consisted of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. In growingNitrosopumiluscultures, hydrophobic amino acids were likely released as a result of passive diffusion corresponding to ammonia oxidation activity, while glycine was continuously released at high rates. Our results suggest that AOA release several ecologically and biochemically relevant metabolites, potentially fueling heterotrophic prokaryotes in the ocean.
Peptide Secondary Structure Prediction using Evolutionary Information
Authors: Singh Harinder , Singh Sandeep , Singh Raghava Gajendra Pal
Published: February 2019

BACKGROUND

In the past, large numbers of methods have been developed for predicting secondary structure of proteins. Best of author’s knowledge no method has been specifically developed for predicting secondary structure of peptides. We analyzed secondary structure of peptides and proteins; it was observed that same peptide in protein adopt different secondary structures. Considering the wide application of peptides in therapeutic market, we made attempt to develop a method called PEP2D for predicting secondary structure of peptides.

RESULTS

In this study, 3107 unique peptides have been used to train, test and evaluate peptide secondary structure prediction models. It was observed that regular secondary structure content (e.g., helix, beta-sheet) increased with length of peptides. Firstly, models based on various machine-learning techniques have been developed using binary profile of peptides and achieved maximum overall accuracy (Q3) 79.5%. The performance of models further improved from 79.5% to 83.5% using evolutionary information in the form of PSSM profile. We also evaluate performance of protein secondary structure prediction method PSIPRED on our dataset and achieved maximum accuracy 76.9%; particularly poor (Q3 71.4%) for small peptides having length less than 10 residues. Overall, PEP2D has better prediction of beta-sheets (Q3 74%) and coil region (Q3 87%) of peptides as compare to PSIPRED (Q3 54.4% for beta-sheet and Q3 77.9% for coil). We also measure performance of PSIPRED and PEP2D in terms of segment overlap (SOV); achieved 69.3 and 76.7 respectively.

CONCLUSION

Our observations indicate that there is a need of developing separate method for predicting secondary structure of peptides. It was also observed that models based on PSSM profile perform poor on small peptides in comparison to long peptides. Based on our study, we developed method for predicting secondary structure of peptides. In order to provide service to user, a webserver/standalone has been developed (https://webs.iiitd.edu.in/raghava/pep2d/).
Discovery of conformation-sensitive anti-amyloid protofibril monoclonal antibodies using an engineered chaperone-like amyloid-binding protein
Authors: Vallen Graham W , Bonito-Oliva Alessandra , Agostinelli Rita , Karim Riyaz , Deguzman Jeremy , Kelleher Kerry , Petro Marianne , Lindström Anna-Karin , Graff Caroline , Wood Kathleen M. , Tchistiakova Lioudmila , Marquette Kimberly , Wes Paul D. , Sakmar Thomas P.
Published: February 2019

The hypothesis that amyloid beta peptides (Aβ) are central to the pathogenesis of sporadic Alzheimer’s disease (AD) is still hotly debated. Although several monoclonal antibodies (mAbs) against Aβ have failed in therapeutic clinical trials, two conformation-selective, anti-Aβ mAbs continue to show promise. A significant challenge has been to discover mAbs that preferentially target Aβ protofibrils over natively-folded monomeric peptides or amyloid plaques. We have engineered a novel chaperone-like amyloid-binding protein (CLABP), Nucleobindin 1 (NUCB1), which enables the stabilization of protofibrils, allowing them to be used as immunogens in mice to facilitate the generation of mAbs that recognize Aβ protofibrils. An immunization campaign and subsequent screening funnel identified a panel of mAbs with high-affinity to Aβ. Two mAbs in particular, 1A8 and 7C8, displayed significant conformation sensitivity and preferentially bound Aβ protofibrils over monomers. Furthermore, 1A8 delayed Aβ aggregation, but did not prevent eventual fibril formation, while 7C8 significantly and dose-dependently reduced fibril formation by inhibiting both primary and secondary nucleation. Both mAbs protected against protofibril-induced cytotoxicityin vitro,and showed distinctive staining patterns by immunohistochemistry in PS1/APP mice and in post-mortem AD brain tissue. In summary, we describe a novel method to stabilize soluble Aβ protofibrils for use in immunization campaigns. We hypothesize that the stabilized protofibrils retain the neoepitopes of the Aβ protofibril and the aggregates found in mouse models of disease and post-mortem AD brain tissue.
Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination
Authors: Hoehn Kenneth B , Vander Heiden Jason A. , Zhou Julian Q. , Lunter Gerton , Pybus Oliver G. , Kleinstein Steven H.
Published: February 2019

In order to produce effective antibodies, B cells undergo rapid somatic hypermutation (SHM) and selection for binding affinity to antigen via a process called affinity maturation. The similarities between this process and evolution by natural selection have led many groups to use evolutionary and phylogenetic methods to characterize the development of immunological memory, vaccination, and other processes that depend on affinity maturation. However, these applications are limited by several features of affinity maturation that violate assumptions in standard phylogenetic models. Further, most phylogenetic models are designed to be applied to individual lineages comprising genetically diverse sequences, while B cell repertoires often consist of hundreds to thousands of separate low-diversity lineages. Here, we introduce a hierarchical phylogenetic framework that incorporates the unique features of SHM, and integrates information from all lineages in a repertoire to more precisely estimate model parameters. We demonstrate the power of this approach by characterizing previously un-described phenomena in affinity maturation. First, we find evidence consistent with age related changes in SHM hot-and cold-spot motifs. Second, we identify a consistent relationship between increased tree length and signs of increased negative selection, apparent in the repertoires of both healthy subjects and those undergoing active immune responses. This suggests that B cell lineages shift towards negative selection over time as a general feature of affinity maturation. Our study provides a framework for undertaking repertoire-wide phylogenetic testing of SHM hypotheses, and provides a new means of charactering the process of mutation and selection during affinity maturation.
Sensorimotor system engagement during ASL sign perception: an EEG study in deaf signers and hearing non-signers
Authors: Kubicek Emily , Quandt Lorna
Published: February 2019

When a person observes someone else performing an action, the observer’s sensorimotor cortex activates as if the observer is the one performing the action, a phenomenon known as action simulation. While this process has been well-established for basic (e.g. grasping) and complex (e.g. dancing) actions, it remains unknown if the framework of action simulation is applicable to visual languages such as American Sign Language (ASL). We conducted an EEG experiment with deaf signers and hearing non-signers to compare overall sensorimotor EEG between groups, and to test whether sensorimotor systems are differentially sensitive to signs that are produced with one hand (“1H”) or two hands (“2H”). We predicted greater alpha and beta event-related desynchronization (previously correlated with action simulation) during the perception of 2H ASL signs compared to 1H ASL signs, due to greater demands on sensorimotor processing systems required for producing two-handed actions. We recorded EEG from both groups as they observed videos of ASL signs, half 1H and half 2H. Event-related spectral perturbations (ERSPs) in the alpha and beta ranges were computed for the two conditions at central electrode sites overlying the sensorimotor cortex. Sensorimotor EEG responses in both Hearing and Deaf groups were sensitive to the observed gross motor characteristics of the observed signs. We show for the first time that despite hearing non-signers showing overall more sensorimotor cortex involvement during sign observation, mirroring-related processes are in fact involved when deaf signers observe signs.
Tuned normalization in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior
Authors: Maniscalco Brian , Odegaard Brian , Grimaldi Piercesare , Cho Seong Hah , Basso Michele A. , Lau Hakwan , Peters Megan A. K.
Published: February 2019

Current dominant views hold that perceptual confidence reflects the probability that a decision is correct. Although these views have enjoyed some empirical support, recent behavioral results indicate that confidence and the probability of being correct can be dissociated. An alternative hypothesis suggests that confidence instead reflects the magnitude of evidence in favor of a decision while being relatively insensitive to the evidence opposing the decision. We considered how this alternative hypothesis might be biologically instantiated by developing a simple leaky competing accumulator neural network model incorporating a known property of sensory neurons: tuned normalization. The key idea of the model is that each accumulator neuron’s normalization ‘tuning’ dictates its contribution to perceptual decisions versus confidence judgments. We demonstrate that this biologically plausible model can account for several counterintuitive findings reported in the literature, where confidence and decision accuracy were shown to dissociate -- and that the differential contribution a neuron makes to decisions versus confidence judgments based on its normalization tuning is vital to capturing some of these effects. One critical prediction of the model is that systematic variability in normalization tuning exists not only in sensory cortices but also in the decision-making circuitry. We tested and validated this prediction in macaque superior colliculus (SC; a region implicated in decision-making). The confirmation of this novel prediction provides direct support for our model. These findings suggest that the brain has developed and implements this alternative, heuristic theory of perceptual confidence computation by capitalizing on the diversity of neural resources available.

Significance

The dominant view of perceptual confidence proposes that confidence optimally reflects the probability that a decision is correct. But recent empirical evidence suggests that perceptual confidence exhibits a suboptimal ‘confirmation bias’, just as in human decision-making in general. We tested how this ‘bias’ might be neurally implemented by building a biologically plausible neural network model, and showed that the ‘bias’ emerges when each neuron’s degree of divisive normalization dictates how it drives decisions versus confidence judgments. We confirmed the model’s biological substrate using electrophysiological recordings in monkeys. These results challenge the dominant model, suggesting that the brain instead capitalizes on the diversity of available machinery (i.e., neuronal resources) to implementheuristic-- not optimal -- strategies to compute subjective confidence.
Accurate inference of tree topologies from multiple sequence alignments using deep learning
Authors: Suvorov Anton , Hochuli Joshua , Schrider Daniel R.
Published: February 2019

Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several “zones” of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. Here we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. While numerous practical challenges remain, these findings suggest that deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.
Tsr4 is a cytoplasmic chaperone for the ribosomal protein Rps2 inSaccharomyces cerevisiae
Authors: Black Joshua J. , Musalgaonkar Sharmishtha , Johnson Arlen W.
Published: February 2019

Eukaryotic ribosome biogenesis requires the action of approximately 200trans-acting factors and the incorporation of 79 ribosomal proteins (RPs). The delivery of RPs to pre-ribosomes is a major challenge for the cell because RPs are often highly basic and contain intrinsically disordered regions prone to nonspecific interactions and aggregation. To counteract this, eukaryotes developed dedicated chaperones for certain RPs that promote their solubility and expression, often by binding eukaryotic-specific extensions of the RPs. Rps2 (uS5) is a universally conserved RP that assembles into nuclear pre-40S subunits. However, a chaperone for Rps2 had not been identified. Our lab previously characterized Tsr4 as a 40S biogenesis factor of unknown function. Here, we report that Tsr4 co-translationally associates with Rps2. Rps2 harbors a eukaryotic-specific N-terminal extension that was critical for its interaction with Tsr4. Moreover, Tsr4 perturbation resulted in decreased Rps2 levels and phenocopied Rps2 depletion. Despite Rps2 joining nuclear pre-40S particles, Tsr4 appeared to be restricted to the cytoplasmic. Thus, we conclude that Tsr4 is a cytoplasmic chaperone dedicated to Rps2.
RASSF1A is required for the maintenance of nuclear actin levels
Authors: Chatzifrangkeskou Maria , Pefani Dafni-Eleftheria , Eyres Michael , Vendrell Iolanda , Fischer Roman , Pankova Daniela , O’Neill Eric
Published: February 2019

Nuclear actin participates in many essential cellular processes including gene transcription, chromatic remodelling and mRNA processing. Actin shuttles into and out the nucleus through the action of dedicated transport receptors importin-9 and exportin-6, but how this transport is regulated remains unclear. Here we show that RASSF1A is a novel regulator of actin nucleocytoplasmic trafficking and is required for the active maintenance of nuclear actin levels through supporting binding of exportin-6 (XPO6) to RAN GTPase. RASSF1A (Ras association domain family 1 isoform A) is a tumour suppressor gene frequently silenced by promoter hypermethylation in all major solid cancers. Specifically, we demonstrate that endogenous RASSF1A localises to the nuclear envelope (NE) and is required for nucleo-cytoplasmic actin transport and the concomitant regulation of Myocardin-related transcription factor A (MRTF-A), a coactivator of the transcription factor serum response factor (SRF). The RASSF1A/RAN/XPO6/nuclear actin pathway is aberrant in cancer cells where RASSF1A expression is lost and correlates with reduced MTRF/SRF activity leading to cell adhesion defects. Taken together, we have identified a previously unknown mechanism by which the nuclear actin pool is regulated and uncovered a previously unknown link of RASSF1A and MTRF/SRF in tumour suppression.
In vitro characterization of the colibactin-activating peptidase ClbP enables development of a fluorogenic activity probe
Authors: Volpe Matthew R. , Wilson Matthew R. , Brotherton Carolyn A. , Winter Ethan S. , Johnson Sheila E. , Balskus Emily P.
Published: February 2019

The gut bacterial genotoxin colibactin has been linked to the development of colorectal cancer. In the final stages of colibactin’s biosynthesis, an inactive precursor (pre-colibactin) undergoes proteolytic cleavage by ClbP, an unusual inner-membrane-bound periplasmic peptidase, to generate the active genotoxin. This enzyme presents an opportunity to monitor and modulate colibactin biosynthesis, but its active form has not been studied in vitro and limited tools exist to measure its activity. Here, we describe the in vitro biochemical characterization of catalytically active, full-length ClbP. We elucidate its substrate preferences and use this information to develop a fluorogenic activity probe. This tool will enable the discovery of ClbP inhibitors and streamline identification of colibactin-producing bacteria.
The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data
Authors: Buffalo Vince , Coop Graham
Published: February 2019

Populations can adapt over short, ecological timescales via standing genetic variation. Genomic data collected over tens of generations in both natural and lab populations is increasingly used to find selected loci underpinning such rapid adaptation. Although selection on large effect loci may be detectable in such data, often the fitness differences between individuals have a polygenic architecture, such that selection at any one locus leads to allele frequency changes that are too subtle to distinguish from genetic drift. However, one promising signal comes from the fact that selection on polygenic traits leads to heritable fitness backgrounds that neutral alleles can become stochastically associated with. These associations perturb neutral allele frequency trajectories, creating autocovariance across generations that can be directly measured from temporal genomic data. We develop theory that predicts the magnitude of these temporal autocovariances, showing that it is determined by the level of additive genetic variation, recombination, and linkage disequilibria in a region. Furthermore, by using analytic expressions for the temporal variances and autocovariances in allele frequency, we demonstrate one can estimate the additive genetic variation for fitness and the drift-effective population size from temporal genomic data. Finally, we also show how the proportion of total variation in allele frequency change due to linked selection can be estimated from temporal data. Temporal genomic data offers strong opportunities to identify the role linked selection has on genome-wide diversity over short timescales, and can help bridge population genetic and quantitative genetic studies of adaptation.
A Bayesian framework for unifying data cleaning, source separation and imaging of electroencephalographic signals
Authors: Ojeda Alejandro , Klug Marius , Kreutz-Delgado Kenneth , Gramann Klaus , Mishra Jyoti
Published: February 2019

Electroencephalographic (EEG) source imaging depends upon sophisticated signal processing algorithms for data cleaning, source separation, and localization. Typically, these problems are addressed separately using a variety of heuristics, making it difficult to systematize a methodology for extracting robust EEG source estimates on a wide range of experimental paradigms. In this paper, we propose a unifying Bayesian framework in which these apparently dissimilar problems can be understood and solved in a principled manner using a single algorithm. We explicitly model the effect of non-brain sources by augmenting the lead field matrix with a dictionary of stereotypical artifact scalp projections. We propose to populate the artifact dictionary with non-brain scalp projections obtained by running Independent Component Analysis (ICA) on an EEG database. Within a parametric empirical Bayes (PEB) framework, we use an anatomical brain atlas to parameterize a source prior distribution that encourages sparsity in the number of cortical regions. We show that, in our inversion algorithm, PEB+ (PEB with the addition of artifact modeling), the sparsity prior has the property of inducing the segregation of the cortical activity into a few maximally independent components with known anatomical support. Artifacts produced by electrooculographic and electromyographic activity as well as single-channel spikes are also segregated into their respective components. Of theoretical relevance, we use our framework to point out the connections between Infomax ICA and distributed source imaging. We use real data to demonstrate that PEB+ outperforms Infomax for source separation on short segments of data and, unlike the popular Artifact Subspace Removal algorithm, it can reduce artifacts without significantly distorting clean epochs. Finally, we analyze mobile brain/body imaging data to characterize the brain dynamics supporting heading computation during full-body rotations. In this example, we run PEB+ followed by the spectral analysis of the activity in the retrosplenial cortex, largely replicating the findings of previous experimental literature.
Super-resolution displacement mapping of unbound single molecules reveals nanoscale heterogeneities in intracellular diffusivity
Authors: Xiang Limin , Chen Kun , Yan Rui , Li Wan , Xu Ke
Published: February 2019

Intracellular diffusion underlies vital processes of the cell. However, it remains difficult to elucidate how an average-sized protein diffuses in the cell with good spatial resolution and sensitivity. Here we report single-molecule displacement/diffusivity mapping (SMdM), a super-resolution strategy that enables the nanoscale mapping of intracellular diffusivity through the local statistics of instantaneous displacements of freely diffusing single molecules. We thus show that diffusion in the cytoplasm and in the nucleus to both be spatially heterogeneous at the nanoscale, and such variations in local diffusivity correlate strongly with the ultrastructure of the actin cytoskeleton and the chromosome, respectively. Moreover, we identify the net charge of the diffuser as a key determinant of diffusion rate: intriguingly, the possession of positive, but not negative, net charges significantly impedes diffusion, and the exact degree of slowdown is determined by the specific subcellular environments.
Communication between distinct subunit interfaces of the cohesin complex promotes its topological entrapment of DNA
Authors: Guacci Vincent , Chatterjee Fiona , Robison Brett , Koshland Douglas
Published: February 2019

Cohesin mediates higher-order chromosome structure. Its biological activities require topological entrapment of DNA within a lumen(s) formed by cohesin subunits. The reversible dissociation of cohesin’s Smc3p and Mcd1p subunits are postulated to form a regulated gate that allows DNA entry and exit into the lumen. We assessed gate-independent functions of this interface in yeast using a fusion protein that joins Smc3p to Mcd1p. We show that in vivo all the regulators of cohesin promote DNA binding of cohesion by mechanisms independent of opening this gate. Furthermore, we show that this interface has a gate-independent activity essential for cohesin to bind chromosomes. We propose this interface regulates DNA entrapment by controlling the opening and closing of one or more distal interfaces formed by cohesin subunits, likely by inducing a conformation change in cohesin. Furthermore, cohesin regulators modulate the interface to control both DNA entrapment and cohesin functions after DNA binding.
The Role of Proactive and Reactive Cognitive Control for Target Selection in Multiple-Target Search
Authors: Ort Eduard , Fahrenfort Johannes J. , Reeder Reshanne , Pollmann Stefan , Olivers Christian N. L.
Published: February 2019

Cognitive control can involve proactive (preparatory) and reactive (corrective) mechanisms. Using a gaze-contingent eye tracking paradigm combined with fMRI, we investigated the involvement of these different modes of control and their underlying neural networks, when switching between different targets in multiple-target search. Participants simultaneously searched for two possible targets presented among distractors, and selected one of them. In one condition, only one of the targets was available in each display, so that the choice was imposed, and reactive control would be required. In the other condition, both targets were present, giving observers free choice over target selection, and allowing for proactive control. Switch costs emerged only when targets were imposed and not when target selection was free. We found differential levels of activity in the frontoparietal control network depending on whether target switches were free or imposed. Furthermore, we observed core regions of the default mode network to be active during target repetitions, indicating reduced control on these trials. Free and imposed switches jointly activated parietal and posterior frontal cortices, while free switches additionally activated anterior frontal cortices. These findings highlight unique contributions of proactive and reactive control during visual search.
Structure-guided function discovery of an NRPS-like glycine betaine reductase for choline biosynthesis in fungi
Authors: Hai Yang , Huang Arthur , Tang Yi
Published: February 2019

Nonribosomal peptide synthetases (NRPS) and NRPS-like enzymes have diverse functions in primary and secondary metabolism. By using a structure-guided approach, we uncovered the function of an NRPS-like enzyme with unusual domain architecture, catalyzing two sequential two-electron reductions of glycine betaine to choline. Structural analysis based on homology model suggests cation-π interactions as the major substrate specificity determinant, which was verified using substrate analogs and inhibitors. Bioinformatic analysis indicates this NRPS-like glycine betaine reductase is highly conserved and widespread in fungi kingdom. Genetic knockout experiments confirmed its role in choline biosynthesis and maintaining glycine betaine homeostasis in fungi. Our findings demonstrate that the oxidative choline-glycine betaine degradation pathway can operate in a fully reversible fashion and provide new insights in understanding fungal choline metabolism. The use of an NRPS-like enzyme for reductive choline formation is energetically efficient compared to known pathways. Our discovery also underscores the capabilities of structure-guided approach in assigning function of uncharacterized multidomain proteins, which can potentially aid functional discovery of new enzymes by genome mining.
Assessing a commercial capillary electrophoresis interface (ZipChip) for shotgun proteomic applications
Authors: Rinas Aimee , Jenkins Conor , Orsburn Ben
Published: February 2019

Capillary electrophoresis coupled electrospray ionization mass spectrometry (CE-MS) has long existed as a theoretical alternative to liquid chromatography coupled mass spectrometry (LC-MS). Until recently, however, the coupling of these technologies has occupied only a small niche within specific applications. A recent innovation in CE-MS is the ZipChip interface system from 908 devices that was pioneered by the Ramsay lab at NC State. This newly available source offers advantages over previous CE-MS interfaces including both relative ease of use and direct compatibility to thousands of mass spectrometers currently in use throughout the world with no hardware alterations. The ZipChip CE-MS has been demonstrated in recent studies to provide high resolution and rapid separations for the analysis of intact proteins, glycoproteins and glycosylated peptides, with more applications likely on the way. In this study we assess the capabilities of the ZipChip system in the context of high throughput global shotgun proteomics experiments. We find that on a high field Orbitrap system we can repeatedly identify as many as 800 unique protein groups in an experiment using a run time of 12 minutes. We find the ZipChip CE-MS system to be widely applicable for both data dependent and data independent acquisition experiments as well as targeted experiments. We conclude that the ZipChip is an attractive alternative solution to traditional nanoflow ESI-MS/MS for the analysis of the genomes of single celled organisms and for offline fractionation of eukaryotic proteomes.
A small viral potassium ion channel with an inherent inward rectification
Authors: Eckert Denise , Schulze Tobias , Stahl Julian , Rauh Oliver , Van Etten James L , Hertel Brigitte , Schroeder Indra , Moroni Anna , Thiel Gerhard
Published: February 2019

Some algal viruses have coding sequences for K+channels with structural and functional characteristics of pore modules of complex K+channels. Here we exploit the immense structural diversity of natural channel orthologs to discover new basic principles of structure/function correlates in K+channels. The comparative analysis of three similar K+channels with monomer sizes ≤ 86 amino acids (AA) shows that one channel (Kmpv1) generates an ohmic conductance in HEK293 cells while the other two channels (KmpvSP1, KmpvPL1) exhibit typical features of canonical Kir channels. Like Kir channels, the rectification of the viral channels is a function of the K+driving force. Reconstitution of KmpvSP1and KmpvPL1in planar lipid bilayers showed rapid channel fluctuations only at voltages negative of the K+reversal voltage. This rectification was maintained in KCl buffer with 1 mM EDTA, which excludes blocking cations as the source of rectification. This means that rectification of the viral channels must be, unlike Kir channels, an inherent property of the channel proteins. The structural basis for rectification was investigated by a chimera between rectifying and non-rectifying channels as well as point mutations, which made the rectifying channels similar to the ohmic conducting channel. The results of these experiments exclude the domain, which connects the two transmembrane helixes and which includes the pore helix and the selectivity filter, as playing a major role in rectification; inward rectification must be conferred by the transmembrane domains. The finding that a swapping of the AA, which is typical for the two inward rectifiers, with the respective AA from Kmpv1did not compromise rectification suggests that tertiary or quaternary structural interactions are responsible for this type of gating.
HH-suite3 for fast remote homology detection and deep protein annotation
Authors: Steinegger Martin , Meier Markus , Mirdita Milot , Vöhringer Harald , Haunsberger Stephan J. , Söding Johannes
Published: February 2019

Background

HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous sequences.

Results

We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. This accelerated HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ~10× faster than PSI-BLAST and ~20× faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over servers in a cluster using OpenMP and message passing interface (MPI). The free, open-source, GNU GPL(v3)-licensed software is available at https://github.com/soedinglab/hh-suite.

Conclusion

The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.