bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Authors: Hill Jason , Lillie Mette , Pettersson Mats E , Rubin Carl-Johan , Grant B Rosemary , Grant Peter R , Andersson Leif , Jern Patric
Published: March 2022

Endogenous retroviruses (ERVs) are inherited remnants of past retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. The utility of ERVs as markers of host genome evolution is augmented by their ability to reveal historic retrovirus-host interactions, given that ERVs are examples of active retroviruses at the time of germline invasion. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system as a natural model for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We found shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggest historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, as well as across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Ecological and evolutionary consequences of selective interspecific information use
Authors: Hämäläinen Reetta , Kajanus Mira H. , Forsman Jukka T. , Kivelä Sami M. , Seppänen Janne-Tuomas , Loukola Olli J.
Published: March 2022

II.

Abstact

The ecology of social information use has been studied in many intra- and interspecific contexts, while the evolutionary consequences of social information use remain less understood. Furthermore, selective social information use, where individuals are discriminative in their decision-making on how to use social information, has been overlooked in interspecific context. In particular, the intentional decision to reject a behavioural trait observed via social information, has gained less attention, although it has recently been shown to occur in various taxa. We develop an individual-based simulation model to explore in which circumstances social information use leads to different coevolutionary outcomes among populations of two species. The initial phenotypes and the balance between costs of competition and benefits of social information use determine whether selection leads to trait divergence, convergence or coevolutionary arms race between two species. Based on existing literature, we propose that selective decisions of individuals, including active rejection, may have far-reaching fitness consequences, potentially leading to similar evolutionary consequences among the populations of the information source and the user as predicted by our model. Overall, we argue that the eco-evolutionary consequences of selective interspecific social information use may be much more prevalent than thus far considered.
Metabolism of glucose activates TORC1 through multiple mechanisms in Saccharomyces cerevisiae
Authors: Alfatah Mohammad , Cui Liang , Hui Goh Corinna Jie , Wong Jin Huei , Lewis Jacqueline , Poh Wei Jie , Arumugam Prakash
Published: March 2022

Target of Rapamycin Complex 1 (TORC1) is a conserved eukaryotic protein complex that links the presence of nutrients with cell growth. In Saccharomyces cerevisiae, TORC1 activity is positively regulated by the presence of amino acids and glucose in the medium. However, mechanisms underlying nutrient-induced TORC1 activation remain poorly understood. By utilizing a TORC1 activation assay, we demonstrate that differential metabolism of glucose activates TORC1 through three distinct pathways in yeast. The first ‘canonical Rag GTPase-dependent pathway’ requires conversion of glucose to fructose 1,6-bisphosphate which activates TORC1 via the Rag GTPase heterodimer Gtr1GTP/Gtr2GDP. The second ‘non-canonical Rag GTPase-dependent pathway’ requires conversion of glucose to glucose 6-phosphate which activates TORC1 via Gtr1GTP/Gtr2GTP. The third ‘Rag GTPase-independent pathway’ requires complete glycolysis and vacuolar ATPase reassembly for TORC1 activation. Glucose-induced TORC1 activation can be uncoupled from glucose-induced AMPK inactivation. We have established a roadmap to deconstruct the link between glucose metabolism and TORC1 activation.
Paf1C denoises transcription and growth patterns to achieve organ shape reproducibility
Authors: Trinh Duy-Chi , Martin Marjolaine , Bald Lotte , Maizel Alexis , Trehin Christophe , Hamant Olivier
Published: March 2022

In multicellular systems, all cells exhibit transcriptional noise. However, its exact contribution to morphogenesis often remains unclear, especially in animals where cells can also move. Here we take advantage of walled plant cells, where transcriptional noise happens in tissues with a fixed topology. Using synchronously growing guard cells in stomata, we demonstrate that mutation in VIP3, a subunit of the conserved polymerase-associated factor 1 complex (Paf1C), increases transcriptional noise in Arabidopsis. This conclusion could be generalized to other group of cells at the shoot apex. Such noise translates into growth and shape defects. Indeed, in vip3 sepals, we measured higher growth heterogeneity between adjacent cells, with molecular evidence of increased local mechanical conflicts. This even culminated with the presence of negatively growing cells in specific growth conditions. Interestingly, such increased local noise makes the regional pattern of growth less clear-cut. Reduced regional conflicts lead to delay in organ growth arrest, ultimately making final organ shapes and sizes more variable. We propose that transcriptional noise is managed by Paf1C to ensure organ robustness by building up mechanical conflicts at the regional scale, instead of the local scale.

HIGHLIGHTS

Paf1C controls transcriptional noise in Arabidopsis

Paf1C reduces growth heterogeneity and dampens local mechanical conflicts

Impairing both Paf1C and microtubules can trigger negative growth in Arabidopsis

Scaling up local conflicts to regional ones with sharp boundaries contributes to organ shape robustness
TNFR2 costimulation differentially impacts regulatory and conventional CD4+ T-cell metabolism
Authors: Mensink Mark , Zaal Esther A. , Tran Ngoc Minh Thi , Schrama Ellen , Berkers Celia R. , Borst Jannie , de Kivit Sander
Published: March 2022

CD4+ conventional T cells (Tconvs) mediate adaptive immune responses, whereas regulatory T cells (Tregs) suppress those responses to safeguard the body from autoimmunity and inflammatory diseases. The opposing activities of Tconvs and Tregs depend on the stage of the immune response and their environment, with an orchestrating role for cytokine- and costimulatory receptors. Nutrient availability also impacts T-cell functionality via metabolic and biosynthetic processes that are largely unexplored. Many data argue that costimulation by Tumor Necrosis Factor Receptor 2 (TNFR2) favors support of Treg over Tconv responses and therefore TNFR2 is a key clinical target. Here, we review the pertinent literature on this topic and highlight the newly identified role of TNFR2 as a metabolic regulator for thymus-derived (t)Tregs. We present novel transcriptomic and metabolomic data that show the differential impact of TNFR2 on Tconv and tTreg gene expression and reveal distinct metabolic impact on both cell types.
circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner
Authors: Josipovic Natasa , Ebbesen Karoline K. , Zirkel Anne , Mackay-Danieli Adi , Dieterich Christoph , Kurian Leo , Hansen Thomas B. , Papantonis Argyris
Published: March 2022

Circular RNAs are endogenous long-lived and abundant non-coding species. Despite their prevalence, only few circRNAs have been dissected mechanistically to date. Here, we catalogued nascent RNA-enriched circRNAs from primary human cells and functionally assign a role to circRAB3IP in sustaining cellular homeostasis. We combined “omics” and functional experiments to show how circRAB3IP depletion deregulates hundreds of genes, suppresses cell cycle progression, and induces senescence-associated gene expression changes. Conversely, excess circRAB3IP delivered to endothelial cells via extracellular vesicles suffices for accelerating their division. We attribute these effects to the interplay between circRAB3IP and the general splicing factor SF3B1, which impacts transcript usage of cell cycle-related genes. Together, our findings link the maintenance of cell homeostasis to the tightly regulated titers of a single circRNA.
Digital twins and hybrid modelling for simulation of physiological variables and stroke risk
Authors: Herrgårdh Tilda , Hunter Elizabeth , Tunedal Kajsa , Örman Håkan , Amann Julia , Navarro Francisco Abad , Martinez-Costa Catalina , Kelleher John D. , Cedersund Gunnar
Published: March 2022

One of the more interesting ideas for achieving personalized, preventive, and participatory medicine is the concept of a digital twin. A digital twin is a personalized computer model of a patient. So far, digital twins have been constructed using either mechanistic models, which can simulate the trajectory of physiological and biochemical processes in a person, or using machine learning models, which for example can be used to estimate the risk of having a stroke given a cross-section profile at a given timepoint. These two modelling approaches have complementary strengths which can be combined into a hybrid model. However, even though hybrid modelling combining mechanistic modelling and machine learning have been proposed, there are few, if any, real examples of hybrid digital twins available. We now present such a hybrid model for the simulation of ischemic stroke. On the mechanistic side, we develop a new model for blood pressure and integrate this with an existing multi-level and multi-timescale model for the development of type 2 diabetes. This mechanistic model can simulate the evolution of known physiological risk factors (such as weight, diabetes development, and blood pressure) through time, under different intervention scenarios, involving a change in diet, exercise, and certain medications. These forecast trajectories of the physiological risk factors are then used by a machine learning model to calculate the 5-year risk of stroke, which thus also can be calculated for each timepoint in the simulated scenarios. We discuss and illustrate practical issues with clinical implementation, such as data gathering and harmonization. By improving patients’ understanding of their body and health, the digital twin can serve as a valuable tool for patient education and as a conversation aid during the clinical encounter. As such, it can facilitate shared decision-making, promote behavior change towards a healthy lifestyle, and improve adherence to prescribed medications.
Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting
Authors: Van den Broeck Lisa , Schwartz Michael F , Krishnamoorthy Srikumar , Spurney Ryan J , Tahir Maimouna Abderamane , Melvin Charles , Gobble Mariah , Peters Rachel , Muhammad Atiyya , Li Baochun , Stuiver Maarten , Horn Timothy , Sozzani Rosangela
Published: March 2022

Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis root cells and soybean meristematic cells. To analyze the large image datasets generated during these long-term viability studies, we developed an open source high-throughput image analysis pipeline. Furthermore, we showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration.
Genetic glyco-profiling and rewiring of insulated flagellin glycosylation pathways
Authors: Kint Nicolas , Dubois Thomas , Viollier Patrick H.
Published: March 2022

Glycosylation of surface structures diversifies cells chemically and physically. Sialic acids commonly serve as glycosyl donors, particularly pseudaminic (Pse) or legionaminic acid (Leg) that prominently decorate eubacterial and archaeal surface layers or appendages. We investigated a new class of FlmG protein glycosyltransferases that modify flagellin, the structural subunit of the flagellar filament. Functional insulation of orthologous Pse and Leg biosynthesis pathways accounted for the flagellin glycosylation specificity and motility conferred by the cognate FlmG in the α-proteobacteria Caulobacter crescentus and Brevundimonas subvibrioides, respectively. Exploiting these functions, we conducted genetic glyco-profiling to classify Pse or Leg biosynthesis pathways and we used heterologous reconstitution experiments to unearth a signature determinant of Leg biosynthesis in eubacteria and archaea. These findings and our chimeric FlmG analyses reveal two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that accepts either Leg or Pse and that uses specialized flagellin-binding domain to identify the substrate.
Effects of variability in manually contoured spinal cord masks on fMRI co-registration and interpretation
Authors: Hoggarth Mark A. , Wang Max C. , Hemmerling Kimberly J. , Vigotsky Andrew D. , Smith Zachary A. , Parrish Todd B. , Weber Kenneth A. , Bright Molly G.
Published: March 2022

Functional magnetic resonance imaging (fMRI) of the human spinal cord (SC) is a unique non-invasive method for characterizing neurovascular responses to stimuli. Group-analysis of SC fMRI data involves co-registration of subject-level data to standard space, which requires manual masking of the cord and may result in bias of group-level SC fMRI results. To test this, we examined variability in SC masks drawn in fMRI data from 21 healthy participants from a completed study mapping responses to sensory stimuli of the C7 dermatome. Masks were drawn on temporal mean functional image by eight raters with varying levels of neuroimaging experience, and the rater from the original study acted as a reference. Spatial agreement between rater and reference masks was measured using the Dice Similarity Coefficient, and the influence of rater and dataset was examined using ANOVA. Each rater’s masks were used to register functional data to the PAM50 template. Gray matter-white matter signal contrast of registered functional data was used to evaluate the spatial normalization accuracy across raters. Subject- and group-level analyses of activation during left- and right-sided sensory stimuli were performed for each rater’s co-registered data. Agreement with the reference SC mask was associated with both rater (F(7,140) = 32.12, P < 2×10−16, η2 = 0.29) and dataset (F(20,140) = 20.58, P < 2×10−16, η2 = 0.53). Dataset variations may reflect image quality metrics: the ratio between the signal intensity of spinal cord voxels and surrounding cerebrospinal fluid was correlated with DSC results (p<0.001). As predicted, variability in the manually-drawn masks influenced spatial normalization, and GM:WM contrast in the registered data showed significant effects of rater and dataset (rater: F(8,160) = 23.57, P < 2×10−16, η2 = 0.24; dataset: F(20,160) = 22.00, P < 2×10−16, η2 = 0.56). Registration differences propagated into subject-level activation maps which showed rater-dependent agreement with the reference. Although group-level activation maps differed between raters, no systematic bias was identified. Increasing consistency in manual contouring of spinal cord fMRI data improved co-registration and inter-rater agreement in activation mapping, however our results suggest that improvements in image acquisition and post-processing are also critical to address.
Spatiotemporal patterns of sleep spindle activity in human anterior thalamus and cortex
Authors: Bernhard Hannah , Schaper Frederic L. W. V. J. , Janssen Marcus L. F. , Gommer Erik D. , Jansma Bernadette M. , Van Kranen-Mastenbroek Vivianne , Rouhl Rob P. W. , Weerd Peter de , Reithler Joel , Roberts Mark J. ,   DBS study group
Published: March 2022

Sleep spindles (8 - 16 Hz) are transient electrophysiological events during non-rapid eye movement sleep. While sleep spindles are routinely observed in the cortex using scalp electroencephalography (EEG), recordings of their thalamic counterparts have not been widely studied in humans. Based on a few existing studies, it has been hypothesized that spindles occur as largely local phenomena. We investigated intra-thalamic and thalamocortical spindle co-occurrence, which may underlie thalamocortical communication. We obtained scalp EEG and thalamic recordings from 7 patients that received bilateral deep brain stimulation (DBS) electrodes to the anterior thalamus for the treatment of drug resistant focal epilepsy. Spindles were categorized into subtypes based on their main frequency (i.e., slow (10±2 Hz) or fast (14±2 Hz)) and their level of thalamic involvement (spanning one channel, or spreading uni- or bilaterally within the thalamus). For the first time, we contrasted observed spindle patterns with permuted data to estimate random spindle co-occurrence. We found that multichannel spindle patterns were systematically coordinated at the thalamic and thalamocortical level. Importantly, distinct topographical patterns of thalamocortical spindle overlap were associated with slow and fast subtypes of spindles. These observations provide further evidence for coordinated spindle activity in thalamocortical networks.

Highlights

Sleep spindles were measured in human anterior thalamus and on the scalp

Both fast and slow spindles occurred in the anterior thalamus

> 25% of spindles spanned multiple channels in thalamus and cortex

A novel statistical approach confirmed that spindle co-occurrences were not random

Cortical spindle patterns depended on thalamic involvement and spindle frequency
PIP4K2B is a mechanosensor and induces heterochromatin-driven nuclear softening through UHRF1
Authors: Poli Alessandro , Pennacchio Fabrizio A. , Nastaly Paulina , Ghisleni Andrea , Crestani Michele , Pramotton Francesca M. , Iannelli Fabio , Beznusenko Galina , Mironov Alexander A. , Panzetta Valeria , Fusco Sabato , Sheth Bhavwanti , Netti Paolo A. , Poulikakos Dimos , Ferrari Aldo , Gauthier Nils , Divecha Nullin , Maiuri Paolo
Published: March 2022

Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated phosphoinositide kinases able to phosphorylate PtdIns5P to PtdIns(4, 5)P2. In cancer patients their expression is typically associated with bad prognosis. Among the three PIP4K isoforms expressed in mammalian cells, PIP4K2B is the one with more prominent nuclear localization. Here, we unveil the role for PIP4K2B as mechanosensor. PIP4K2B protein level, indeed, strongly decreases in cells growing on soft substrates. Its direct silencing or pharmacological inhibition, mimicking cell response to soft, triggers a concomitant reduction of the epigenetic regulator UHRF1 and induces changes in nuclear polarity, nuclear envelope tension and chromatin compaction. This substantial rewiring of the nucleus mechanical state drives YAP cytoplasmic retention and impairment of its activity as transcriptional regulator, finally leading to defects in cell spreading and motility. Since YAP signalling is essential for initiation and growth of human malignancies, our data suggest that potential therapeutic approaches targeting PIP4K2B could be beneficial in the control of the altered mechanical properties of cancer cells.
Degeneracy in the neurological model of auditory speech repetition
Authors: Sajid Noor , Gajardo-Vidal Andrea , Ekert Justyna O. , Lorca-Puls Diego L. ,   PLORAS team, Hope Thomas M. H. , Green David W. , Friston Karl J. , Price Cathy J.
Published: March 2022

In the neurological model of language, repeating heard speech involves four left hemisphere regions: primary auditory cortex for processing sounds; Wernicke’s area for processing auditory images of speech; Broca’s area for processing motor images of speech; and primary motor cortex for overt speech articulation. Previous functional-MRI (fMRI) studies confirm that auditory repetition activates these regions. Here, we used dynamic causal modelling (DCM) to test how the four regions interact with each other during single word and pseudoword auditory repetition. Contrary to expectation, we found that, for both word and pseudoword repetition, the effective connectivity between Wernicke’s and Broca’s areas was predominantly bidirectional and inhibitory; activity in the motor cortex could be driven by either Wernicke’s area or Broca’s area; and the latter effect varied both within and between individuals. Such variability speaks to degenerate functional architectures that support auditory repetition and may explain resilience to functional loss after brain damage.
Myosin waves and a mechanical asymmetry guide the oscillatory migration of Drosophila cardiac progenitors
Authors: Balaghi Negar , Erdemci-Tandogan Gonca , McFaul Christopher , Fernandez-Gonzalez Rodrigo
Published: March 2022

Heart development begins with the formation of a tube, as cardiac progenitors migrate from opposite sides of the embryo and meet medially. Defective cardiac progenitor movements cause congenital heart defects. However, the mechanisms of cell migration during early heart development remain poorly understood. We investigated the mechanisms of movement of the Drosophila cardiac progenitors, the cardioblasts. Using quantitative time-lapse microscopy, we found that cardioblasts did not advance monotonically. Instead, cardioblasts took periodic forward and backward steps as they migrated. The forward steps were greater in both amplitude and duration, resulting in net forward movement of the cells. The molecular motor non-muscle myosin II displayed an alternating pattern of localization between the leading and trailing ends of migrating cardioblasts, forming oscillatory waves that traversed the cells. The alternating pattern of myosin polarity was associated with the alternative contraction and relaxation of the leading and trailing edges of the cell. Mathematical modelling predicted that forward migration requires the presence of a stiff boundary at the trailing edge of the cardioblasts. Consistent with this, we found a supracellular actin cable at the trailing edge of the cardioblasts. When we reduced the tension sustained by the actin cable, the amplitude of the backward steps of cardioblasts increased, thus reducing the net forward speed of migration. Together, our results indicate that periodic cell shape changes coupled with a polarized actin cable produce asymmetrical forces that guide cardioblast migration.
PeerPub: A device for concurrent operant oral self-administration by multiple rats
Authors: Lemen Paige M. , Ni Jie , Huang Jun , Chen Hao
Published: March 2022

The social environment has long been recognized to play an important role in substance abuse disorders (SUD). Operant conditioning is the most widely used rodent model of SUD. However, most operant chambers do not accommodate more than one rat at a time. Here, we introduce PeerPub – a novel social operant chamber. PeerPub uses a touch sensor to record the number of licks on drinking spouts. It then delivers a drop of solution with a fixed volume as the reward to the tip of the spout when the number of licks meets the requirement of a reinforcement schedule. A radio-frequency identification (RFID) chip implanted on top of each rat’s skull tracks the identity of the rat. The system is controlled by a Raspberry Pi computer. We tested PeerPub using male Wistar Kyoto rats in daily one-hour sessions where supersac, a solution containing glucose and saccharin, was delivered under a fixed ratio 5 schedule. We found that male rats consumed more supersac in group housing rather than in isolated conditions. These data demonstrated the utility of PeerPub in modeling the interaction between motivated behavior and social context. We anticipate devices like PeerPub will help demonstrate the role of the social environment in SUD phenotypes. The design of PeerPub is available at http://github.com/nijie321/PeerPub
UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS
Authors: Black Holly H. , Roberts Julia E. , Leslie Shannon N. , Campodonico Will , Ebmeier Christopher C. , Lau Cristina I. , Whiteley Alexandra M.
Published: March 2022

Amyotrophic Lateral Sclerosis (ALS) is a fatal, neurodegenerative disease characterized by progressive motor neuron dysfunction and loss. A portion of ALS is caused by mutation of the proteasome shuttle factor Ubiquilin 2 (UBQLN2), but the molecular pathway leading from UBQLN2 dysfunction to disease remains unclear. Here, we demonstrate a function of UBQLN2 in regulating activity of the domesticated gag-pol retrotransposon ‘paternally expressed gene 10’ (PEG10) in human cells and tissues. In cells, the PEG10 gag-pol protein cleaves itself in a mechanism reminiscent of retrotransposon self-processing to generate a liberated ‘nucleocapsid’ fragment, which uniquely localizes to the nucleus and changes expression of genes involved in axon remodeling. In spinal cord tissue from ALS patients, PEG10 gag-pol is elevated compared to healthy controls. These findings implicate the retrotransposon-like activity of PEG10 as a contributing mechanism in ALS through regulation of gene expression, and restraint of PEG10 as a primary function of UBQLN2.
Unleashing the Potential of Noncanonical Amino Acid Biosynthesis for Creation of Cells with Site-Specific Tyrosine Sulfation
Authors: Chen Yuda , Jin Shikai , Zhang Mengxi , Wu Kuan-lin , Chang Anna , Wang Shichao , Tian Zeru , Wolynes Peter G. , Xiao Han
Published: March 2022

Incorporation of noncanonical amino acids (ncAAs) into proteins holds great promise for modulating the structure and function of those proteins and for influencing evolutionary dynamics in organisms. Despite significant progress in improving the efficiency of translational machinery needed for incorporating ncAAs, exogenous feeding of high concentrations of chemically-synthesized ncAAs, especially in the case of polar ncAAs, is required to ensure adequate intracellular ncAA levels. Here, we report the creation of autonomous cells, both prokaryotic and eukaryotic, with the ability to biosynthesize and genetically encode sulfotyrosine (sTyr), an important protein post-translational modification with low membrane permeability. We discovered the first enzyme catalyzing tyrosine sulfation, sulfotransferase 1C1 from Nipponia nippon (NnSULT1C1), using a sequence similarity network (SSN). The unique specificity of NnSULT1C1 for tyrosine has been systematically explored using both bioinformatics and computational methods. This NnSULT1C1 was introduced into both bacterial and mammalian cells so as to yield organisms capable of biosynthesizing high levels of intracellular sTyr. These engineered cells produced site-specifically sulfated proteins at a higher yield than cells fed exogenously even with the highest level of sTyr reported in literature. We have used these autonomous cells to prepare highly potent thrombin inhibitors with site-specific sulfation. By enhancing ncAA incorporation efficiency, this added ability of cells to biosynthesize ncAAs and genetically incorporate them into proteins greatly extends the utility of genetic code expansion methods.

TOC
An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics
Authors: Shaver Amanda O. , Garcia Brianna M. , Gouveia Goncalo J. , Morse Alison M. , Liu Zihao , Asef Carter K. , Borges Ricardo M. , Leach Franklin E. , Andersen Erik C. , Amster I. Jonathan , Fernández Facundo M. , Edison Arthur S. , McIntyre Lauren M.
Published: March 2022

Large-scale untargeted metabolomics studies suffer from individual variation, batch effects and instrument variability, making comparisons of common spectral features across studies difficult. One solution is to compare studies after compound identification. However, compound identification is expensive and time consuming. We successfully identify common spectral features across multiple studies, with a generalizable experimental design approach. First, we included an anchor strain, PD1074, during sample and data collection. Second, we collected data in blocks with multiple controls. These anchors enabled us to successfully integrate three studies of Caenorhabditis elegans for nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) data from five different assays. We found 34% and 14% of features to be significant in LC-MS and NMR, respectively. Between 20-50% of spectral features differ in a mutant and among a set of genetically diverse natural strains, suggesting this reduced set of spectral features are excellent targets for compound identification.

GRAPHICAL ABSTRACT

Fourteen C. elegans strains are used in three individual studies. PD1074, the anchor control strain (orange), is grown alongside test strains (green, yellow, purple). Multiple biological replicates of PD1074 captures environmental variation in growth conditions. Non-polar and polar metabolic data across the three studies (i.e., natural strains, central metabolism mutants, and UGT mutants) were collected by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Data acquisition controls in each block included biological reference material and pooled PD1074 samples. Biological replicates of PD1074 (n = 42 for LC-MS, n = 52 for NMR) were included in all batches. Meta-analysis provided comparable inferences to mixed effects models, and the estimated relative effects of each test strain to PD1074 and straightforward comparisons of test strains across experiments.
ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data
Authors: Fry Joshua , Li Yangyang , Yang Rendong
Published: March 2022

Exitron splicing is a type of alternative splicing where coding sequences are spliced out. Recently, exitron splicing has been shown to increase proteome plasticity and play a role in cancer. Long-read RNA-seq is well suited for quantification and discovery of alternative splicing events; however, there are currently no tools available for detection and annotation of exitrons in long-read RNA-seq data. Here we present ScanExitronLR, an application for the characterization and quantification of exitron splicing events in long-reads. From a BAM alignment file, reference genome and reference gene annotation, ScanExitronLR outputs exitron events at the transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. A companion tool, AnnotateExitron, reports exitron annotations such as truncation or frameshift type, nonsense-mediated decay status, and Pfam domain interruptions. We demonstrate that ScanExitronLR performs better on noisy long-reads than currently published exitron detection algorithms designed for short-read data.

Availability and Implementation

ScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index.

Contact

yang4414@umn.edu

Supplementary Information

Supplementary data are available at Bioinformatics online.
Coregistration of heading to visual cues in retrosplenial cortex
Authors: Sit Kevin K. , Goard Michael J.
Published: March 2022

Spatial cognition depends on an accurate representation of orientation within an environment. Head direction cells in distributed brain regions receive a range of sensory inputs, but visual input is particularly important for aligning their responses to environmental landmarks. To investigate how population-level heading responses are aligned to visual input, we recorded from retrosplenial cortex (RSC) of head-fixed mice in a moving environment using two-photon calcium imaging. We show that RSC neurons are tuned to the animal’s relative orientation in the environment, even in the absence of head movement. Next, we found that RSC receives functionally distinct projections from visual and thalamic areas, and contains several functional classes of neurons. While some functional classes mirror RSC inputs, a newly discovered class coregisters visual and thalamic signals. Finally, decoding analyses reveal unique contributions to heading from each class. Our results suggest an RSC circuit for anchoring heading representations to environmental visual landmarks.
HIV-1 CD4-binding site germline antibody–Env structures inform vaccine design
Authors: Dam Kim-Marie A. , Barnes Christopher O. , Gristick Harry B. , Schoofs Till , Nussenzweig Michel C. , Bjorkman Pamela J.
Published: March 2022

BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we solved 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures revealed critical Env contacts by BG24iGL and identified antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24iGL variants bound to Envs with CD4bs glycans present provided insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276gp120 glycan. Together, these findings revealed Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.
RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity
Authors: Adler Benjamin A. , Hessler Tomas , Cress Brady F , Mutalik Vivek K. , Barrangou Rodolphe , Banfield Jillian , Doudna Jennifer A
Published: March 2022

CRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against invasive phages through general, non-specific RNA degradation upon complementary target transcript binding. Despite being RNA nucleases, Cas13 effectors are capable of inhibiting the infection of dsDNA phages but have only been investigated across a relatively small sampling of phage diversity. Here, we employ a systematic, phage-centric approach to determine the anti-phage capacity of Cas13 and find LbuCas13a to be a remarkably potent phage inhibitor. LbuCas13a confers robust, consistent antiviral activity regardless of gene essentiality, gene expression timing or target sequence location. Furthermore, after challenging LbuCas13a with eight diverse E. coli phages distributed across E. coli phage phylogenetic groups, we find no apparent phage-encoded limits to its potent antiviral activity. In contrast to other Class 2 CRISPR-Cas proteins, these results suggest that DNA phages are generally vulnerable to Cas13a targeting. Leveraging this effective anti-phage activity, LbuCas13a can be used seamlessly as a counter-selection agent for broad-spectrum phage editing. Using a two-step phage editing and enrichment approach, we show that LbuCas13a enables markerless genome edits in phages with exceptionally high efficiency and precision, including edits as small as a single codon. By taking advantage of the broad vulnerability of RNA during viral infection, Cas13a enables a generalizable strategy for editing the most abundant and diverse biological entities on Earth.
High-resolution Ribosome Profiling Reveals Translational Selectivity for Transcripts in Bovine Preimplantation Embryo Development
Authors: Zhu Linkai , Zhou Tong , Iyyappan Rajan , Ming Hao , Wang Yinjuan , Dvoran Michal , Chen Qi , Roberts R. Michael , Susor Andrej , Jiang Zongliang
Published: March 2022

High resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome, polysome- and non-polysome-bound RNA profiles of bovine oocytes (GV and MII stage) and early embryos at 2-, 8-cell, morula, and blastocyst stage, and revealed four modes of translational selectivity: i. selective translation of non-abundant mRNAs, ii. active, but modest translation of a selection of highly expressed mRNAs, iii. translationally suppressed abundant to moderately abundant mRNAs, and iv. mRNAs associated specifically with monosomes. A strong translational selection of low abundance mRNAs encoding protein components involved in metabolic pathways and lysosome was found throughout bovine oocyte and preimplantation development. In particular, genes encoding components involved in mitochondrial function were prioritized for translation. Notably, transcripts encoding proteins regulating chromatin modifications selectively translated in oocytes. We found that the translational dynamics largely reflects transcriptional profiles in oocytes and 2-cell embryos, but observed marked shift in translational control in 8-cell embryos associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become better synchronized in morulae and blastocysts. Together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.

Significance Statement

Translational control during preimplantation embryo development is poorly understood, mostly due to the scarcity of samples and the corresponding inability to analyze low quantities of these materials. By developing a low-input method, we have been able to explore the transcriptome, polysome- and non-polysome-bound RNA profiles of bovine oocytes (GV and MII stage) and preimplantation embryos at 2-, 8-cell, morula, and blastocyst stages. We reveal four different modes of translational selectivity, plus novel temporal regulatory mechanisms during early embryo development. The spatiotemporal translation dynamics of bovine oocytes and preimplantation embryos offer an entirely new insight into mammalian embryo development research and new possibilities for improving efficiency of assisted reproduction technologies (ARTs).
Limitations of principal components in quantitative genetic association models for human studies
Authors: Yao Yiqi , Ochoa Alejandro
Published: March 2022

Principal Component Analysis (PCA) and the Linear Mixed-effects Model (LMM), sometimes in combination, are the most common genetic association models. Previous PCA-LMM comparisons give mixed results, unclear guidance, and have several limitations, including not varying the number of principal components (PCs), simulating simple population structures, and inconsistent use of real data and power evaluations. We evaluate PCA and LMM both varying number of PCs in realistic genotype and complex trait simulations including admixed families, subpopulation trees, and real multiethnic human datasets with simulated traits. We find that LMM without PCs usually performs best, with the largest effects in family simulations and real human datasets and traits without environment effects. Poor PCA performance on human datasets is driven by large numbers of distant relatives more than the smaller number of closer relatives. While PCA was known to fail on family data, we report strong effects of family relatedness in genetically diverse human datasets, not avoided by pruning close relatives. Environment effects driven by geography and ethnicity are better modeled with LMM including those labels instead of PCs. This work better characterizes the severe limitations of PCA compared to LMM in modeling the complex relatedness structures of multiethnic human data for association studies.
Multiplealrgenes exhibit allorecognition-associated variation in the colonial cnidarianHydractinia
Authors: Rodriguez-Valbuena Henry , Gonzalez-Muñoz Andrea , Cadavid Luis F.
Published: March 2022

The genetics of allorecognition has been determined from inbred lines ofHydractinia symbiolongicarpus, in which genetic control is attributed mainly to the highly polymorphic lociallorecognition 1 (alr1)andallorecognition 2 (alr2)located within the Allorecognition Complex (ARC). While allelic variation atalr1andalr2can predict the phenotypes in inbred lines, these two loci do not entirely predict the allorecognition phenotypes in wild-type colonies and their progeny, suggesting the presence of additional uncharacterized genes that improve the prediction of these phenotypes. Comparative genomics analyses were used to identify coding sequence differences in assembled chromosomal intervals of the ARC and genomic scaffold sequences between two incompatibleH. symbiolongicarpussiblings from a backcross population. New IgSF-like genes are reported for the ARC, five of these genes are closely related to thealr1andalr2genes, suggesting the presence of multiplealr-typegenes within this complex. Cloning evidence revealed that the allelic polymorphism of eight Ig-SF-like genes is associated with allorecognition phenotypes in a backcross population ofH. symbiolongicarpus. Remarkably, alternative splicing was found as a mechanism that contributes to the functional variability of these genes by changing putative activating receptors to inhibitory receptors, or generating secreted isoforms of allorecognition proteins. Our findings demonstrate that allorecognition inH. symbiolongicarpusis a multigenic phenomenon controlled by genetic variation in at least eight genes in the ARC complex, as well as putative uncharacterized variation outside of this region.
Infection dynamics of co-transmitted reproductive symbionts are mediated by sex, tissue, and development
Authors: Jones Megan W , Fricke Laura C , Thorpe Cody J , Vander Esch Lauren O , Lindsey Amelia RI
Published: March 2022

One of the most prevalent intracellular infections on earth is with Wolbachia: a bacterium in the Rickettsiales that infects a range of insects, crustaceans, chelicerates, and nematodes. Wolbachia is maternally transmitted to offspring and has profound effects on the reproduction and physiology of its hosts, which can result in reproductive isolation, altered vectorial capacity, mitochondrial sweeps, and even host speciation. Some populations stably harbor multiple Wolbachia strains, which can further contribute to reproductive isolation and altered host physiology. However, almost nothing is known about the requirements for multiple intracellular microbes to be stably maintained across generations while they likely compete for space and resources. Here we use a coinfection of two Wolbachia strains (“wHa” and “wNo”) in Drosophila simulans to define the infection and transmission dynamics of an evolutionarily stable double infection. We find that a combination of sex, tissue, and host development contribute to the infection dynamics of the two microbes and that these infections exhibit a degree of niche partitioning across host tissues. wHa is present at a significantly higher titer than wNo in most tissues and developmental stages, but wNo is uniquely dominant in ovaries. Unexpectedly, the ratio of wHa to wNo in embryos does not reflect those observed in the ovaries, indicative of strain-specific transmission dynamics. Understanding how Wolbachia strains interact to establish and maintain stable infections has important implications for the development and effective implementation of Wolbachia-based vector biocontrol strategies, as well as more broadly defining how cooperation and conflict shape intracellular communities.

IMPORTANCE

Wolbachia are maternally transmitted intracellular bacteria that manipulate the reproduction and physiology of arthropods, resulting in drastic effects on the fitness, evolution, and even speciation of their hosts. Some hosts naturally harbor multiple strains of Wolbachia that are stably transmitted across generations, but almost nothing is known about the factors that limit or promote these co-infections which can have profound effects on the host’s biology and evolution, and are under consideration as an insect-management tool. Here we define the infection dynamics of a known stably transmitted double infection in Drosophila simulans with an eye towards understanding the patterns of infection that might facilitate compatibility between the two microbes. We find that a combination of sex, tissue, and development all contribute how the coinfection establishes.
Conserved GYXLI motif of FlhA is involved in dynamic domain motions of FlhA required for flagellar protein export
Authors: Minamino Tohru , Kinoshita Miki , Inoue Yumi , Kitao Akio , Namba Keiichi
Published: March 2022

Flagellar structural subunits are transported via the flagellar type III secretion system (fT3SS) and assemble at the distal end of the growing flagellar structure. The C-terminal cytoplasmic domain of FlhA (FlhAC) serves as a docking platform for export substrates and flagellar chaperones and plays an important role in hierarchical protein targeting and export. FlhAC consists of domains D1, D2, D3, and D4 and adopts open and closed conformations. Gly-368 of Salmonella FlhA is located within the highly conserved GYXLI motif and is critical for the dynamic domain motions of FlhAC. However, it remains unclear how it works. Here, we report that periodic conformational changes of the GYXLI motif induce a remodeling of hydrophobic side-chain interaction networks in FlhAC and promotes the cyclic open-close domain motions of FlhAC. The temperature- sensitive flhA(G368C) mutation stabilized a completely closed conformation at 42°C through strong hydrophobic interactions between Gln-498 of domain D1 and Pro-667 of domain D4 and between Phe-459 of domain D2 and Pro-646 of domain D4, thereby inhibiting flagellar protein export by the fT3SS. Its intragenic suppressor mutations reorganized the hydrophobic interaction networks in the closed FlhAC structure, restoring the protein export activity of the fT3SS to a significant degree. Furthermore, the conformational flexibility of the GYXLI motif was critical for flagellar protein export. We propose that the conserved GYXLI motif acts as a structural switch to induce the dynamic domain motions of FlhAC required for efficient and rapid protein export by the fT3SS.

IMPORTANCE

Many motile bacteria employ the flagellar type III secretion system (fT3SS) to construct flagella beyond the cytoplasmic membrane. The C-terminal cytoplasmic domain of FlhA (FlhAC), a transmembrane subunit of the fT3SS, provides binding-sites for export substrates and flagellar export chaperones to coordinate flagellar protein export with assembly. FlhAC undergoes cyclic open- close domain motions. The highly conserved Gly-368 residue of FlhA is postulated to be critical for dynamic domain motions of FlhAC. However, it remains unknown how it works. Here, we carried out mutational analysis of FlhAC combined with molecular dynamics simulation and provide evidence that the conformational flexibility of FlhAC by Gly-368 is important for remodeling hydrophobic side-chain interaction networks in FlhAC to facilitate its cyclic open-close domain motions, allowing the fT3SS to transport flagellar structural subunits for efficient and rapid flagellar assembly.