bluuebunny/crossref_metadata_2025 huggingface dataset:
APOBEC3A drives acquired resistance to targeted therapies in non-small cell lung cancer
Authors: Isozaki Hideko , Abbasi Ammal , Nikpour Naveed , Langenbucher Adam , Su Wenjia , Stanzione Marcello , Cabanos Heidie Frisco , Siddiqui Faria M. , Phan Nicole , Jalili Pégah , Oh Sunwoo , Timonina Daria , Bilton Samantha , Gomez-Caraballo Maria , Archibald Hannah L. , Nangia Varuna , Dionne Kristin , Riley Amanda , Lawlor Matthew , Banwait Mandeep Kaur , Cobb Rosemary G. , Zou Lee , Dyson Nicholas J. , Ott Christopher J. , Benes Cyril , Getz Gad , Chan Chang S. , Shaw Alice T. , Lin Jessica J. , Sequist Lecia V. , Piotrowska Zofia , Engelman Jeffrey A. , Lee Jake June-Koo , Maruvka Yosef , Buisson Rémi , Lawrence Michael S. , Hata Aaron N.
Published: January 2021

Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1‒6, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. The extent to which therapy actively drives tumor evolution by promoting mutagenic processes7or simply provides the selective pressure necessary for the outgrowth of drug-resistant clones8remains an open question. Here, we report that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Induction of A3A facilitated the formation of double-strand DNA breaks (DSBs) in cycling drug-treated cells, and fully resistant clones that evolved from drug-tolerant intermediates exhibited an elevated burden of chromosomal aberrations such as copy number alterations and structural variations. Preventing therapy-induced A3A mutagenesis either by gene deletion or RNAi-mediated suppression delayed the emergence of drug resistance. Finally, we observed accumulation of A3A mutations in lung cancer patients who developed drug resistance after treatment with sequential targeted therapies. These data suggest that induction of A3A mutagenesis in response to targeted therapy treatment may facilitate the development of acquired resistance in non-small-cell lung cancer. Thus, suppressing expression or enzymatic activity of A3A may represent a potential therapeutic strategy to prevent or delay acquired resistance to lung cancer targeted therapy.
Association between land use, land cover, plant genera, and pollinator abundance in mixed-use landscapes
Authors: Diengdoh Vishesh L. , Brook Barry W. , Hunt Mark , Ondei Stefania
Published: January 2021

Pollinators are globally threatened by land-use change, but its effect varies depending on the taxa and the intensity of habitat degradation. However, pollinator-landscape studies typically focus on regions of intensive human activities and on a few focal species. Evaluating pollinator responses in landscapes with moderate land-use changes and on multiple pollinator groups would therefore fill an important knowledge gap. This study aims to determine the predictive capacity and effect of habitat characteristics on the relative abundance of multiple pollinator groups in mixed-use landscapes. To do this, we collected field data on the relative abundance of nectivorous birds, bees, beetles, and butterflies across the Tasman Peninsula (Tasmania, Australia). We then applied Random Forests to resolve the effects of land use (protected areas, plantation, and pasture), land cover at different radii (100 m and 2000 m), and plant genera on pollinator abundance. Overall, land cover and plant genera were more important predictors of pollinator abundance than land use. And the effect of land use, land cover, and plant genera varied depending on the pollinating group. Pollinator groups were associated with a range of plant genera, with the native generaAcacia, Leptospermum, Leucopogon, Melaleuca, Pomaderris, andPultenaeabeing among the most important predictors. Our results highlight that one size does not fit all—that is pollinator response to different landscape characteristics vary, emphasise the importance of considering multiple habitat factors to manage and support a dynamic pollinator community, and demonstrates how land management can be informed using predictive modelling.
Ocular elongation and retraction in foveated reptiles
Authors: Rasys Ashley M. , Pau Shana H. , Irwin Katherine E. , Luo Sherry , Trainor Paul A. , Menke Douglas B. , Lauderdale James D.
Published: January 2021

Background

Pronounced asymmetric changes in ocular globe size during eye development have been observed in a number of species ranging from humans to lizards. In contrast, largely symmetric changes in globe size have been described for other species like rodents. We propose that asymmetric changes in the three-dimensional structure of the developing eye correlate with the types of retinal remodeling needed to produce areas of high photoreceptor density. To test this idea, we systematically examined three-dimensional aspects of globe size as a function of eye development in the bifoveated brown anole,Anolis sagrei.

Results

During embryonic development, the anole eye undergoes dynamic changes in ocular shape. Initially spherical, the eye elongates in the presumptive foveal regions of the retina and then proceeds through a period of retraction that returns the eye to its spherical shape. During this period of retraction, pit formation and photoreceptor cell packing are observed. We found a similar pattern of elongation and retraction associated with the single fovea of the veiled chameleon,Chamaeleo calyptratus.

Conclusions

These results, together with those reported for other foveated species, support the idea that areas of high photoreceptor packing occur in regions where the ocular globe asymmetrically elongates and retracts during development.

Key Findings

The eyes of the brown anole,Anolis sagrei, and veiled chameleon,Chamaeleo calyptratusundergo dynamic asymmetrical changes in ocular shape during development.

In both species, asymmetric elongation and retraction of the ocular globe is associated with fovea morphogenesis.

Pit formation and photoreceptor cell packing in the foveal area occur when the corresponding region of the ocular globe is retracting relative to adjacent regions.
LAM – an image analysis method for regionally defined organ-wide cellular phenotyping of theDrosophilamidgut
Authors: Viitanen Arto , Gullmets Josef , Morikka Jack , Katajisto Pekka , Mattila Jaakko , Hietakangas Ville
Published: January 2021

Intestine is divided into functionally distinct regions along the anteroposterior (A/P) axis. How the regional identity influences the function of intestinal stem cells (ISCs) and their offspring remain largely unresolved. We introduce an imaging-based method, ‘Linear Analysis of Midgut’ (LAM), which allows quantitative regionally defined cellular phenotyping of the wholeDrosophilamidgut. LAM transforms image-derived cellular data from three-dimensional midguts into a linearized representation, binning it into segments along the A/P axis. Through automated multi-variate determination of regional borders, LAM allows mapping and comparing cellular features and frequencies with subregional resolution. Through the use of LAM, we quantify the distributions of ISCs, enteroblasts and enteroendocrine cells in a steady state midgut, and reveal unprecedented regional heterogeneity in the ISC response to aDrosophilamodel of colitis. Taken together, LAM is a powerful tool for organ-wide quantitative analysis of the regional heterogeneity of midgut cells.

Graphical abstract
Rab11a mediates cell-cell spread and reassortment of influenza A virus genomes via tunneling nanotubes
Authors: Ganti Ketaki , Han Julianna , Manicassamy Balaji , Lowen Anice C.
Published: January 2021

Influenza A virus (IAV) genomes comprise eight negative strand RNAs packaged into virions in the form of viral ribonucleoproteins (vRNPs). Rab11a plays a crucial role in the transport of vRNPs from the nucleus to the plasma membrane via microtubules, allowing assembly and virus production. Here, we identify a novel function for Rab11a in the inter-cellular transport of IAV vRNPs using tunneling nanotubes (TNTs) as molecular highways. TNTs are F-Actin rich tubules that link the cytoplasm of nearby cells. In IAV-infected cells, Rab11a was visualized together with vRNPs in these actin-rich intercellular connections. To better examine viral spread via TNTs, we devised an infection system in which conventional, virion-mediated, spread was not possible. Namely, we generated HA-deficient reporter viruses which are unable to produce progeny virions but whose genomes can be replicated and trafficked. In this system, vRNP transfer to neighboring cells was observed and this transfer was found to be dependent on both actin and Rab11a. Generation of infectious virus via TNT transfer was confirmed using donor cells infected with HA-deficient virus and recipient cells stably expressing HA protein. Mixing donor cells infected with genetically distinct IAVs furthermore revealed the potential for Rab11a and TNTs to serve as a conduit for genome mixing and reassortment in IAV infections. These data therefore reveal a novel role for Rab11a in the IAV life cycle, which could have significant implications for within-host spread, genome reassortment and immune evasion.

Author Summary

Influenza A viruses infect epithelial cells of the upper and lower respiratory tract in humans. Infection is propagated by the generation of viral particles from infected cells, which disseminate within the tissue. Disseminating particles can encounter obstacles in the extracellular environment, including mucus, ciliary movement, antibody neutralization and uptake by phagocytic immune cells. An alternative mode of spread, which avoids these hazards, involves direct transport of viral components between cells. This cell-cell spread of infection is not a well understood process. In this study we demonstrate that the host factor Rab11a mediates the transport of viral genomes in the cell-cell spread of infection. Rab11a is already known to play a pro-viral role in the transport of viral genomes to the plasma membrane for assembly into virus particles. Here, we see that this same transport mechanism is co-opted for direct cell-cell spread through cellular connections called tunneling nanotubes. We show that complexes of Rab11a and viral components can be trafficked across tunneling nanotubes, transmitting infection without the formation of virus particles. Importantly, this route of spread often seeds viral genomes from multiple donor cells into recipient cells, which in turn increases viral genetic diversity.
Automatic and unbiased segmentation and quantification of myofibers in skeletal muscle
Authors: Waisman Ariel , Norris Alessandra , Costa Martín Elías , Kopinke Daniel
Published: January 2021

Skeletal muscle has the remarkable ability to regenerate. However, with age and disease muscle strength and function decline. Myofiber size, which is affected by injury and disease, is a critical measurement to assess muscle health. Here, we test and apply Cellpose, a recently developed deep learning algorithm, to automatically segment myofibers within murine skeletal muscle. We first show that tissue fixation is necessary to preserve cellular structures such as primary cilia, small cellular antennae, and adipocyte lipid droplets. However, fixation generates heterogeneous myofiber labeling, which impedes intensity-based segmentation. We demonstrate that Cellpose efficiently delineates thousands of individual myofibers outlined by a variety of markers, even within fixed tissue with highly uneven myofiber staining. We created a novel ImageJ plugin (LabelsToRois) that allows processing multiple Cellpose segmentation images in batch. The plugin also contains a semi-automatic erosion function to correct for the area bias introduced by the different stainings, identifying myofibers as accurately as human experts. We successfully applied our segmentation pipeline to uncover myofiber size differences between two different muscle injury models, cardiotoxin and glycerol. Thus, Cellpose combined with LabelsToRois allows for fast, unbiased, and reproducible myofiber quantification for a variety of staining and fixation conditions.
Fine-scale changes in speed and altitude suggest protean movements in homing pigeon flights
Authors: Garde Baptiste , Wilson Rory P. , Lempidakis Emmanouil , Börger Luca , Portugal Steven J. , Hedenström Anders , Dell’Omo Giacomo , Quetting Michael , Wikelski Martin , Shepard Emily L. C.
Published: January 2021

The flight speeds that animals should adopt to minimise energy expenditure in different scenarios can be predicted by the curve of power against speed. However, relatively few studies have examined how animals respond to the landscape below them, which could affect speed through modifications in climb rate and perceived predation risk. We equipped homing pigeons(Columba livia)with high frequency loggers to examine how flight speed varies in relation to topography and land cover, predicting that these parameters may have a substantial impact on flight speed and hence cost. Pigeons showed mixed evidence for an energy saving strategy, as they minimised climb rates by starting their ascent ahead of hills, but selected rapid speeds in their ascents. Birds did not modify their speed substantially in relation to land cover, but higher speeds were observed during descending flight, highlighting the importance to consider the rate of change in altitude before estimating power use from speed. Finally, we document an unexpected variability in speed and altitude over fine scales; a source of substantial inefficiency. We suggest this may a form of protean behaviour adopted to reduce predation risk when flocking is not an option, and that such a strategy could be widespread.
Upregulation of eIF4E, but not other translation initiation factors, in dendritic spines during memory consolidation
Authors: Gindina Sofya , Botsford Benjamin , Cowansage Kiriana , LeDoux Joseph , Klann Eric , Hoeffer Charles , Ostroff Linnaea
Published: January 2021

Local translation can provide a rapid, spatially targeted supply of new proteins in distal dendrites to support synaptic changes that underlie learning. Learning and memory are especially sensitive to manipulations of translational control mechanisms, particularly those that target the initiation step, and translation initiation at synapses could be a means of maintaining synapse specificity during plasticity. Initiation predominantly occurs via recruitment of ribosomes to the 5’ mRNA cap by complexes of eukaryotic initiation factors (eIFs), and the interaction between eIF4E and eIF4G1 is a particularly important target of translational control pathways. Pharmacological inhibition of eIF4E-eIF4G1 binding impairs consolidation of memory for aversive Pavlovian conditioning as well as the accompanying increase in polyribosomes in the heads of dendritic spines in the lateral amygdala (LA). This is consistent with a role for initiation at synapses in memory formation, but whether eIFs are even present near synapses is unknown. To determine whether dendritic spines contain eIFs and whether eIF distribution is affected by learning, we combined immunolabeling with serial section transmission electron microscopy (ssTEM) volume reconstructions of LA dendrites after Pavlovian conditioning. Labeling for eIF4E, eIF4G1, and eIF2α – another key target of regulation – occurred in roughly half of dendritic spines, but learning effects were only found for eIF4E, which was upregulated in the heads of dendritic spines. Our results support the possibility of regulated translation initiation as a means of synapse-specific protein targeting during learning and are consistent with the model of eIF4E availability as a central point of control.
Human neuronal networks on micro-electrode arrays are a highly robust tool to study disease-specific genotype-phenotype correlationsin vitro
Authors: Mossink B. , Verboven A.H.A. , van Hugte E.J.H. , Gunnewiek T.M. Klein , Parodi G. , Linda K. , Schoenmaker C. , Kleefstra T. , Kozicz T. , van Bokhoven H. , Schubert D. , Kasri N. Nadif , Frega M.
Published: January 2021

Micro-electrode arrays (MEAs) are increasingly used to characterize neuronal network activity of human induced pluripotent stem-cell (hiPSC)-derived neurons. Despite their gain in popularity, MEA recordings from hiPSC-derived neuronal networks are not always used to their full potential in respect to experimental design, execution and data analysis. Therefore, we benchmarked the robustness and sensitivity of MEA-derived neuronal activity patterns derived from ten healthy individual control lines. We provide recommendations on experimental design and analysis to achieve standardization. With such standardization, MEAs can be used as a reliable platform to distinguish (disease-specific) network phenotypes. In conclusion, we show that MEAs are a powerful and robust tool to uncover functional neuronal network phenotypes from hiPSC-derived neuronal networks, and provide an important resource to advance the hiPSC field towards the use of MEAs for disease-phenotyping and drug discovery.
AdipoAtlas: A Reference Lipidome for Human White Adipose Tissue
Authors: Lange Mike , Angelidou Georgia , Ni Zhixu , Criscuolo Angela , Schiller Jürgen , Blüher Matthias , Fedorova Maria
Published: January 2021

Obesity, characterized by expansion and metabolic dysregulation of white adipose tissue (WAT), has reached pandemic proportions and acts as a primer for a wide range of metabolic disorders. Remodelling of WAT lipidome in obesity and associated comorbidities can explain disease etiology and provide valuable diagnostic and prognostic markers. To support understanding of WAT lipidome remodelling at the molecular level, we performed in-depth lipidomics profiling of human subcutaneous and visceral WAT of lean and obese individuals. Tissue-tailored preanalytical and analytical workflows allowed accurate identification and semi-absolute quantification of 1636 and 737 lipid molecular species, respectively, and summarized here in a form of human WAT reference lipidome. Deep lipidomic profiling allowed to identify main lipid (sub)classes undergoing depot/phenotype specific remodelling. Furthermore, previously unanticipated diversity of WAT ceramides was uncovered. AdipoAtlas reference lipidome will serve as a data-rich resource for the development of WAT-specific high-throughput methods and as a scaffold for systems medicine data integration.
Food and temperature change photoperiodic responses in two vole species: different roles for hypothalamic genes
Authors: van Rosmalen Laura , Hut Roelof A.
Published: January 2021

Seasonal timing of reproduction in voles is driven by photoperiod. Here we hypothesize that a negative energy balance can modify spring-programmed photoperiodic responses in the hypothalamus, controlling reproductive organ development. We manipulated energy balance by the ‘work-for-food’ protocol, in which voles were exposed to increasing levels of food scarcity at different ambient temperatures under long photoperiod. We reveal that common (Microtus arvalis) and tundra voles (Microtus oeconomus), reduce photoperiodic induced pars tuberalis thyroid-stimulating hormone β-subunit (Tshβ) expression to inhibit gonadal development when food is scarce. Reduction in gonadal size is more pronounced in tundra voles, in which the hypothalamic Kisspeptin (Kiss1) system seems involved in downregulating gonadal development, especially in males. Low temperature additionally leads to decreased hypothalamic RF-amide related peptide (Rfrp3) levels, which may facilitate further suppression of gonadal growth. Shutting off the photoperiodic-axis when food is scarce in spring may be an adaptive response to save energy, leading to delayed reproductive organ development until food resources are sufficient for reproduction, lactation and offspring survival. Defining the mechanisms through which metabolic cues modify photoperiodic responses will be important for a better understanding of how environmental cues impact reproduction.

Summary statement

This study provides a better understanding of the molecular mechanism through which metabolic cues can modify photoperiodic responses, to adaptively adjust timing of reproductive organ development
Simulating lesion-dependent functional recovery mechanisms
Authors: Sajid Noor , Holmes Emma , Hope Thomas M. , Fountas Zafeirios , Price Cathy J. , Friston Karl J.
Published: January 2021

Functional recovery after brain damage varies widely and depends on many factors, including lesion site and extent. When a neuronal system is damaged, recovery may occur by engaging residual (e.g., perilesional) components. When damage is extensive, recovery depends on the availability of other intact neural structures that can reproduce the same functional output (i.e., degeneracy). A system’s response to damage may occur rapidly, require learning or both. Here, we simulate functional recovery from four different types of lesions, using a generative model of word repetition that comprised a default premorbid system and a less used alternative system. The synthetic lesions (i) completely disengaged the premorbid system, leaving the alternative system intact, (ii) partially damaged both premorbid and alternative systems, and (iii) limited the experience-dependent plasticity of both. The results, across 1000 trials, demonstrate that (i) a complete disconnection of the premorbid system naturally invoked the engagement of the other, (ii) incomplete damage to both systems had a much more devastating long-term effect on model performance and (iii) the effect of reducing learning capacity within each system. These findings contribute to formal frameworks for interpreting the effect of different types of lesions.
ImPartial: Partial Annotations for Cell Instance Segmentation
Authors: Martinez Natalia , Sapiro Guillermo , Tannenbaum Allen , Hollmann Travis J. , Nadeem Saad
Published: January 2021

Segmenting noisy multiplex spatial tissue images constitutes a challenging task, since the characteristics of both the noise and the biology being imaged differs significantly across tissues and modalities; this is compounded by the high monetary and time costs associated with manual annotations. It is therefore imperative to build algorithms that can accurately segment the noisy images based on a small number of annotations. Recently techniques to derive such an algorithm from a few scribbled annotations have been proposed, mostly relying on the refinement and estimation of pseudo-labels. Other techniques leverage the success of self-supervised denoising as a parallel task to potentially improve the segmentation objective when few annotations are available. In this paper, we propose a method that augments the segmentation objective via self-supervised multi-channel quantized imputation, meaning that each class of the segmentation objective can be characterized by a mixture of distributions. This approach leverages the observation that perfect pixel-wise reconstruction or denoising of the image is not needed for accurate segmentation, and introduces a self-supervised classification objective that better aligns with the overall segmentation goal. We demonstrate the superior performance of our approach for a variety of cancer datasets acquired with different highly-multiplexed imaging modalities in real clinical settings. Code for our method along with a benchmarking dataset is available athttps://github.com/natalialmg/ImPartial.
Codominance of two symbiont genera within the same coral host is associated with elevated symbiont productivity and lower host susceptibility to thermal stress
Authors: Abbott Evelyn , Dixon Groves , Matz Mikhail
Published: January 2021

In recent years, as sea surface temperature increases, many coral species that used to harbor symbionts of the genusCladocopiumhave become colonized with the thermally tolerant genus,Durusdinium.Here, we asked how the symbionts of one genus react to the presence of another symbiont genus within the same coral host, and what effect this interaction has on the host. We used previously published transcriptomic data fromAcropora hyacinthuscorals hostingCladocopiumand/orDurusdiniumsymbionts and looked at gene expression in all three symbiotic partners depending on the relative proportion of the two symbiont genera within the same host. We find that bothCladocopiumandDurusdiniumchange their expression the most when their proportions within the host are nearly equal (the state that we call “codominance”): both genera elevate expression of photosynthesis and ribosomal genes, suggesting increase in photosynthesis and growth (i.e. higher productivity). At the same time, the coral host also elevates production of ribosomes suggesting faster cellular growth, and, when heated, shows less pronounced stress response. These results can be explained in two alternative ways. One explanation is that increased competition between codominant symbionts switches them to the higher productivity mode, which benefits the host, making it more resilient to stress. Alternatively, the symbionts’ elevated productivity might be not the cause but the consequence of the host being particularly healthy. Under this explanation, rapid growth of the healthy host creates new space, lowering the symbioints’ competition and thus promoting their growth, which allows for codominance to happen where one genus would otherwise outcompete another. The latter explanation is supported by the fact that codominance is associated with lower symbiont densities, assessed as relative proportions of symbiont reads in the data. Irrespective of the causation direction, the presence of mixed symbiont communities could potentially be used as an instant indicator of coral well-being, which would be a useful tool for coral conservation and restoration.
PASV: Automatic protein partitioning and validation using conserved residues
Authors: Moore Ryan M. , Harrison Amelia O. , Nasko Daniel J. , Chopyk Jessica , Cebeci Metehan , Ferrell Barbra D. , Polson Shawn W. , Wommack K. Eric
Published: January 2021

Background

Increasingly, researchers use protein-coding genes from targeted PCR amplification or direct metagenomic sequencing in community and population ecology. Analysis of protein-coding genes presents different challenges from those encountered in traditional SSU rRNA studies. Most protein-coding sequences are annotated based on homology to other computationally-annotated sequences, which can lead to inaccurate annotations. Therefore, the results of sensitive homology searches must be validated to remove false-positives and assess functionality. Multiple lines of in silico evidence can be gathered by examining conserved domains and residues identified through biochemical investigations. However, manually validating sequences in this way can be time consuming and error prone, especially in large environmental studies.

Results

An automated pipeline for protein active site validation (PASV) was developed to improve validation and partitioning accuracy for protein-coding sequences, combining multiple sequence alignment with expert domain knowledge. PASV was tested using commonly misannotated proteins: ribonucleotide reductase (RNR), alternative oxidase (AOX), and plastid terminal oxidase (PTOX). PASV partitioned 9,906 putative Class I alpha and Class II RNR sequences from bycatch in a global viral metagenomic investigation with >99% true positive and true negative rates. PASV predicted the class of 2,579 RNR sequences in >98% agreement with manual annotations. PASV correctly partitioned all 336 tested AOX and PTOX sequences.

Conclusions

PASV provides an automated and accurate way to address post-homology search validation and partitioning of protein-coding marker genes. Source code is released under the MIT license and is found with documentation and usage examples on GitHub at https://github.com/mooreryan/pasv.
Direct simulation of a stochastically driven multi-step birth-death process
Authors: Gorin Gennady , Pachter Lior
Published: January 2021

1

The description of transcription as a stochastic process provides a framework for the analysis of intrinsic and extrinsic noise in cells. To better understand the behaviors and possible extensions of existing models, we design an exact stochastic simulation algorithm for a multimolecular transcriptional system with an Ornstein-Uhlenbeck birth rate that is implemented via a special function-based time-stepping algorithm. We demonstrate that its joint copy-number distributions reduce to analytically well-studied cases in several limiting regimes, and suggest avenues for generalizations.
Regulation by Progestins, Corticosteroids and RU486 of Activation of Elephant Shark and Human Progesterone Receptors: An Evolutionary Perspective
Authors: Lin Xiaozhi , Takagi Wataru , Hyodo Susumu , Ijiri Shigeho , Katsu Yoshinao , Baker Michael E.
Published: January 2021

We investigated progestin and corticosteroid activation of the progesterone receptor (PR) from elephant shark, a cartilaginous fish belonging to the oldest group of jawed vertebrates. Comparison with human PR provides insights into the evolution of steroid activation of human PR. At 1 nM steroid, elephant shark PR is activated by progesterone, 17-hydroxy-progesterone, 20β-hydroxy-progesterone, 11-deoxycorticosterone (21-hydroxyprogesterone) and 11-deoxycortisol. Human PR, in comparison, is activated at 1 nM steroid, only by progesterone and 11-deoxycorticosterone, indicating increased progestin and corticosteroid specificity during the evolution of human PR. RU486, an important clinical antagonist of human PR, did not inhibit progesterone activation of elephant shark PR. Cys-528 in elephant shark PR corresponds to Gly-722 in human PR, which is essential for RU486 inhibition of human PR. Confirming the importance of Cys-528 in elephant shark PR, RU486 inhibited progesterone activation of the Cys528Gly mutant PR. Compared to wild-type human PR, there was an increase in activation of human Gly722Cys PR by11-deoxycortisol and a decrease in activation by corticosterone, which may have been important in selection for the mutation corresponding to human glycine-722 PR that first evolved in platypus PR, a basal mammal.
How to align arthropod legs
Authors: Bruce Heather S.
Published: January 2021

How to align leg segments between the four groups of arthropods (insects, crustaceans, myriapods, and chelicerates) has tantalized generations of researchers, as this would answer over a century of speculation about the origins and homologies of the fascinating diversity of arthropod appendages and outgrowths. Here we compare the expression and loss-of-function phenotypes of leg patterning genes in crustaceans, insects, and arachnids using our own and previously published data. We find that all arthropod leg segments correspond to each other in a one-to-one fashion. This alignment suggests that chelicerates with seven leg segments incorporated a proximal leg segment into the body wall. In addition, this alignment suggests that insect and myriapod tracheae are convergent and homologous structures: each evolved via the independent internalization of an ancestral gill (respiratory exite) on the proximal-most leg segment of their shared ancestor. A framework for understanding the homologies of arthropod appendages opens up a powerful system for studying the origins of novel structures, the plasticity of morphogenetic fields across vast phylogenetic distances, and the convergent evolution of shared ancestral developmental fields.
High-throughput functional characterization of visceral afferents by optical recordings from thoracolumbar and lumbosacral dorsal root ganglions
Authors: Bian Zichao , Guo Tiantian , Jiang Shaowei , Chen Longtu , Liu Jia , Zheng Guoan , Feng Bin
Published: January 2021

Functional understanding of visceral afferents is important for developing new treatment to visceral hypersensitivity and pain. The sparse distribution of visceral afferents in dorsal root ganglions (DRGs) has challenged conventional electrophysiological recordings. Alternatively, Ca2+indicators like GCaMP6f allow functional characterization by optical recordings. Here we report a turnkey microscopy system that enables simultaneous Ca2+imaging at two parallel focal planes from intact DRG. By using consumer-grade optical components, the microscopy system is cost effective and can be made broadly available without loss of capacity. It records low-intensity fluorescent signals at a wide field of view (1.9 x 1.3 mm) to cover a whole mouse DRG, with a high pixel resolution of 0.7 micron/pixel, a fast frame rate of 50 frames/sec, and the capability of remote focusing without perturbing the sample. The wide scanning range (100 mm) of the motorized sample stage allows convenient recordings of multiple DRGs in thoracic, lumbar, and sacral vertebrae. As a demonstration, we characterized mechanical neural encoding of visceral afferents innervating distal colon and rectum (colorectum) in GCaMP6f mice driven by VGLUT2 promotor. A post-processing routine is developed for conducting unsupervised detection of visceral afferent responses from GCaMP6f recordings, which also compensates the motion artefacts caused by mechanical stimulation of the colorectum. The reported system offers a cost-effective solution for high-throughput recordings of visceral afferent activities from a large volume of DRG tissues. We anticipate a wide application of this microscopy system to expedite our functional understanding of visceral innervations in both health and diseases.
Abrupt increase in the UK coronavirus death-case ratio in December 2020
Authors: Wallace David J , Ackland Graeme J
Published: January 2021

1

Objective

to determine the statistical relationship between reported deaths and infections in the UK coronavirus outbreak

Design

Publicly available UK government data is used to determine a relationship between reported cases and deaths, taking into account various UK regions, age profiles and prevalence of the variant of concern (VOC) B.1.1.7.

Main Outcome Measures

Establishing a simple statistical relationship between detected cases and subsequent mortality.

Results

Throughout October and November 2020, deaths in England are well described as 1/55th of detected cases from 12 days previously. After that, the relationship no longer holds and deaths are significantly higher. This is especially true in regions affected by the VOC B.1.1.7

Conclusions

In early December, some new factor emerged to increase the case-fatality rate in the UK.

Summary Box

What is already known on this topic

The infection-mortality ratio enables one to predict future deaths based on current infections. Incomplete monitoring of infection may be sufficient to predict future trends.

What the study adds

For the specific case of the second wave of coronavirus infection in the UK, we show a clear mathematical relationship between detected infections (positive tests) and subsequent deaths. This relationship begins to fail in December, with unexpectedly high death rates. This may be correlated in time and region with the emergence of the Variant of Concern B 1.1.7.
Detection and removal of pacing artifacts prior to automated analysis of 12-lead ECG
Authors: Haq Kazi T. , Javadekar Neeraj , Tereshchenko Larisa G.
Published: January 2021

Background

Pacing artifacts must be excluded from the analysis of paced ECG waveform. This study aimed to develop and validate an algorithm to identify and remove the pacing artifacts on ECG.

Methods

We developed a semi-automatic algorithm that identifies the onset and offset of a pacing artifact based on the ECG signal’ slope steepness and designed a graphical user interface that permits quality control and fine-tuning the constraining threshold values. We used 1,054 ECGs from the retrospective, multicenter cohort study “Global Electrical Heterogeneity and Clinical Outcomes,” including 3,825 atrial and 10,031 ventricular pacing artifacts for the algorithm development and 22 ECGs including 108 atrial and 241 ventricular pacing artifacts for validation. Validation was performed per digital sample. We used the kappa-statistic of interrater agreement between manually labeled sample (ground-truth) and automated detection.

Results

The constraining parameter values were for onset threshold 13.06±6.21 μV/ms, offset threshold 34.77±17.80 μV/ms, and maximum window size 27.23 ± 3.53 ms. The automated algorithm detected a digital sample belonging to pacing artifact with a sensitivity of 74.5% and specificity of 99.6% and classified correctly 98.8% of digital samples (ROC AUC 0.871; 95%CI 0.853-0.878). The kappa-statistic was 0.785, indicating substantial agreement. The agreement was on 98.81% digital samples, significantly (P<0.00001) larger than the random agreement on 94.43% of digital samples.

Conclusions

The semi-automated algorithm can detect and remove ECG pacing artifacts with high accuracy and provide a user-friendly interface for quality control.

Highlights

We developed and validated a semi-automated algorithm to detect and remove pacing spike artifacts from a digital ECG signal.

The semi-automated algorithm can detect and remove pacing spike artifacts with high accuracy and provide a user-friendly interface for quality control.
The photosensitive phase acts as a sensitive window for seasonal multisensory neuroplasticity in male and female starlings
Authors: Orije Jasmien , Cardon Emilie , Hamaide Julie , Jonckers Elisabeth , Darras Veerle M. , Verhoye Marleen , Van der Linden Annemie
Published: January 2021

Traditionally, research unraveling seasonal neuroplasticity in songbirds has focused on the male song control system and testosterone. We longitudinally monitored the song and neuroplasticity in male and female starlings during multiple photoperiods using Diffusion Tensor and Fixel-Based techniques. These exploratory data-driven whole-brain methods resulted in a population-based tractogram uncovering microstructural sexual dimorphisms in the song control system and beyond. Male brains showed microstructural hemispheric asymmetries, whereas females had higher interhemispheric connectivity, which could not be attributed to brain size differences. Only females with large brains sing but differ from males in their song behavior by showing involvement of the hippocampus. Both sexes experienced multisensory neuroplasticity in the song control, auditory and visual system, and the cerebellum, mainly during the photosensitive period. This period with low gonadal hormones might represent a ‘sensitive window’ during which different sensory and motor systems in telencephalon and cerebellum can be seasonally re-shaped in both sexes.
Tristetraprolin prevents gastric metaplasia in mice by suppressing pathogenic inflammation
Authors: Busada Jonathan T. , Kadka Stuti , Peterson Kylie N. , Stumpo Deborah J. , Zhou Lecong , Cidlowski John A. , Blackshear Perry J.
Published: January 2021

Aberrant immune activation is associated with numerous inflammatory and autoimmune diseases and contributes to cancer development and progression. Within the stomach, inflammation drives a well-established sequence from gastritis to metaplasia, eventually resulting in adenocarcinoma. Unfortunately, the processes that regulate gastric inflammation and prevent carcinogenesis remain unknown. Tristetraprolin (TTP) is an RNA-binding protein that promotes the turnover of numerous pro-inflammatory and oncogenic mRNAs. Here, we utilized a TTP-overexpressing model, the TTPΔARE mouse, to examine whether TTP can protect the stomach from adrenalectomy (ADX)-induced gastric inflammation and spasmolytic polypeptide-expressing metaplasia (SPEM). We found that TTPΔARE mice were completely protected from ADX-induced gastric inflammation and SPEM. RNA sequencing revealed that TTP overexpression suppressed the expression of genes associated with the innate immune response. Finally, we show that protection from gastric inflammation was only partially due to suppression ofTnf, a well-known TTP target. Our results demonstrate that TTP exerts broad anti-inflammatory effects in the stomach and suggest that therapies that increase TTP expression may be effective treatments of pro-neoplastic gastric inflammation.
A rational blueprint for the design of chemically-controlled protein switches
Authors: Shui Sailan , Gainza Pablo , Scheller Leo , Yang Che , Kurumida Yoichi , Rosset Stéphane , Georgeon Sandrine , Correia Bruno E.
Published: January 2021

Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. However, the repertoire of small-molecule protein switches is insufficient for many applications, including those in the translational spaces, where properties such as safety, immunogenicity, drug half-life, and drug side-effects are critical. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions as OFF- and ON-switches. The designed binders and drug-receptors form chemically-disruptable heterodimers (CDH) which dissociate in the presence of small molecules. To design ON-switches, we converted the CDHs into a multi-domain architecture which we refer to asactivation by inhibitor releaseswitches (AIR) that incorporate a rationally designed drug-insensitive receptor protein. CDHs and AIRs showed excellent performance as drug responsive switches to control combinations of synthetic circuits in mammalian cells. This approach effectively expands the chemical space and logic responses in living cells and provides a blueprint to develop new ON- and OFF-switches for basic and translational applications.
Clustering FunFams using sequence embeddings improves EC purity
Authors: Littmann Maria , Bordin Nicola , Heinzinger Michael , Schütze Konstantin , Dallago Christian , Orengo Christine , Rost Burkhard
Published: January 2021

Motivation

Classifying proteins into functional families can improve our understanding of protein function and can allow transferring annotations within one family. For this, functional families need to be “pure”, i.e., contain only proteins with identical function. Functional Families (FunFams) cluster proteins within CATH superfamilies into such groups of proteins sharing function. 11% of all FunFams (22,830 of 203,639) contain EC annotations and of those, 7% (1,526 of 22,830) have inconsistent functional annotations.

Results

We propose an approach to further cluster FunFams into functionally more consistent sub-families by encoding their sequences through embeddings. These embeddings originate from language models transferring knowledge gained from predicting missing amino acids in a sequence (ProtBERT) and have been further optimized to distinguish between proteins belonging to the same or a different CATH superfamily (PB-Tucker). Using distances between embeddings and DBSCAN to cluster FunFams and identify outliers, doubled the number of pure clusters per FunFam compared to random clustering. Our approach was not limited to FunFams but also succeeded on families created using sequence similarity alone. Complementing EC annotations, we observed similar results for binding annotations. Thus, we expect an increased purity also for other aspects of function. Our results can help generating FunFams; the resulting clusters with improved functional consistency allow more reliable inference of annotations. We expect this approach to succeed equally for any other grouping of proteins by their phenotypes.

Availability

Code and embeddings are available via GitHub:https://github.com/Rostlab/FunFamsClustering
Femtosecond laser microdissection isolating regeneratingC. elegansneurons for single cell RNA sequencing
Authors: Zhao Peisen , Martin Chris , Ma Ke-Yue , Jiang Ning , Ben-Yakar Adela
Published: January 2021

Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single neuron resolution in small model organisms such asCaenorhabditis elegans. Existing cell isolation techniques cannot isolate regenerating neurons from the nematode. We present femtosecond laser microdissection (fs-LM), a new single cell isolation method that dissects intact cells directly from living tissue by leveraging the micron-scale precision of fs-laser ablation. We show that fs-LM facilitated sensitive and specific gene expression profiling by single cell RNA-sequencing, while mitigating the stress related transcriptional artifacts induced by tissue dissociation. Single cell RNA-sequencing of fs-LM isolated regeneratingC. elegansneurons revealed transcriptional program leading to successful regeneration in wild-type animals or regeneration failure in animals lacking DLK-1/p38 kinase. The ability of fs-LM to isolate specific neurons based on phenotype of interest allowed us to study the molecular basis of regeneration heterogeneity displayed by neurons of the same type. We identified gene modules whose expression patterns were correlated with axon regrowth rate at a single neuron level. Our results establish fs-LM as a highly specific single cell isolation method ideal for precision and phenotype-driven studies.
Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation
Authors: Cholico Giovan N. , Fling Russ R. , Zacharewski Nicholas A. , Fader Kelly A. , Nault Rance , Zacharewski Tim
Published: January 2021

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a persistent environmental contaminant, induces steatosis by increasing hepatic uptake of dietary and mobilized peripheral fats, inhibiting lipoprotein export, and repressing β-oxidation. In this study, the mechanism of β-oxidation inhibition was investigated by testing the hypothesis that TCDD dose-dependently repressed straight-chain fatty acid oxidation gene expression in mice following oral gavage every 4 days for 28 days. Untargeted metabolomic analysis revealed a dose-dependent decrease in hepatic acyl-CoA levels, while octenoyl-CoA and dicarboxylic acid levels increased. TCDD also dose-dependently repressed the hepatic gene expression associated with triacylglycerol and cholesterol ester hydrolysis, fatty acid binding proteins, fatty acid activation, and 3-ketoacyl-CoA thiolysis while inducing acyl-CoA hydrolysis. Moreover, octenoyl-CoA blocked the hydration of crotonyl-CoA suggesting short chain enoyl-CoA hydratase (ECHS1) activity was inhibited. Collectively, the integration of metabolomics and RNA-seq data suggested TCDD induced a futile cycle of fatty acid activation and acyl-CoA hydrolysis resulting in incomplete β-oxidation, and the accumulation octenoyl-CoA levels that inhibited the activity of short chain enoyl-CoA hydratase (ECHS1).
Species ecology explains the various spatial components of genetic diversity in tropical reef fishes
Authors: Donati Giulia Francesca Azzurra , Zemp Niklaus , Manel Stéphanie , Poirier Maude , Claverie Thomas , Ferraton Franck , Gaboriau Théo , Govinden Rodney , Hagen Oskar , Ibrahim Shameel , Mouillot David , Leblond Julien , Julius Pagu , Velez Laure , Zareer Irthisham , Ziyad Adam , Leprieur Fabien , Albouy Camille , Pellissier Loïc
Published: January 2021

Intraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between theα, βandγcomponents of genetic diversity, which we subsequently link to six ecological traits. In contrast to what is expected by the neutral theory of molecular evolution, we find that theαandγcomponents of genetic diversity are negatively associated with species abundance, which can be explained by larger variance in reproductive success in large populations and/or higher introgression in less frequent species. Pelagic larval duration, an important dispersal trait in marine fishes, is found to be negatively related to geneticβdiversity, as expected by theory. We conclude that the neutral theory of molecular evolution may not be sufficient to explain genetic diversity in tropical reef fishes and that additional processes influence those relationships.