bluuebunny/crossref_metadata_2025 huggingface dataset:
A non-transcriptional function of Yap orchestrates the DNA replication program
Authors: García Rodrigo Meléndez , Haccard Olivier , Chesneau Albert , Narassimprakash Hemalatha , Roger Jérôme E , Perron Muriel , Marheineke Kathrin , Bronchain Odile
Published: November 2021

In multicellular eukaryotic organisms, the initiation of DNA replication occurs asynchronously throughout S-phase according to a regulated replication timing program. Here, using Xenopus egg extracts, we showed that Yap (Yes-associated protein 1), a downstream effector of the Hippo signaling pathway, is required for the control of DNA replication dynamics. We found that Yap is recruited to chromatin at the start of DNA replication and that Yap depletion accelerates DNA replication dynamics by increasing the number of activated replication origins. Furthermore, we identified Rif1, a major regulator of the DNA replication timing program, as a novel Yap binding protein. In Xenopus embryos, using a Trim-Away approach during cleavage stages devoid of transcription, we found that both Yap and Rif1 depletion trigger an acceleration of cell divisions, suggesting a shorter S-phase by alterations of the replication program. Finally, our data show that Rif1 knockdown leads to defects in the partitioning of early versus late replication foci in retinal stem cells, as we previously showed for Yap. Altogether, our findings unveil a non-transcriptional role for Yap in regulating replication dynamics. We propose that Yap and Rif1 function as breaks to control the DNA replication program in early embryos and post-embryonic stem cells.

Highlights

Yap is recruited to chromatin during DNA replication dependent on pre-replicative complex assembly.

Yap controls DNA replication dynamics by limiting origin firing.

The replication timing regulatory factor 1, Rif1, is a novel Yap binding-partner.

Both Yap and Rif1 regulate the length of the first embryonic cell cycles.

Like Yap, Rif1 controls retinal stem cell DNA replication timing.
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
Authors: Salter Jessie F. , Hosner Peter A. , Tsai Whitney L. E. , McCormack John E. , Braun Edward L. , Kimball Rebecca T. , Brumfield Robb T. , Faircloth Brant C.
Published: November 2021

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
Filtration extraction method using microfluidic channel for measuring environmental DNA
Authors: Fukuzawa Takashi , Kameda Yuichi , Nagata Hisao , Nishizawa Naofumi , Doi Hideyuki
Published: November 2021

The environmental DNA (eDNA) method, which is widely applied for biomonitoring, is limited to laboratory analysis and processing. In this study, we developed a filtration/extraction component using a microfluidic channel, Biryu-Chip (BC), and a filtration/extraction method, BC method, to minimize the volume of the sample necessary for DNA extraction and subsequent PCR amplification. We tested the performance of the BC method and compared it with the Sterivex filtration/extraction method using aquarium and river water samples. We observed that using the BC method, the same concentration of the extracted DNA was obtained with 1/20–1/40 of the filtration volume of the Sterivex method, suggesting that the BC method can be widely used for eDNA measurement. In addition, we could perform on-site measurements of eDNA within 30 min using a mobile PCR device. Using the BC method, filtration and extraction could be performed easily and quickly. The PCR results obtained by the BC method were similar to those obtained by the Sterivex method. The BC method required fewer steps and therefore, the risk of DNA contamination could be reduced. When combined with a mobile PCR, the BC method can be applied to easily detect eDNA within 30 min from a few 10 mL of the water sample, even on-site.
Accuracy and data efficiency in deep learning models of protein expression
Authors: Nikolados Evangelos-Marios , Wongprommoon Arin , Mac Aodha Oisin , Cambray Guillaume , Oyarzún Diego A.
Published: November 2021

Many applications of synthetic biology involve engineering microbial strains to express high-value proteins. Thanks to advances in rapid DNA synthesis and sequencing, deep learning has emerged as a promising approach to build sequence-to-expression models for strain design and optimization. Such models, however, require large amounts of training data that are costly to acquire, which creates substantial entry barriers for many laboratories. Here, we study the relation between model accuracy and data efficiency in a large panel of machine learning models of varied complexity, from penalized linear regressors to deep neural networks. Our analysis is based on data from a large genotype-phenotype screen inEscherichia coli, which was generated with a design-of-experiments approach to balance coverage and depth of the genotypic space. We sampled these data to emulate scenarios with a limited number of DNA sequences for training, as commonly encountered in strain engineering applications. Our results suggest that classic, non-deep, models can achieve good prediction accuracy with much smaller datasets than previously thought, and provide robust evidence that convolutional neural networks further improve performance with the same amount of data. Using methods from Explainable AI and model benchmarking, we show that convolutional neural networks have an improved ability to discriminate between input sequences and extract sequence features that are highly predictive of protein expression. We moreover show that controlled sequence diversity leads to important gains in data efficiency, and validated this principle in a separate genotype-phenotype screen inSaccharomyces cerevisiae.These results provide practitioners with guidelines for designing experimental screens that strike a balance between cost and quality of training data, laying the groundwork for wider adoption of deep learning across the biotechnology sector.
TIS Transformer: Remapping the Human Proteome Using Deep Learning
Authors: Clauwaert Jim , Gupta Ramneek , McVey Zahra , Menschaert Gerben
Published: November 2021

Abstract

The correct mapping of the proteome is an important step towards advancing our understanding of biological systems and cellular mechanisms. Methods that provide better mappings can fuel important processes such as drug discovery and disease understanding. Currently, true determination of translation initiation sites is primarily achieved byin vivoexperiments. Here we propose TIS Transformer, a deep learning model for the determination of translation start sites solely utilizing the information embedded in the transcript nucleotide sequence. The method is built upon deep learning techniques first designed for natural language processing. We prove this approach to be best suited for learning the semantics of translation, outperforming previous approaches by a large margin. We demonstrate that limitations in the model performance is primarily due to the presence of low quality annotations against which the model is evaluated against. Advantages of the method are its ability to detect key features of the translation process and multiple coding sequences on a transcript. These include micropeptides encoded by short Open Reading Frames, either alongside a canonical coding sequence or within long non-coding RNAs. To demonstrate the use of our methods, we applied TIS Transformer to remap the full human proteome.
Earliest photic zone niches probed by ancestral microbial rhodopsins
Authors: Sephus Cathryn D. , Fer Evrim , Garcia Amanda K. , Adam Zachary R. , Schwieterman Edward W. , Kaçar Betül
Published: November 2021

For billions of years, life has continuously adapted to dynamic physical conditions near the Earth’s surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth’s earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as “paleosensors” for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.
ZARP: An automated workflow for processing of RNA-seq data
Authors: Katsantoni Maria , Gypas Foivos , Herrmann Christina J. , Burri Dominik , Bak Maciej , Iborra Paula , Agarwal Krish , Ataman Meric , Börsch Anastasiya , Zavolan Mihaela , Kanitz Alexander
Published: November 2021

RNA sequencing (RNA-seq) is a crucial technique for many scientific studies and multiple models, and software packages have been developed for the processing and analysis of such data. Given the plethora of available tools, choosing the most appropriate ones is a time-consuming process that requires an in-depth understanding of the data, as well as of the principles and parameters of each tool. In addition, packages designed for individual tasks are developed in different programming languages and have dependencies of various degrees of complexity, which renders their installation and execution challenging for users with limited computational expertise. The use of workflow languages and execution engines with support for virtualization and encapsulation options such as containers and Conda environments facilitates these tasks considerably. Computational workflows defined in those languages can be reliably shared with the scientific community, enhancing reusability, while improving reproducibility of results by making individual analysis steps more transparent.

Here we present ZARP, a general purpose RNA-seq analysis workflow which builds on state-of-the-art software in the field to facilitate the analysis of RNA-seq data sets. ZARP is developed in the Snakemake workflow language using best software development practices. It can run locally or in a cluster environment, generating extensive reports not only of the data but also of the options utilized. It is built using modern technologies with the ultimate goal to reduce the hands-on time for bioinformaticians and non-expert users. ZARP is available under a permissive Open Source license and open to contributions by the scientific community.

Contact

mihaela.zavolan@unibas.ch, alexander.kanitz@unibas.ch
Epigenetic machinery is functionally conserved in cephalopods
Authors: Macchi Filippo , Edsinger Eric , Sadler Kirsten C.
Published: November 2021

Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet little is known about the epigenome in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental and regenerative processes, but using molecular approaches in such studies is hindered by the lack of knowledge about genome organization and gene regulation in these animals. We combined bioinformatic and molecular analysis of Octopus bimaculoides to identify gene expression signatures for 12 adult tissues and a hatchling, and investigate the presence and pattern of DNA methylation and histone methylation marks across tissues. This revealed a dynamic gene expression profile encoding several epigenetic regulators, including DNA methylation maintenance factors that were highly conserved and functional in cephalopods, as shown by detection of 5-methyl-cytosine in multiple tissues of octopus, squid and bobtail squid. WGBS of octopus brain and RRBS from a hatchling revealed that less than 10% of CpGs are methylated, highlighting a non-random distribution in the genome of all tissues, with enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Each DNA methylation pattern encompassed genes with distinct functions and, strikingly, many of these genes showed similar expression levels across tissues. In contrast to the static pattern of DNA methylation, the histone marks H3K27me3, H3K9me3 and H3K4me3 were detected at different levels in diverse cephalopod tissues. This suggests the methylome and histone code cooperate to regulate tissue specific gene expression in a way that may be unique to cephalopods.
scCODE: an R package for personalized differentially expressed gene detection on single-cell RNA-sequencing data
Authors: Zou Jiawei , Wang Miaochen , Zhang Zhen , Liu Zheqi , Zhang Xiaobin , Hua Rong , Chen Ke , Zou Xin , Hao Jie
Published: November 2021

Differential expression (DE) gene detection in single-cell RNA-seq (scRNA-seq) data is a key step to understand the biological question investigated. We find that DE methods together with gene filtering have profound impact on DE gene identification, and different datasets will benefit from personalized DE gene detection strategies. Existing tools don’t take gene filtering into consideration, and couldn’t evaluate DE performance on real datasets without prior knowledge of true results. Based on two new metrics, we propose scCODE (single cell Consensus Optimization of Differentially Expressed gene detection), an R package to automatically optimize DE gene detection for each experimental scRNA-seq dataset.
Mechanistic insights into global suppressors of protein folding defects
Authors: Chattopadhyay Gopinath , Bhowmick Jayantika , Manjunath Kavyashree , Ahmed Shahbaz , Goyal Parveen , Varadarajan Raghavan
Published: November 2021

Most amino acid substitutions in a protein either lead to partial loss of function or are near neutral. Several studies have shown the existence of second-site mutations that can rescue defects caused by diverse loss of function mutations. Such global suppressor mutations are key drivers of protein evolution. However, the mechanisms responsible for such suppression remain poorly understood. To address this, we characterized multiple suppressor mutations both in isolation and in combination with inactive mutants. We examined six global suppressors of the bacterial toxin CcdB, the known M182T global suppressor of TEM-1 β-lactamase, the N239Y global suppressor of p53-DBD and three suppressors of the SARS-CoV-2 spike Receptor Binding Domain. The suppressors both alone, and in conjunction with inactive mutants, stabilise the protein both thermodynamically and kinetically in-vitro, predominantly through acceleration of the refolding rate. When coupled to inactive mutants they promote increased in-vivo solubilities as well as regain-of-function phenotypes. In the case of CcdB, where novel suppressors were isolated, we determined the crystal structures of three such suppressors to obtain insight into the specific molecular interactions responsible for the observed effects. While most individual suppressors result in small stability enhancements relative to wildtype, which can be combined to yield significant stability increases, thermodynamic stabilisation is neither necessary nor sufficient for suppressor action.
Probabilistic representations as building blocks for higher-level vision
Authors: Chetverikov Andrey , Kristjánsson Árni
Published: November 2021

Current theories of perception suggest that the brain represents features of the world as probability distributions, but can such uncertain foundations provide the basis for everyday vision? Perceiving objects and scenes requires knowing not just how features (e.g., colors) are distributed but also where they are and which other features they are combined with. Using a Bayesian computational model, we recover probabilistic representations used by human observers to search for odd stimuli among distractors. Importantly, we found that the brain integrates information between feature dimensions and spatial locations, leading to more precise representations compared to when information integration is not possible. We also uncover representational asymmetries and biases, showing their spatial organization and arguing against simplified “summary statistics” accounts. Our results confirm that probabilistically encoded visual features are bound with other features and to particular locations, proving how probabilistic representations can be a foundation for higher-level vision.
Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy
Authors: Gavrilov Yulian , Kümmerer Felix , Orioli Simone , Prestel Andreas , Lindorff-Larsen Kresten , Teilum Kaare
Published: November 2021

The conformational heterogeneity of a folded protein can affect both its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here we have examined whether changed native state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side-chains with molecular dynamics simulations to quantify the native state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: A reduction in conformational dynamics (and entropy) of the native state of L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native state entropy might be needed to improve the predictions of the effect of mutations on protein stability.
An insight into new glycotherapeutic in glial inflammation: Understanding the role of glycosylation from acute to chronic phase of inflammation
Authors: Patil Vaibhav , Bohara Raghvendra , Winter Carla , Kilcoyne Michelle , McMahon Siobhan , Pandit Abhay
Published: November 2021

Glycosylation plays a critical role during inflammation and glial scar formation upon spinal cord injury (SCI) disease progression. Astrocytes and microglia are involved in this cascade to modulate the inflammation and tissue remodelling from acute to chronic phases. Therefore, understating the glycan changes in these glial cells is paramount. Herein a lectin microarray was undertaken using a cytokine-driven inflammatory MGC model, revealing considerable differential glycosylation from the acute to the chronic phase in a cytokine-combination generated inflamed MGC model. It was found that several N- and O-linked glycans associated with glia during SCI were differentially regulated. Pearson’s correlation hierarchical clustering showed that groups were separated into several clusters, illustrating the heterogenicity among the control, cytokine combination, and LPS treated groups and the day on which treatment was given. Control and LPS treatments were observed to be in dense clusters. This was further confirmed with lectin immunostaining in which GalNAc, GlcNAc, mannose, fucose and sialic acid-binding residues were detected in astrocytes and microglia. However, this modification (upregulation of sialic acid expression) was inhibited by the sialyltransferase inhibitor which indeed modulates the mitochondrial functions. The present study is the first functional investigation of glycosylation modulation in a MGC (MGC) model which elucidates the role of the glycome in neuroinflammation and identified potential therapeutic targets for future glycol-therapeutics in neuroinflammation
Evolution of enzyme levels in metabolic pathways: A theoretical approach. Part 2
Authors: Coton Charlotte , Dillmann Christine , de Vienne Dominique
Published: November 2021

Metabolism is essential for cell function and adaptation. Because of their central role in metabolism, kinetic parameters and enzyme concentrations are under constant selective pressure to adapt the fluxes of the metabolic networks to the needs of the organism. In the line of various studies dealing with enzyme evolution, we recently developed a model of evolution of enzyme concentrations under selection for increased flux, considered as a proxy of fitness (Coton et al. 2021). Taking into account two realistic cellular constraints, competition for resources and co-regulations, we determined the evolutionary equilibria and the ranges of neutral variations of enzyme concentrations. In this article, we give more generality to this model, by considering that the enzymes of a pathway can belong to different groups of co-regulation. We determined the equilibria and showed that the constraints modify the adaptive landscape by limiting the number of independent dimensions. We also showed that any trade-off between enzyme concentration is sufficient to limit the flux and to relax selection for increasing other enzyme concentrations. Even though the model is based on simplifying assumptions, the complexity of the relationship between enzyme concentrations prevents the analysis of selective neutrality.
The spotlight of attention turns from rhythmic exploration-exploitation to a stable exploitation state
Authors: Melcón María , van Bree Sander , Sánchez-Carro Yolanda , Barreiro-Fernández Laura , Kolibius Luca D. , Alzueta Elisabet , Wimber Maria , Capilla Almudena , Hanslmayr Simon
Published: November 2021

While traditional studies claim that visuospatial attention stays fixed at one location at a time, recent research has rather shown that attention rhythmically fluctuates between different locations at rates of prominent brain rhythms. However, little is known about the temporal dynamics of this fluctuation and, particularly, whether it changes over time. Thus, we addressed this question by investigating how visuospatial attention behaves over space and time. We recorded electroencephalographic activity of twenty-seven human participants while they performed a visuospatial cueing task, where attention was covertly oriented to the left or right visual field. In order to decode the spatial locus of attention from neural activity, we trained and tested a classifier on every timepoint of the orienting period, from the attentional cue to stimulus onset. This resulted in one temporal generalization matrix per participant, which was time-frequency decomposed to identify the sampling rhythm. Finally, a searchlight analysis was conducted to reveal the brain regions responsible for attention allocation. Our results show a dynamic evolution of the attentional spotlight, distinguishing between two states. In an early time window, attention explored both cued and uncued hemifield rhythmically at ~10 Hz. In a later time window attention focused on the cued hemifield. Classification was driven by occipital sources, while frontal regions exclusively became involved just before the spotlight settled onto the cued location. Together, our results define attentional sampling as a quasi-rhythmic dynamic process characterized by an initial rhythmic exploration-exploitation state, which is followed by a stable exploitation state.
Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict
Authors: Knyshov Alexander , Hrytsenko Yana , Literman Robert , Schwartz Rachel S.
Published: November 2021

The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In this study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. The results suggest that the data has statistical support for two hypotheses for the placements of treeshrews, sister to Primatomorpha and to Primatomorpha+Glires. While we observe differences in properties of loci of different types (e.g., CDS, intron, etc.) with respect to the strength of the signal, the support for any particular topology is not dependent on the properties of the data. Rather, we show that the method of phylogenetic signal assessment, as well as whether the signal is measured using the full dataset or only loci with the strongest signal, impact the results much more.
Metaeffector interactions modulate the type III effector-triggered immunity load of Pseudomonas syringae
Authors: Martel Alexandre , Laflamme Bradley , Breit-McNally Clare , Lonjon Fabien , Desveaux Darrell , Guttman David S.
Published: November 2021

The bacterial plant pathogen Pseudomonas syringae requires type III secreted effectors (T3SEs) for pathogenesis. However, a major facet of plant immunity entails the recognition of a subset of P. syringae’s T3SEs by intracellular host receptors in a process called Effector- Triggered Immunity (ETI). Prior work has shown that ETI-eliciting T3SEs are pervasive in the P. syringae species complex raising the question of how P. syringae mitigates its ETI load to become a successful pathogen. While pathogens can evade ETI by T3SE mutation, recombination, or loss, there is increasing evidence that effector-effector (a.k.a., metaeffector) interactions can suppress ETI. To study the ETI-suppression potential of P. syringae T3SE repertoires, we compared the ETI-elicitation profiles of two genetically divergent strains: P. syringae pv. tomato DC3000 (PtoDC3000) and P. syringae pv. maculicola ES4326 (PmaES4326), which are both virulent on Arabidopsis thaliana but harbour largely distinct effector repertoires. Of the 529 T3SE alleles screened on A. thaliana Col-0 from the P. syringae T3SE compendium (PsyTEC) [1], 69 alleles from 21 T3SE families elicited ETI in at least one of the two strain backgrounds, while 50 elicited ETI in both backgrounds, resulting in 19 differential ETI responses including two novel ETI-eliciting families: AvrPto1 and HopT1. Although most of these differences were quantitative, three ETI responses were completely absent in one of the pathogenic backgrounds. We performed ETI suppression screens to test if metaeffector interactions contributed to these ETI differences, and found that HopQ1a suppressed AvrPto1m-mediated ETI, while HopG1c and HopF1g suppressed HopT1b-mediated ETI. Overall, these results show that P. syringae strains leverage metaeffector interactions and ETI suppression to overcome the ETI load associated with their native T3SE repertoires.
Sustained attention as measured by RT variability is a strong modulator for the P600, but not the N400
Authors: Contier Friederike , Weymar Mathias , Wartenburger Isabell , Rabovsky Milena
Published: November 2021

The functional significance of the two prominent language-related ERP components N400 and P600 is still under debate. It has recently been suggested that one important dimension along which the two vary is in terms of automaticity versus attentional control, with N400 amplitudes reflecting more automatic and P600 amplitudes reflecting more controlled aspects of sentence comprehension. The availability of executive resources necessary for controlled processes depends on sustained attention, which fluctuates over time. Here, we thus tested whether P600 and N400 amplitudes depend on the level of sustained attention. We re-analyzed EEG and behavioral data from a sentence processing task by Sassenhagen & Bornkessel-Schlesewsky (2015, Cortex), which included sentences with morphosyntactic and semantic violations. Participants read sentences phrase by phrase and indicated whether a sentence contained any type of anomaly as soon as they had the relevant information. To quantify the varying degree of sustained attention, we extracted a moving reaction time coefficient of variation over the entire course of the task. We found that the P600 amplitude was significantly larger during periods of low reaction time variability (high sustained attention) than in periods of high reaction time variability (low sustained attention). In contrast, the amplitude of the N400 was not affected by reaction time variability. These results thus suggest that the P600 component is sensitive to sustained attention while the N400 component is not, which provides independent evidence for accounts suggesting that P600 amplitudes reflect more controlled and N400 amplitudes more automatic aspects of sentence comprehension.
Heat stress leads to rapid lipid remodelling and transcriptional adaptations in Nicotiana tabacum pollen tubes
Authors: Krawczyk Hannah Elisa , Rotsch Alexander Helmut , Herrfurth Cornelia , Scholz Patricia , Shomroni Orr , Salinas-Riester Gabriela , Feussner Ivo , Ischebeck Till
Published: November 2021

After reaching the stigma, pollen grains germinate and form a pollen tube that transports the sperm cells to the ovule. Due to selection pressure between pollen tubes, they likely evolved mechanisms to quickly adapt to temperature changes to sustain an elongation at the highest possible rate. We investigated these adaptions in Nicotiana tabacum pollen tubes grown in vitro under 22 °C and 37 °C by a multi-omic approach including lipidomic, metabolomic and transcriptomic analysis. Both glycerophospholipids and galactoglycerolipids increased in saturated acyl chains under heat stress while triacylglycerols changed less in respect to desaturation but showed higher levels. Free sterol composition was altered, and sterol ester levels decreased. The levels of sterylglycosides and several sphingolipid classes and species were augmented. Most amino acids increased during heat stress, including the non-codogenic amino acids γ-amino butyrate and pipecolate. Furthermore, the sugars sedoheptulose and sucrose showed higher levels. Also the transcriptome underwent pronounced changes with 1,570 of 24,013 genes being differentially up- and 813 being downregulated. Transcripts coding for heat shock proteins and many transcriptional regulators were most strongly upregulated, but also transcripts that have so far not been linked to heat stress. Transcripts involved in triacylglycerol synthesis were increased, while the modulation of acyl chain desaturation seemed not to be transcriptionally controlled indicating other means of regulation.

One sentence summary

Nicotiana tabacum pollen tubes react to heat stress with metabolomic adaptations, transcriptional adjustments, and a rapid and reversible lipid remodelling.
nucGEMs probe the biophysical properties of the nucleoplasm
Authors: Shu Tong , Szórádi Tamás , Kidiyoor Gururaj R. , Xie Ying , Herzog Nora L. , Bazley Andrew , Bonucci Martina , Keegan Sarah , Saxena Shivanjali , Ettefa Farida , Brittingham Gregory , Lemiere Joël , Fenyö David , Chang Fred , Delarue Morgan , Holt Liam J.
Published: November 2021

The cell interior is highly crowded and far from thermodynamic equilibrium. This environment can dramatically impact molecular motion and assembly, and therefore influence subcellular organization and biochemical reaction rates. These effects depend strongly on length-scale, with the least information available at the important mesoscale (10-100 nanometers), which corresponds to the size of crucial regulatory molecules such as RNA polymerase II. It has been challenging to study the mesoscale physical properties of the nucleoplasm because previous methods were labor-intensive and perturbative. Here, we report nuclear Genetically Encoded Multimeric nanoparticles (nucGEMs). Introduction of a single gene leads to continuous production and assembly of protein-based bright fluorescent nanoparticles of 40 nm diameter. We implemented nucGEMs in budding and fission yeast and in mammalian cell lines. We found differences in particle motility between the nucleus and the cytosol at the mesoscale, that mitotic chromosome condensation ejects nucGEMs from the nucleus, and that nucGEMs are excluded from heterochromatin and the nucleolus. nucGEMs enable hundreds of nuclear rheology experiments per hour, and allow evolutionary comparison of the physical properties of the cytosol and nucleoplasm.
Adaptive ratchets and the evolution of molecular complexity
Authors: Röschinger Tom , Tovar Roberto Morán , Pompei Simone , Lässig Michael
Published: November 2021

Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or peptides binding a cognate recognition target of sufficient sequence similarity. Such sites are simple, ubiquitous modules of sequence information, cellular function, and evolution. Here we show that recognition sites, if coupled to a time-dependent target, can rapidly evolve to complex states with larger code length and smaller coding density than sites recognising a static target. The underlying fitness model contains selection for recognition, which depends on the sequence similarity between site and target, and a uniform cost per unit of code length. Site sequences are shown to evolve in a specific adaptive ratchet, which produces selection of different strength for code extensions and compressions. Ratchet evolution increases the adaptive width of evolved sites, accelerating the adaptation to moving targets and facilitating refinement and innovation of recognition functions. We apply these results to the recognition of fast-evolving antigens by the human immune system. Our analysis shows how molecular complexity can evolve as a collateral to selection for function in a dynamic environment.
Designing and comparing cleaning pipelines for TMS-EEG data: a theoretical overview and practical example
Authors: Rogasch Nigel C. , Biabani Mana , Mutanen Tuomas P.
Published: November 2021

Combining transcranial magnetic stimulation (TMS) with electroencephalography (EEG) is growing in popularity as a method for probing the reactivity and connectivity of neural circuits in basic and clinical research. However, using EEG to measure the neural responses to TMS is challenging due to the unique artifacts introduced by combining the two techniques. In this paper, we overview the artifacts present in TMS-EEG data and the offline cleaning methods used to suppress these unwanted signals. We then describe how open science practices, including the development of open-source toolboxes designed for TMS-EEG analysis (e.g., TESA - the TMS-EEG signal analyser), have improved the availability and reproducibility of TMS-EEG cleaning methods. We provide theoretical and practical considerations for designing TMS-EEG cleaning pipelines and then give an example of how to compare different pipelines using TESA. We show that changing even a single step in a pipeline designed to suppress decay artifacts results in TMS-evoked potentials (TEPs) with small differences in amplitude and spatial topography. The variability in TEPs resulting from the choice of cleaning pipeline has important implications for comparing TMS-EEG findings between research groups which use different online and offline approaches. Finally, we discuss the challenges of validating cleaning pipelines and recommend that researchers compare outcomes from TMS-EEG experiments using multiple pipelines to ensure findings are not related to the choice of cleaning methods. We conclude that the continued improvement, availability, and validation of cleaning pipelines is essential to ensure TMS-EEG reaches its full potential as a method for studying human neurophysiology.

Highlights

Concurrent TMS-EEG is challenging due to artifacts in the recorded signals.

We overview offline methods for cleaning TEPs and provide tips on pipeline design.

We use TESA to compare pipelines and show changing a single step alters TEPs.

We discuss the challenges in validating pipelines for TMS-EEG analysis.

We suggest using multiple pipelines to minimise the impact of method choice on TEPs.
Optimizing reaction coordinate by flux maximization in the transition path ensemble
Authors: Li Wenjin
Published: November 2021

Transition path ensemble is a collection of reactive trajectories, all of which largely keep going forward along the transition channel from the reactant state to the product one, and is believed to possess the information necessary for the identification of reaction coordinate. Previously, the full coordinates (both position and momentum) of the snapshots in the transition path ensemble were utilized to obtain the reaction coordinate (J. Chem. Phys. 2016, 144, 114103; J. Chem. Phys. 2018, 148, 084105). Here, with the conformational (or position) coordinates alone, it is demonstrated that the reaction coordinate can be optimized by maximizing the flux of a given coordinate in the transition path ensemble. In the application to alanine dipeptide in vacuum, dihderal angles ϕ and θ were identified to be the two best reaction coordinates, which was consistent with the results in existing studies. A linear combination of these two coordinates gave a better reaction coordinate, which is highly correlated with committor. Most importantly, the method obtained a linear combination of pairwise distances between heavy atoms, which was highly correlated with committor as well. The standard deviation of committor at the transition region defined by the optimized reaction coordinate is as small as 0.08. In addition, the effects of practical factors, such as the choice of transition path sub-ensembles and saving interval between frames in transition paths, on reaction coordinate optimization were also considered.
Joint estimation of selection intensity and mutation rate under balancing selection with applications to HLA
Authors: Slatkin Montgomery
Published: November 2021

A composite likelihood method is introduced for jointly estimating the intensity of selection and the rate of mutation, both scaled by the effective population size, when there is balancing selection at a single multi-allelic locus in an isolated population at demographic equilibrium. The performance of the method is tested using simulated data. Average estimated mutation rates and selection intensities are close to the true values but there is considerable variation about the averages. Allowing for both population growth and population subdivision do not result in qualitative differences but the estimated mutation rates and selection intensities do not in general reflect the current effective population size. The method is applied to three class I (HLA-A, HLA-B and HLA-C) and two class II loci (HLA-DRB1 and HLA-DQA1) in the 1000 Genomes populations. Allowing for asymmetric balancing selection has only a slight effect on the results from the symmetric model. Mutations that restore symmetry of the selection model are preferentially retained because of the tendency of natural selection to maximize average fitness. However, slight differences in selective effects result in much longer persistence time of some alleles. Trans-species polymorphism (TSP), which is characteristic of MHC in vertebrates, is more likely when there are small differences in allelic fitness than when complete symmetry is assumed. Therefore, variation in allelic fitness expands the range of parameter values consistent with observations of TSP.
Model for ring closure in ER tubular network dynamics
Authors: Zucker Ben , Golani Gonen , Kozlov Michael M.
Published: November 2021

Tubular networks of endoplasmic reticulum (ER) are dynamic structures whose steady-state conformations are maintained by a dynamic balance between the persistent generation and vanishing of the network elements. While factors producing the ER tubules and inter-tubular junctions have been investigated, the mechanisms behind their elimination remained unknown. Here we addressed the ER ring closure, the process resulting in the tubule and junction removal through constriction of the network unit-cells into junctional knots followed by the knot remodeling into regular junctions. We considered the ring closure to be driven by the tension existing in ER membranes. We modeled, computationally, the structures of the junctional knots containing internal nanopores and analyzed their tension dependence. We predicted an effective interaction between the nanopores facilitating the knot tightening and collapse of additional network unit cells. We analyzed the process of the pore sealing through membrane fission resulting in formation of regular junctions. Considering the hemi-fission as the rate-limiting stage of the fission reaction, we evaluated the membrane tensions guarantying the spontaneous character of the pore sealing. We concluded that feasible membrane tensions explain all stages of the ER ring closure.
Three orphan histidine kinases inhibit Clostridioides difficile sporulation
Authors: Edwards Adrianne N. , Wetzel Daniela , DiCandia Michael A. , McBride Shonna M.
Published: November 2021

The ability of the anaerobic gastrointestinal pathogen, Clostridioides difficile, to survive outside the host relies on the formation of dormant endospores. Spore formation is contingent on the activation of a conserved transcription factor, Spo0A, by phosphorylation. Multiple kinases and phosphatases regulate Spo0A activity in other spore-forming organisms; however, these factors are not well conserved in C. difficile. Previously, we discovered that deletion of a conserved phosphotransfer protein, CD1492, increases sporulation, indicating that CD1492 inhibits C. difficile spore formation. In this study, we investigate the functions of additional conserved orphan phosphotransfer proteins, CD2492, CD1579, and CD1949 which are hypothesized to regulate Spo0A phosphorylation. Disruption of the conserved phosphotransfer protein, CD2492, also increased sporulation frequency, similarly to the CD1492 mutant, and in contrast to a previous study. A CD1492 CD2492 mutant phenocopied the sporulation and gene expression patterns of the single mutants, suggesting that these proteins function in the same genetic pathway to repress sporulation. Deletion of the conserved CD1579 phosphotransfer protein also variably increased sporulation frequency; however, knockdown of CD1949 expression did not influence sporulation. We provide evidence that CD1492, CD2492 and CD1579 function as phosphatases, as mutation of the conserved histidine residue for phosphate transfer abolished CD2492 function, and expression of the CD1492 or CD2492 histidine site-directed mutants or the wild-type CD1579 allele in a parent strain resulted in a dominant negative hypersporulation phenotype. Altogether, at least three phosphotransfer proteins, CD1492, CD2492 and CD1579 (herein, PtpA, PtpB and PtpC) repress C. difficile sporulation initiation by regulating activity of Spo0A.

IMPORTANCE

The formation of inactive spores is critical for the long-term survival of the gastrointestinal pathogen Clostridioides difficile. The onset of sporulation is controlled by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple kinases and phosphatases control Spo0A phosphorylation; however, this regulatory pathway is not defined in C. difficile. We show that two conserved phosphotransfer proteins, CD1492 (PtpA) and CD2492 (PtpB), function in the same regulatory pathway to repress sporulation by preventing Spo0A phosphorylation. We show that another conserved phosphotransfer protein, CD1579 (PtpC), also represses sporulation, and we eliminate the possibility that a fourth orphan histidine kinase protein, CD1949, impacts C. difficile sporulation. These results support the idea that C. difficile inhibits sporulation initiation through multiple phosphatases.