bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-modal and multi-subject modular organization of human brain networks
Authors: Puxeddu Maria Grazia , Faskowitz Joshua , Sporns Olaf , Astolfi Laura , Betzel Richard F.
Published: January 2022

The human brain is a complex network of anatomically interconnected brain areas. Spontaneous neural activity is constrained by this architecture, giving rise to patterns of statistical dependencies between the activity of remote neural elements. The non-trivial relationship between structural and functional connectivity poses many unsolved challenges about cognition, disease, development, learning and aging. While numerous studies have focused on statistical relationships between edge weights in anatomical and functional networks, less is known about dependencies between their modules and communities. In this work, we investigate and characterize the relationship between anatomical and functional modular organization of the human brain, developing a novel multi-layer framework that expands the classical concept of multi-layer modularity optimization. By simultaneously mapping anatomical and functional networks estimated from different subjects into communities, this approach allows us to carry out a multi-subject and multi-modal analysis of the brain’s modular organization. Here, we investigate the relationship between anatomical and functional modules during resting state, finding unique and shared structures. The proposed framework constitutes a methodological advance in the context of multi-layer network analysis and paves the way to further investigate the relationship between structural and functional network organization in clinical cohorts, during cognitively demanding tasks, and in developmental or lifespan studies.
The genomic basis of the plant island syndrome in Darwin’s giant daisies
Authors: Cerca José , Petersen Bent , Lazaro Guevara José Miguel , Rivera-Colón Angel , Birkeland Siri , Vizueta Joel , Li Siyu , Loureiro João , Kosawang Chatchai , Díaz Patricia Jaramillo , Rivas-Torres Gonzalo , Fernández-Mazuecos Mario , Vargas Pablo , McCauley Ross , Petersen Gitte , Santos-Bay Luisa , Wales Nathan , Catchen Julian , Machado Daniel , Nowak Michael D. , Suh Alexander , Sinha Neelima , Nielsen Lene R. , Seberg Ole , Gilbert M. Thomas P. , Leebens-Mack James H. , Rieseberg Loren , Martin Michael D.
Published: January 2022

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galápagos endemicScalesia atractyloidesArnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements,k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of allScalesiaspecies on the Galápagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwin’s giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.
Evolutionary convergence of a neural mechanism in the cavefish lateral line system
Authors: Lunsford Elias T. , Paz Alexandra , Keene Alex C. , Liao James C.
Published: January 2022

Animals can evolve dramatic sensory functions in response to environmental constraints, but little is known about the neural mechanisms underlying these changes. The Mexican tetra, Astyanax mexicanus, is a leading model to study genetic, behavioral, and physiological evolution by comparing eyed surface populations and blind cave populations. We compared neurophysiological responses of posterior lateral line afferent neurons and motor neurons across A. mexicanus populations to reveal how shifts in sensory function may shape behavioral diversity. These studies indicate differences in intrinsic afferent signaling and gain control across populations. Elevated endogenous afferent activity identified a lower response threshold in the lateral line of blind cavefish relative to surface fish. We next measured the effect of inhibitory corollary discharges from hindbrain efferent neurons onto afferents during locomotion. We discovered that three independently-derived cavefish populations have evolved persistent afferent activity during locomotion, suggesting for the first time that regression of the efferent system can be an evolutionary mechanism for neural adaptation of a vertebrate sensory system.
Cognitive Deficits and Altered Cholinergic Innervation in Young Adult Mice Carrying a Parkinson’s Disease LRRK2-G2019S Knockin Mutation
Authors: Hussein Ayan , Tielemans Alexander , Baxter Mark G. , Benson Deanna L. , Huntley George W.
Published: January 2022

Impaired executive function is a common and debilitating non-motor symptom of idiopathic and hereditary Parkinson’s disease (PD), but there is little understanding of the underlying pathophysiological mechanisms and circuits. The G2019S mutation in the kinase domain of leucine-rich repeat kinase 2 (LRRK2) greatly increases risk for late-onset PD, and non-manifesting LRRK2-G2019S carriers also exhibit early and significant cognitive impairment. Here, we subjected young adult mice carrying a Lrrk2-G2019S knockin mutation to touchscreen-based operant tasks that measure attention, goal-directed learning and cognitive flexibility, all of which rely on prefrontal-striatal connectivity and are strongly modulated by cholinergic innervation. In a visuospatial attention task, mutant mice exhibited significantly more omissions and longer response latencies than controls that could not be attributed to deficits in motivation, visual sensory perception per se or locomotion, thereby suggesting impairment in divided attention and slower information processing speed. Pretreating mice with the acetylcholinesterase inhibitor donepezil normalized both higher omission rates and longer reward latencies in the mutants, but did not affect any performance metric in controls. Strikingly, cholinergic fiber density in mPFC and dorsomedial striatum was significantly sparser in mutants than in controls, while further behavioral interrogation of the mutants revealed significant impairments in action-outcome associations but preserved cognitive flexibility. These data suggest that the G2019S mutation impacts cholinergic innervation and impairs corticostriatal network function in young adulthood that may contribute to early PD-associated cognitive deficits.

STATEMENT OF SIGNIFICANCE

The LRRK2-G2019S mutation causes hereditary Parkinson’s disease and is found in some idiopathic cases. Early cognitive impairment is a common symptom of hereditary and idiopathic PD, yet there is little mechanistic understanding of such impairment. Here, we tested young adult Lrrk2-G2019S knockin mice in a series of touchscreen-based visuospatial tasks. We found that mutants exhibited significant deficits in attention and goal-directed learning, and had significantly slower information processing speed. Treatment with an acetylcholinesterase inhibitor reversed some of these behavioral deficits, while anatomical analyses showed significantly sparser cholinergic innervation of brain structures important for executive function. These findings suggest the G2019S mutation alters cholinergic signaling in young adulthood, and thus may contribute to early PD-associated impairment in several cognitive domains.
Direct type I Interferon signaling in hepatocytes control malaria
Authors: Marques-da-Silva Camila , Peissig Kristen , Walker Michael P. , Shiau Justine , Kyle Dennis E. , Vijay Rahul , Lindner Scott E. , Kurup Samarchith P.
Published: January 2022

Malaria is a devastating disease impacting over half of the world’s population. Plasmodium parasites that cause malaria undergo obligatory development and replication in hepatocytes before infecting red blood cells and initiating clinical disease. While type I interferons (IFNs) are known to facilitate innate immune control to Plasmodium in the liver, how they do so has remained unresolved, preventing the manipulation of such responses to combat malaria. Utilizing transcriptomics, infection studies, and a novel transgenic Plasmodium strain that exports and traffics Cre recombinase, we show that direct type I IFN signaling in Plasmodium-infected hepatocytes is necessary and sufficient to control malaria. We also show that the majority of infected hepatocytes naturally eliminate Plasmodium infection, revealing the potential existence of anti-malarial cell-autonomous immune responses in such hepatocytes. These discoveries challenge the existing paradigms in Plasmodium immunobiology and are expected to inspire new anti-malarial drugs and vaccine strategies.
Genetic Regulation of Circular RNA Expression in Human Aortic Smooth Muscle Cells and Vascular Traits
Authors: Aherrahrou Redouane , Lue Dillon , Civelek Mete
Published: January 2022

Background

Circular RNAs (circRNAs) are a class of non-coding RNAs that have cell-type specific expression and are relevant in cardiovascular disease. Aortic smooth muscle cells (SMCs) play a crucial role in cardiovascular disease by differentiating from a quiescent to proliferative phenotype. The role of circRNAs in SMCs and their relevance to cardiovascular disease is largely unexplored.

Results

In this study, we employ a systems genetics approach to identify circRNA transcripts at a genome wide level and their relevance in cardiovascular traits. We quantified circRNA expression across 151 quiescent and proliferative human aortic SMCs from multiethnic donors. We identified 1,589 expressed circRNAs. Between quiescent and proliferative SMCs, we identified 173 circRNAs which were differentially expressed. To characterize the genetic regulation of circRNA expression, we associated the genotypes of 6.3 million single nucleotide polymorphisms (SNPs) with circRNA abundance and found 96 circRNAs which were associated with genetic loci. Three SNPs were associated with circRNA expression in proliferative SMCs but not in quiescent SMCs. We identified 6 SNPs which had distinct association directions with circRNA isoforms from the same gene. Lastly, to identify the relevance of circRNAs in cardiovascular disease, we overlapped genetic loci associated with circRNA expression with vascular disease related GWAS loci. We identified 7 blood pressure, 1 myocardial infarction, and 3 coronary artery disease loci which were associated with a circRNA transcript (circZKSCAN1, circFOXK2, circANKRD36, circLARP4, circCEP85L, circGTF3C2, circPDS5A, circSLC4A7, and chr17:42610108|42659552) but not mRNA transcript.

Conclusions

Overall, our results provide mechanistic insight into the regulation of circRNA expression and the genetic basis of cardiovascular disease.
Eco-evolutionary feedbacks in the human gut microbiome
Authors: Good Benjamin H. , Rosenfeld Layton B.
Published: January 2022

Gut microbiota can evolve within their hosts on human-relevant timescales. Yet little is known about how these changes influence (or are influenced by) the composition of their surrounding community. Here, by combining ecological and evolutionary analyses of a large cohort of human gut metagenomes, we show that the short-term evolution of the microbiota is linked with shifts in its ecological structure. These correlations are not simply explained by expansions of the evolving species, and often involve additional fluctuations in distantly related taxa. We show that similar feedbacks naturally emerge in simple resource competition models, even in the absence of cross-feeding or predation. These results suggest that the structure and function of host microbiota may be shaped by their local evolutionary history, which could have important implications for personalized medicine and microbiome engineering.
Permethylation of ribonucleosides provides enhanced mass spectrometry quantification of post-transcriptional modifications
Authors: Xie Yixuan , Janssen Kevin A. , Scacchetti Alessandro , Bonasio Roberto , Garcia Benjamin A
Published: January 2022

Chemical modifications of RNA are associated with fundamental biological processes such as RNA splicing, export, translation, degradation, as well as human disease states such as cancer. However, the analysis of ribonucleoside modifications is impeded due to the hydrophilicity of the ribonucleoside molecules. In this research, we used solid-phase permethylation to derivatize the ribonucleosides, and the permethylated ribonucleosides, which were then quantitively analyzed using a liquid chromatography−tandem mass spectrometry (LC−MS/MS)-based method. The solid-phase permethylation efficiently derivatized the ribonucleosides, and more than 60 RNA modifications were simultaneously monitored using ultrahigh-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QqQ-MS) performed in the dynamic multiple reaction monitoring (dMRM) mode. Because of the increased hydrophobicity of permethylated ribonucleosides, this method enhanced retention, separation, and ionization efficiency, resulting in improved detection and quantification when compared to existing analytical strategies of RNA modifications. We applied this new approach to measure the extent of cytosine methylation and hydroxymethylation in RNA obtained from mouse embryonic stem cells with genetic deficiencies in ten-eleven translocation (TET) enzymes. The results matched previously performed analyses and highlighted the sensitivity, efficacy, and robustness of the new method. The advantage of this method enables comprehensive analysis of RNA modifications in biological samples.

Abstract Figure
Determinants of SARS-CoV-2 nasopharyngeal testing in a rural community sample susceptible of first infection: the CHRIS COVID-19 study
Authors: Giardiello Daniele , Melotti Roberto , Barbieri Giulia , Gögele Martin , Weichenberger Christian X. , Foco Luisa , Bottigliengo Daniele , Barin Laura , Lundin Rebecca , Pramstaller Peter P. , Pattaro Cristian
Published: January 2022

To characterize COVID-19 epidemiology, numerous population-based studies have been undertaken to model the risk of SARS-CoV-2 infection. Less is known about what may drive the probability to undergo testing. Understanding how much testing is driven by contextual or individual conditions is important to delineate the role of individual behavior and to shape public health interventions and resource allocation. In the Val Venosta/Vinschgau district (South Tyrol, Italy), we conducted a population-representative longitudinal study on 697 individuals susceptible to first infection who completed 4,512 repeated online questionnaires at four week intervals between September 2020 and May 2021. Mixed-effects logistic regression models were fitted to investigate associations of self-reported SARS-CoV-2 testing with individual characteristics (social, demographic, and biological) and contextual determinants. Testing was associated with month of reporting, reflecting the timing of both the pandemic intensity and public health interventions, COVID-19-related symptoms (odds ratio, OR:8.26; 95% confidence interval, CI:6.04–11.31), contacts with infected individuals within home (OR:7.47, 95%CI:3.81–14.62) or outside home (OR:9.87, 95%CI:5.78–16.85), and being retired (OR:0.50, 95%CI:0.34-0.73). Symptoms and next within- and outside-home contacts were the leading determinants of swab testing predisposition in the most acute phase of the pandemics. Testing was not associated with age, sex, education, comorbidities, or lifestyle factors. In the study area, contextual determinants reflecting the course of the pandemic were predominant compared to individual sociodemographic characteristics in explaining the SARS-CoV-2 probability of testing. Decision makers should evaluate whether the intended target groups were correctly prioritized by the testing campaign.
Deletion of Sod1 in motor neurons exacerbates age-related changes in axons and NMJs associated with premature muscle atrophy in aging mice
Authors: Pollock N , Macpherson PC , Staunton CA , Hemmings K , Davis CS , Owen ED , Vasilaki A , Van Remmen H , Richardson A , McArdle A , Brooks SV , Jackson MJ
Published: January 2022

Whole body knock out of Cu, Zn superoxide dismutase1 (Sod1KO) results in accelerated, age-related loss of muscle mass and function associated with a breakdown of neuromuscular junctions (NMJ) similar to sarcopenia. In order to determine whether altered redox in motor neurons is integral to this phenotype, an inducible neuron specific deletion of Sod1 (i-mnSod1KO) was compared with wild type (WT) mice of different ages (adult, mid-age and old) and whole body Sod1KO mice. Nerve oxidative damage, motor neuron numbers and structural changes to neurons and NMJ were examined.

Deletion of neuronal Sod1 (induced by tamoxifen injection at 6 months of age) caused the exaggerated, age-associated loss of muscle mass and force generation previously reported. No effect of age or lack of neuronal Sod1 was seen on oxidation in the sciatic nerve assessed by electron paramagnetic resonance of the in vivo spin probe 1-hydroxy-3-carboxy-2,2,5,5 tetramethylpyrrolidine (CPH), analysis of protein 3-nitrotyrosines or carbonyl content. i-mnSod1KO mice showed increased numbers of denervated NMJs, a reduced number of large axons and increased number of small axons compared with age-matched old WT mice. A large proportion of the remaining innervated NMJs in i-mnSod1KO mice also displayed a much simpler structure than that seen in WT mice.

Thus, while Sod1KO mice recapitulate substantially the neuromuscular phenotypes of old WT mice, deletion of Sod1 specifically in neurons induces exaggerated loss of muscle mass and force only in old (24-29 month) mice indicating that significant muscle declines require the accumulation of age-related changes such that a threshold is reached past which maintenance of structure and function is not possible.

Significance statement

Sarcopenia is the age-related loss of muscle mass and function. It is a significant contributor to frailty and to increased falls in the elderly. While multifactorial, changes in redox status have been shown to have significant influence over neuromuscular aging, recent work suggests that changes in motor neurons may be the driving factor in muscle atrophy. The current study confirmed that a specific lack of Sod1 in the motor neuron causes significant alteration in axonal architecture and the neuromuscular junctions which can drive reduced muscle mass and function. Pinpointing early changes in motor neurons may provide therapeutic targets critical for maintaining muscle in the elderly.
Microdynamics of lamin A Ig-fold domain regulates higher order assembly of the protein
Authors: Mukherjee Chandrayee , Sengupta Duhita , Maganti Lakshmi , Mahendar M. , Bhattacharyya Dhananjay , Sengupta Kaushik
Published: January 2022

Lamins maintain the shape and rigidity of the nucleus in the form of a proteinaceous scaffold underneath the inner nuclear membrane (INM) and provide anchorage to chromatin and other nuclear proteins. Mutations in the human LMNA gene encoding lamin A/C cause about 16 different diseases with distinct phenotypes collectively termed as laminopathies which affect primarily the muscle tissues as well as adipose tissues, neuromuscular junctions and multiple other organs in progeroid syndromes. Lamins contain several domains of which Ig-fold is one of the well characterized and structured domains that harbours many mutations leading to deleterious interactions with other nuclear proteins. In this work, we have elucidated the effects of 3 such mutations namely R453W, W498C and W498R on the dynamics and flexibility of the Ig-fold domain and the consequent effect on the assembly into lamina by live cell imaging, fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. From our experimental observations, we concluded that R453W has somewhat increased flexibility compared to the other mutants but lower than that of the wild type. This might be attributed due to an alteration of the salt bridges in the Ig fold domain of the mutant. This is the first report where such an alteration in the full length has been documented by gross changes in diffusional properties as a sequel to a mutation in the Ig fold domain
Life history speed, population disappearances and noise-induced ratchet effects
Authors: Greyson-Gaito Christopher J. , Gellner Gabriel , McCann Kevin S.
Published: January 2022

Nature is replete with variation in the body sizes, reproductive output, and generation times of species that produce life history responses known to vary from small and fast to large and slow. Although researchers recognize that life history speed likely dictates fundamental processes in consumer-resource interactions like productivity and stability, theoretical work remains incomplete in this critical area. Here, we examine the role of life history speed on consumer-resource interactions by using a well used mathematical approach that manipulates the speed of the consumer’s growth rate in a consumer-resource interaction. Importantly, this approach holds the isocline geometry intact allowing us to assess the impacts of altered life history speed on stability (coefficient of variation, CV) without changing the underlying qualitative dynamics. Although slowing life history can be initially stabilizing, we find that in stochastic settings slowing ultimately drives highly destabilizing population disappearances, especially under reddened noise. Our results suggest that human-driven reddening of noise may decrease species stability because the autocorrelation of red noise enlarges the period and magnitude of perturbations, overwhelming a species’ natural compensatory responses via a ratchet-like effect. This ratchet-like effect then pushes species’ population dynamics far away from equilibria that can lead to precipitous local extinction.
Experimental disruption of social structure reveals totipotency in the orchid bee, Euglossa dilemma
Authors: Saleh Nicholas W. , Henske Jonas , Ramírez Santiago R.
Published: January 2022

Eusociality has evolved multiple times across the insect phylogeny. Social insects with greater levels of social complexity tend to exhibit specialized castes with low levels of individual phenotypic plasticity. In contrast, species with small, simple social groups may consist of totipotent individuals that can transition among behavioral and reproductive states as the social hierarchy shifts. However, recent work has shown that in some simple social groups, there can still be constraint on individual plasticity, caused by differences in maternal nourishment or initial social interaction. It is not well understood how and when these constraints arise during social evolution, ultimately leading to the evolution of nonreproductive workers. Some species of orchid bees can form social groups of a dominant and 1-2 subordinate helpers where all individuals are reproductive. Females can also disperse on emergence to start their own nest as a solitary foundress, which includes a nonreproductive nest guarding phase not typically expressed by subordinates. Little data exist to characterize the flexibility of orchid bees across these trajectories. Here, using the orchid bee Euglossa dilemma, we conduct an experiment assessing the plasticity of subordinate helpers, finding that they are highly flexible and capable of the behavioral, physiological, transcriptomic, and chemical changes seen in foundresses. Furthermore, we identify genes and gene networks associated with reproductive changes in E. dilemma that overlap with genes associated with worker physiology in eusocial species. Our results provide evidence that the lack of nonreproductive workers in E. dilemma is not due to a lack of subordinate plasticity.
Heterotrimeric G protein α subunit (GPA1) regulates the response to low-nitrogen stress in Arabidopsis by interacting with AtNRT1.4 and AtATG8a
Authors: Luo Mingzhao , Hu Liqin , Li Weiwei , Ge Linhao , Qin Yuhai , Zhou Yongbin , Tang Wensi , Wang Chunxiao , Xu Zhaoshi , Chen Jun , Delaplace Pierre , Ma Youzhi , Chen Ming
Published: January 2022

Efficient nitrogen absorption and utilization are important factors for higher plants to increase yield and reduce eutrophication (caused by excessive use of nitrogen fertilizers). Heterotrimeric G proteins, including three subunits of α, β, and γ, participate in the pathway regulating nitrogen absorption and utilization in plants. However, the regulatory mechanism remains largely obscured. In this study, our results revealed that the G protein α subunit (AtGPA1) mutant gpa1-4 was tolerant to low-nitrogen stress in Arabidopsis. AtGPA1 was shown to directly interact with a nitrate transporter (AtNRT1.4) and a key autophagy-related protein (AtATG8a) on the plasma membrane using the yeast hybrid system and pull-down assay (in vitro) and BiFC assay (in vivo). GUS staining and subcellular localization showed that AtGPA1 and AtNRT1.4 were co-expressed in roots and leaf veins and on the plasma membrane. Under low-nitrate conditions, the single mutant gpa1-4 and NRT1.4RNAi plants (AtNRT1.4RNA interference plants) and the double mutant NRT1.4RNAi/gpa1-4 plants (AtNRT1.4RNA interference plants on a gpa1-4 background) were healthier than the wild type plants. Moreover, the phenotype of the double mutant NRT1.4RNAi/gpa1-4 plants was closer to that of the NRT1.4RNAi plants compared to that of the gpa1-4 mutants. The results of the nitrate efflux rate assay in roots were consistent with the phenotypic changes under low-nitrogen conditions. These results indicated that AtGPA1 is an upstream factor that regulated the response to low-nitrogen stress through interaction with AtNRT1.4. In addition, we found that transgenic plants overexpressing AtATG8a were more tolerant to low-nitrogen stress, and their phenotype was similar to that of gpa1-4 mutants and double mutant ATG8aOX/gpa1-4 plants (AtATG8a overexpressing plants on a gpa1-4 mutant background). Further, autophagosome observations were consistent with the phenotypes in mutant plants, indicating that AtGPA1 regulated the response to low-nitrogen stress in Arabidopsis plants by affecting the autophagosome assembly. Our findings may provide a new model for improving nitrogen-use efficiency through genetical modification to boost crop yields.

One sentence summary

AtGPA1 negative regulates low nitrogen stress response by interaction with a nitrate transporter, AtNRT1.4 and an autophagy-related protein, AtATG8a in Arabidopsis.
Building model prototypes from time-course data
Authors: Veliz-Cuba Alan , Voss Stephen Randal , Murrugarra David
Published: January 2022

A primary challenge in building predictive models from temporal data is selecting the appropriate model topology and the regulatory functions that describe the data. Software packages are available for equation learning of continuous models, but not for discrete models. In this paper we introduce a method for building model prototypes. These model prototypes consist of a wiring diagram and a set of discrete functions that can explain the time course data. The method takes as input a collection of time course data or discretized measurements over time. After network inference, we use our toolbox to simulate the prototype model as a stochastic Boolean model. Our method provides a model that can qualitatively reproduce the patterns of the original data and can further be used for model analysis, making predictions, and designing interventions. We applied our method to a time-course, gene-expression data that were collected during salamander tail regeneration under control and intervention conditions. The inferred model captures important regulations that were previously validated in the research literature and gives novel interactions for future testing. The toolbox for inference and simulations is freely available at github.com/alanavc/prototype-model.
RTEL1 and MCM10 overcome topological stress during vertebrate replication termination
Authors: Campos Lillian V. , Greer Briana H. , Heintzman Darren R. , Kavlashvili Tamar , McDonald W. Hayes , Rose Kristie Lindsey , Eichman Brandt F. , Dewar James M.
Published: January 2022

Topological stress can cause replication forks to stall as they converge upon one another during termination of vertebrate DNA synthesis. However, replication forks ultimately overcome topological stress and complete DNA synthesis, suggesting that alternative mechanisms can overcome topological stress. We performed a proteomic analysis of converging replication forks that were stalled by topological stress in Xenopus egg extracts. We found that the helicase RTEL1 and the replisome protein MCM10 were highly enriched on DNA under these conditions. We show that RTEL1 normally plays a minor role during fork convergence while the role of MCM10 is normally negligible. However, RTEL1 and MCM10 both become crucially important for fork convergence under conditions of topological stress. RTEL1 and MCM10 exert non-additive effects on fork convergence and physically interact, suggesting that they function together. Furthermore, RTEL1 and MCM10 do not impact topoisomerase activity but do promote fork progression through a replication barrier. Thus, RTEL1 and MCM10 appear to play a general role in promoting progression of stalled forks, including when forks stall during termination. Overall, our data identify an alternate mechanism of termination involving RTEL1 and MCM10 that can be used to complete DNA synthesis under conditions of topological stress.
Puromycin is incorporated into regenerating flagella of Chlamydomonas reinhardtii as an indicator of nascent flagellar proteins
Authors: Kubo Tomohiro , Kanou Natsumi , Oda Toshiyuki
Published: January 2022

The unicellular alga Chlamydomonas reinhardtii assembles flagella after pH shock-induced deflagellation, in which process the cell vigorously synthesizes flagellar proteins. Previously, newly synthesized flagellar proteins were chased using radioisotopes. Here, we have developed an alternative, non-radioactive method using the surface sensing of translation (SUnSET) assay, an assay that takes advantage of the incorporation of the antibiotic puromycin into newly synthesized peptides. Just after deflagellation, puromycin-labeled proteins increased dramatically in the cytoplasm and newly assembled flagella. Axonemal incorporation of newly synthesized proteins occurred from the distal tip of the flagellum. Cycloheximide, a protein synthesis inhibitor, almost completely prevented the cellular and flagellar incorporation of puromycin, although, as reported previously, it allowed reassembly of half-length flagella from the cytoplasmic “flagellar precursor” proteins. In contrast to wild-type cells, a cycloheximide-resistant mutant act2 produced nearly full-length flagella containing puromycin-labeled proteins even in the presence of cycloheximide. These and other results demonstrate that the SUnSET method serves as a powerful tool for visualizing flagellar incorporation of nascent proteins in Chlamydomonas.
Assessment of AlphaFold2 residue conformations for human proteins
Authors: Bæk Kristoffer T. , Kepp Kasper P.
Published: January 2022

Motivation

As only 35% of human proteins feature (often partial) PDB structures, the protein structure prediction tool AlphaFold2 (AF2) could have massive impact on human biology and medicine fields, making independent benchmarks of interest. We studied AF2’s ability to describe the backbone solvent exposure as an easily interpretable “natural coordinate” of protein conformation, using human proteins as test case.

Results

After screening for appropriate comparative sets, we matched 1818 human proteins predicted by AF2 against 7585 unique experimental PDBs, and after curation for sequence overlap, we assessed 1264 comparative pairs comprising 115 unique AF2-structures and 652 unique experimental structures. AF2 performed markedly worse for multimers, whereas ligands, cofactors and experimental resolution were interestingly not very important for performance. AF2 performed excellently for monomer proteins. Challenges relating to specific groups of residues and multimers were analyzed. We identify larger errors for lower-confidence scores (pLDDT) and exposed residues, and polar residues (Asp, Glu, Asn e.g.) being less accurately described than hydrophobic residues. Proline conformations were the hardest to predict, probably due to common location in dynamic solvent-accessible parts. In summary, using solvent exposure as a natural metric of local conformation, we quantify the performance of AF2 for human proteins and provide estimates of the expected error as a function of ligand presence, multimer/monomer status, resolution, local residue solvent exposure, pLDDT, and amino acid type. Overall performance was found to be excellent.

Availability and Implementation

Scripts used to perform benchmarking are available athttps://github.com/ktbaek/AlphaFold.
Fast and accurate joint inference of coancestry parameters for populations and/or individuals
Authors: Mary-Huard Tristan , Balding David
Published: January 2022

We introduce a fast, new algorithm for inferring jointly the FST parameters describing genetic distances among a set of populations and/or unrelated diploid individuals, and a tree representing their genetic structure, from allele count data. While the inferred tree typically reflects historical processes of splitting and divergence, its aim is to represent the actual genetic variance, with FST values specified by branch lengths. We generalise two major approaches to defining FST, via correlations and mismatch probabilities of sampled allele pairs, which measure shared and non-shared components of genetic variance. A diploid individual can be treated as a population of two gametes, which allows inference of coancestry coefficients for individuals as well as for populations, or a combination of the two. A simulation study illustrates that our fast method-of-moments estimation of FST values, simultaneously for multiple populations/individuals, gains statistical efficiency over pairwise approaches by pooling information about ancestral allele frequencies. We apply our approach to genome-wide genotypes from the 26 worldwide human populations of the 1000 Genomes Project. We first analyse at the population level, then a subset of individuals and in a final analysis we pool individuals from the more homogeneous populations. This flexible analysis approach gives many advantages over traditional approaches to population structure/coancestry, including visual and quantitative assessments of long-standing questions about the relative magnitudes of within- and between-population genetic differences.

Author summary

We propose new ways to measure, and visualise in a tree, the genetic distances among a set of populations using allele frequency data. The two genomes within a diploid individual can be treated as a small population, which allows a flexible framework for investigating genetic variation within and between populations. Genetic structure can be accurately and efficiently represented in a tree with nodes representing either homogeneous populations or genetically diverse individuals, for example due to admixture. We first generalise the long-established measure of genetic distance, FST, to tree-structured populations and individuals, finding that two measures are required for each pair of populations, corresponding to their shared and and non-shared genetic variation. We show using a simulation study that our novel tree-based estimators are more efficient than current pairwise estimators, and we illustrate the potential for novel ways to explore and visualise genetic variation within and between populations using a worldwide human genetic dataset.
Did Caenorhabditis nematodes recycle transposons to fight pathogens?
Authors: Li Zixin , Rödelsperger Christian
Published: January 2022

Animal genomes consist largely of sequences derived from transposons which were previously considered as junk DNA and active transposons can even be deleterious for organismal fitness. Nevertheless, the huge pool of transposon-derived sequences also forms the raw material for molecular innovations. Here, we follow up on the incidental finding of a transposon-derived DNA binding domain in a subset of F-box genes in Caenorhabditis elegans. Based on phylogenetic analysis, we show that a single gene fusion followed by individual losses explains most members of this novel gene family. Phylogenomic data of available Caenorhabditis genomes allowed us to trace this fusion event to the ancestor of the Elegans group. Additional homology searches suggest endogenous Mariner transposons as the likely source of the coopted sequence. Further bioinformatic characterization of different F-box families by Gene Ontology analysis, gene module comparisons, and literature research identified first evidence that some F-box genes might be involved in innate immunity, as it had been proposed previously based on adaptive signatures of molecular evolution. Specifically, the F-box gene fbxa-158 contains one of the transposon-derived domains and was shown to interact with the components of the intracellular pathogen response machinery targeting Microsporidia and viruses. Thus, cooption of transposon-derived sequences likely contributed to the adaptive evolution of the F-box superfamily in Caenorhabditis nematodes.

Significance statement

When considering transposons as genomic junk or selfish elements that are detrimental for organismal fitness, we often neglect the potential of transposon-derived sequences as a source of molecular innovation. Here, we characterize a case where a transposon-derived sequence has been coopted by one of the largest and fastest evolving gene superfamilies in Caenorhabditis nematodes which include the model organism C. elegans. The resulting chimeric gene family has been stably maintained for about 20 million years and bioinformatic analysis reveals first evidence for potential functions in innate immunity. Thus, strong evolutionary pressure might have forced Caenorhabditis nematodes to recycle transposons in order to fight pathogens.
Effective generation of tumor-infiltrating lymphocyte products from metastatic non-small-cell lung cancer (NSCLC) lesions irrespective of location and previous treatments
Authors: Castenmiller Suzanne M. , de Groot Rosa , Guislain Aurélie , Monkhorst Kim , Hartemink Koen J. , Veenhof Alexander A.F.A. , Smit Egbert F. , Haanen John B.A.G. , Wolkers Monika C.
Published: January 2022

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. Because current treatment regimens show limited success rates, alternative therapeutic approaches are needed. We recently showed that treatment-naive, stage I/II primary NSCLC tumors contain a high percentage of tumor-reactive T cells, and that these tumor-reactive T cells can be effectively expanded and used for the generation of autologous TIL therapy. Whether these promising findings also hold true for metastatic lesions is unknown yet critical for the translation into the clinic. We here studied the lymphocytic composition and the feasibility to generate tumor-responsive TIL products from metastatic NSCLC lesions that were derived from different locations and from patients who had previously received different treatment regimens, or who were treatment naïve. The overall numbers and composition of lymphocyte infiltrates from this various metastatic lesions was by and large comparable to that of early-stage primary NSCLC tumors. With the clinically approved TIL expansion protocol, we effectively expanded TILs from metastatic NSCLC lesions to numbers that were compatible with TIL transfusion, irrespective of the location of the metastasis and of the previous treatment. Importantly, 16 of 21 (76%) tested TIL products displayed anti-tumoral activity, as determined by their production of the key pro-inflammatory cytokines IFN-γ, TNF, IL-2 and of CD137 expression upon incubation with autologous tumor digests by CD8+ and CD4+ T cells. In summary, metastatic NSCLC lesions constitute a viable source for the generation of tumor-reactive TIL products for therapeutic purposes irrespective of their location and the pretreatment regimens.
RNase L-mediated RNA decay alters 3’ end formation and splicing of host mRNAs
Authors: Burke James M. , Ripin Nina , Ferretti Max B. , St Clair Laura A. , Worden-Sapper Emma R. , Sawyer Sara L. , Perera Rushika , Lynch Kristen W. , Parker Roy
Published: January 2022

The antiviral endoribonuclease, RNase L, is a vital component of the mammalian innate immune response that destroys host and viral RNA to reduce viral gene expression. Herein, we show that a consequence of RNase L-mediated decay of cytoplasmic host RNAs is the widespread re-localization of RNA-binding proteins (RBPs) from the cytoplasm to the nucleus, due to the presence of nuclear RNA. Concurrently, we observe global alterations to host RNA processing in the nucleus, including alterations of splicing and 3’ end formation, with the latter leading to downstream of gene (DoG) transcripts. While affecting many host mRNAs, these alterations are pronounced in mRNAs encoding type I and type III interferons and coincide with the retention of their mRNAs in the nucleus. Similar RNA processing defects also occur during infection with either dengue virus or SARS-CoV-2 when RNase L is activated. These findings reveal that the distribution of RBPs between the nucleus and cytosol is fundamentally dictated by the availability of RNA in each compartment and thus viral infections that trigger cytoplasmic RNA degradation alter RNA processing due to the nuclear influx of RNA binding proteins.
Elucidating Heterogeneous Iron Biomineralization Patterns in a Denitrifying As(III)-Oxidizing Bacterium: Implications for Arsenic Immobilization
Authors: Lopez-Adams Rebeca , Fairclough Simon M. , Lyon Ian C. , Haigh Sarah J. , Zhang Jun , Zhao Fang-Jie , Moore Katie L. , Lloyd Jonathan R.
Published: January 2022

Anaerobic nitrate-dependent iron(II) oxidation is a process common to many bacterial species, which promotes the formation of Fe(III) minerals that can influence the fate of soil and groundwater pollutants, such as arsenic. Herein, we investigated simultaneous nitrate-dependent Fe(II) and As(III) oxidation byAcidovoraxsp. strain ST3 with the aim of studying the Fe biominerals formed, their As immobilization capabilities and the metabolic effect on cells. X-ray powder diffraction (XRD) and scanning transmission electron microscopy (STEM) nanodiffraction were applied for biomineral characterization in bulk and at the nanoscale, respectively. NanoSIMS (nanoscale secondary ion mass spectrometry) was used to map the intra and extracellular As and Fe distribution at the single-cell level and to trace metabolically active cells, by incorporation of a13C-labeled substrate (acetate). Metabolic heterogeneity among bacterial cells was detected, with periplasmic Fe mineral encrustation deleterious to cell metabolism. Interestingly, Fe and As were not co-localized in all cells, indicating delocalized sites of As(III) and Fe(II) oxidation. The Fe(III) minerals lepidocrocite and goethite were identified in XRD, although only lepidocrocite was identified via STEM nanodiffraction. Extracellular amorphous nanoparticles were formed earlier and retained more As(III/V) than crystalline “flakes” of lepidocrocite, indicating that longer incubation periods promote the formation of more crystalline minerals with lower As retention capabilities. Thus, the addition of nitrate promotes Fe(II) oxidation and formation of Fe(III) biominerals by ST3 cells which retain As(III/V), and although this process was metabolically detrimental to some cells, it warrants further examination as a viable mechanism for As removal in anoxic environments by biostimulation with nitrate.
Crystal structure and Hirshfeld surface analysis of 5-acetyl-3-amino-6-methyl-N-phenyl-4-[(E)-2-phenylethenyl]thieno[2,3-b]pyridine-2-carboxamide
Authors: Mohamed Shaaban K. , Bakhite Etify A. , Çelikesir Sevim Türktekin , Abdu-Allah Hajjaj H. M. , Akkurt Mehmet , Ibrahim Omaima F. , Mague Joel T. , Al-Waleedy Safiyyah A. H.
Published: January 2022

The asymmetric unit of the title compound, C25H21N3O2S, comprises four molecules. Their conformations differ primarily in the orientations of the styryl and the N-phenylcarboxamido groups. In the crystal, intermolecular N—H...N, C—H...O and C—H...S hydrogen-bonding contacts as well a C—H...π(ring) interactions lead to the formation of a layer structure parallel to (010). Hirshfeld surface analysis revealed that H...H interactions represent the main contributions to the crystal packing.
N-Phenyl-N-[(E)-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)ethenyl]aniline
Authors: Hatayama Yuki , Akagi Kazuto , Okuno Tsunehisa
Published: January 2022

The title compound, C20H24BNO2, has a polarized π-system due to significant resonance between the N—C(H)=C(H)—B and ionic N+=C(H)—C(H)=B− canonical forms. The dihedral angles between the NC2B plane (r.m.s. deviation 0.0223 Å) and the C3N (r.m.s. deviation 0.0025 Å) and BCO2 (r.m.s. deviation 0.0044 Å) planes are 2.51 (12) and 3.09 (19)°, respectively. This indicates the lone pair of the nitrogen atom and a vacant p orbital of the boron atom are conjugated with the central C=C bond. In comparison with the carbazole analogue [Hatayama & Okuno (2012). Acta Cryst. E68, o84], the C—N and C—B bonds are shorter. The results are well explained by the increase in the contribution of the N+=C(H)—C(H)=B− canonical form in the title compound.