bluuebunny/crossref_metadata_2025 huggingface dataset:
The 3D architecture of the pepper (Capsicum annum) genome and its relationship to function and evolution
Authors: Liao Yi , Wang Juntao , Zhu Zhangsheng , Liu Yuanlong , Chen Jinfeng , Zhou Yongfeng , Liu Feng , Lei Jianjun , Gaut Brandon S. , Cao Bihao , Emerson J.J. , Chen Changming
Published: December 2021

The architecture of topologically associating domains (TADs) varies across plant genomes. Understanding the functional consequences of this diversity requires insights into the pattern, structure, and function of TADs. Here, we present a comprehensive investigation of the 3D genome organization of pepper (Capsicum annuum) and its association with gene expression and genomic variants. We report the first chromosome-scale long-read genome assembly of pepper and generate Hi-C contact maps for four tissues. The contact maps indicate that 3D structure varies somewhat across tissues, but generally the genome was segregated into subcompartments that were correlated with transcriptional state. In addition, chromosomes were almost continuously spanned by TADs, with the most prominent found in large genomic regions that were rich in retrotransposons. A substantial fraction of TAD boundaries were demarcated by chromatin loops, suggesting loop extrusion is a major mechanism for TAD formation; many of these loops were bordered by genes, especially in highly repetitive regions, resulting in gene clustering in three dimensional space. Integrated analysis of Hi-C profiles and transcriptomes showed that change in 3D chromatin structures (e.g. subcompartments, TADs, and loops) was not the primary mechanism contributing to differential gene expression between tissues, but chromatin structure does play a role in transcription stability. TAD boundaries were significantly enriched for breaks of synteny and depletion of sequence variation, suggesting that TADs constrain patterns of genome structural evolution in plants. Together, our work provides insights into principles of 3D genome folding in large plant genomes and its association with function and evolution.
Polyclonal pathogen populations accelerate the evolution of antibiotic resistance in patients
Authors: Caballero Julio Diaz , Wheatley Rachel M. , Kapel Natalia , López-Causapé Carla , Van der Schalk Thomas , Quinn Angus , Recanatini Claudia , Xavier Basil Britto , Timbermont Leen , Kluytmans Jan , Ruzin Alexey , Esser Mark , Malhotra-Kumar Surbhi , Oliver Antonio , MacLean R. Craig ,   WP3A working group
Published: December 2021

Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection forde novovariants. Here we show that pulmonary populations of the opportunistic pathogenP. aeruginosaare often polyclonal. Crucially, resistance evolves rapidly in patients colonized by polyclonal populations through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by monoclonal populations due to selection for novel resistance mutations. However, strong trade-offs between resistance and fitness occur in polyclonal populations that can drive the loss of resistant strains. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.

One sentence summary

Antibiotic resistance evolves quickly in patients colonized by polyclonal pathogen populations.
Manipulating Histone Acetylation Leads to Adverse Effects in Hemangiosarcoma Cells
Authors: Suzuki Tamami , Aoshima Keisuke , Yamazaki Jumpei , Kobayashi Atsushi , Kimura Takashi
Published: December 2021

Canine hemangiosarcoma (HSA) is a malignant tumour derived from endothelial cells. No effective treatment has yet been developed because of the lack of understanding of its pathogenesis. Histone acetylation, an epigenetic modification, is highly associated with cancer pathogenesis. Manipulating histone acetylation by histone deacetylase inhibitors (HDACi) or bromodomain and extraterminal domain inhibitors (BETi) is one approach to treat various cancers. However, the role of histone acetylation in HSA remains unknown. This study aimed to investigate how histone acetylation functions in HSA pathogenesis using two HDACi, suberanilohydroxamic acid (SAHA) and valproic acid (VPA), and one BETi, JQ1, in vitro and in vivo. Histone acetylation levels were high in cell lines and heterogeneous in clinical cases. SAHA and JQ1 induced apoptosis in HSA cell lines. SAHA and VPA treatment in HSA cell lines upregulated inflammatory-related genes, thereby attracting macrophages. This implies that SAHA and VPA can induce anti-tumour immunity. JQ1 stimulated autophagy and inhibited the cell cycle. Finally, JQ1 suppressed HSA tumour cell proliferation in vivo. These results suggest that HDACi and BETi can be alternative drugs for HSA treatment. Although further research is required, this study provides useful insights for developing new treatments for HSA.
Ketamine Sedation Facilitates Asleep DBS: a multicenter retrospective study
Authors: Erdman Halen Baker , Kornilov Evgeniya , Kahana Eilat , Zarchi Omer , Reiner Johnathan , Socher Achinoam , Strauss Ido , Israel Zvi , Bergman Hagai , Tamir Idit
Published: December 2021

Deep brain stimulation (DBS) is commonly and safely performed for selective Parkinson’s disease patients. Many centers perform DBS lead positioning exclusively under local anesthesia, to allow for brain microelectrode recordings (MER) and testing of stimulation-related therapeutic and side effects. These measures enable physiological identification of the DBS targets based on electrophysiological properties like firing rates and patterns, optimization of lead placement accuracy, and intra-operative evaluation of therapeutic window. Nevertheless, due to the challenges of awake surgery, some centers use sedation or general anesthesia, despite the distortion of discharge properties, and potential impact on clinical outcomes. Thus, there is a need for a novel anesthesia regimen that enables sedation without compromising intra-operative monitoring. This study investigates the use of low-dose ketamine for conscious sedation during lead positioning in subthalamic nucleus (STN) DBS for Parkinson’s disease patients.

Three anesthetic regimens were retrospectively compared in 38 surgeries across three DBS centers: 1) Interleaved propofol-ketamine (PK), 2) Interleaved propofol-awake (PA), and 3) Fully awake (AA).

All anesthesia regimens achieved satisfactory MER. Automatic detection of STN borders and subdomains using a Hidden Markov Model was similar between the groups. Patients’ symptoms and cooperation during stimulation testing in the ketamine group was not altered. No major adverse effects were reported in the different anesthesia protocols.

These results support the use of low-dose ketamine as a novel alternative for the existing DBS anesthesia regimens, optimizing patient’s experience while preserving lead placement accuracy. A prospective study should be performed to confirm these findings.
The impact of the COVID-19 school closure on adolescents’ use of mental healthcare services in Sweden
Authors: Svaleryd Helena , Björkegren Evelina , Vlachos Jonas
Published: December 2021

Background

School closures used to contain the COVID-19 pandemic may have negative impacts on students’ mental health but credible evidence is scarce. Sweden moved upper-secondary students to remote learning but, as the only country in the OECD, kept schools at lower levers open throughout the pandemic.

Methods

Using nationwide register data, we estimate the difference in the use of mental healthcare services between upper- and lower-secondary students during the pandemic, and relate this to the same group difference prior to the pandemic. For the main analysis, this difference-in-difference approach is applied to the period April-June 2020 when upper-secondary schools were fully closed. We also study the periods July-December 2020 when upper-secondary schools were largely open, and January-March 2021 when they were partially closed. We study the impact on all contacts with hospitals and specialist psychiatric care due to mental and behavioral disorder, as well as prescriptions for antidepressants, insomnia, and ADHD drugs.

Findings

Compared with expected rates, the use of mental healthcare services among upper-secondary students fell by -3.71 [CI95 -5.52 to -1.91] cases per 1000 during April-June 2020, largely due to a reduction in depression and anxiety-related diagnoses (-1.49; CI95 [-2.36 to -0.63]) and prescriptions (-1.80; CI95 [-2.93 to -0.68]). This reduction in the use of mental healthcare services corresponds to a 4.36% CI95 [-6.47 to -2.25]) decrease compared to the level prior to the pandemic. The decrease compared to expected rates persists through July-December 2020 (-3.55%; CI95 [-5.38 to -1.71]) and January-March 2021 (-5.23%; CI95 [-7.24 to -3.21]). The reduction is stronger among students in the 2nd (-5.06%; CI95 [-8.02 to -2.09]) and 3rd (-4.86%; CI95 [-8.19 to -1.53]) year of upper-secondary school. The decrease is concentrated to students who was not in contact with mental healthcare services earlier in the academic year (-16.70%; CI95 [-22.20 to -11.20]). The relative reduction is largest for unplanned care (-13.88%; CI95 [-19.35 to -8.42]) and care at emergency units (-18.19%; CI95 [-26.44 to -9.92]).

Interpretation

Closing upper-secondary schools in Sweden reduced use of mental healthcare services. There is no indication of this being due to reduced accessibility. In a setting with no strict lockdown, moving to online teaching for a limited period did not worsen mental health among students in upper-secondary schools.
Change in Finances, Peer Access, and Mental Health Among Trans and Non-binary People in Canada During COVID-19
Authors: Ghabrial Monica A. , Scheim Ayden I. , Chih Caiden , Santos Heather , Adams Noah James , Bauer Greta R.
Published: December 2021

Purpose

COVID-related stressors associated with loss of income and community are compounded with gender minority stress among trans and non-binary people (TNB) – which may result in mental health burden. The present study examined the effect of COVID-related change in finances and TNB gathering access on anxiety and depression among TNB people.

Methods

Participants were 18 years and older (M age = 30) who completed both pre-pandemic baseline (Fall 2019) and pandemic follow-up (Fall 2020) surveys in the Trans PULSE Canada study. Multivariable regression analyses examined associations between change in (1) finances and (2) access to TNB peers and mental health during the pandemic.

Results

Of 780 participants, 50% reported that COVID had a negative effect on personal income and 58.3% reported loss in access to TNB peer or friend gatherings (in person or online). Depression and anxiety symptoms increased from pre-pandemic to follow-up, and most participants were above measurement cut-offs for clinical levels during the pandemic. Changes in finances and access to peer gatherings were associated with depression symptoms during the pandemic, but effects depended on level of pre-pandemic depression. For participants with high pre-pandemic depression, financial stability was not protective against increased depression at follow-up. Participants experiencing unprecedentedly high levels of depression during COVID may have pursued more TNB gatherings. Neither financial change nor access to TNB gatherings were associated with pandemic anxiety.

Conclusion

Findings suggest need for a multifaceted approach to mental health programmes and services to address structural barriers, including financial support and meaningful TNB community engagement.
Large-scale osteocyte lacunar morphological analysis of transiliac bone in normal and osteoporotic premenopausal women
Authors: Goff Elliott , Cohen Adi , Shane Elizabeth , Recker Robert R. , Kuhn Gisela , Müller Ralph
Published: December 2021

Bone’s adaptation ability is governed by the network of embedded osteocytes that inhabit individual crevasses called lacunae. The morphology of these lacunae and their resident osteocytes are known to change with age and diseases such as postmenopausal osteoporosis. However, it is unclear whether alterations in lacunar morphology are present in younger populations with osteoporosis. To investigate this, we implemented a previously validated methodology to image and quantify the three-dimensional morphometries of lacunae on a large scale (26.2 million cells) with ultra-high-resolution micro-computed tomography (microCT) in transiliac bone biopsies from three groups of premenopausal women: control n=39; idiopathic osteoporosis (IOP) n=45; idiopathic low BMD (ILBMD) n=19. Important lacunar morphometric parameters were measured in both trabecular and cortical bone: lacunar density (Lc.N/BV), lacunar porosity (Lc.TV/BV), lacunar number (Lc.N), lacunar volume (Lc.V), lacunar surface area (Lc.S), lacunar alignment (Lc.θ), lacunar stretch (Lc.St), lacunar oblateness (Lc.Ob), lacunar equancy (Lc.Eq), and lacunar sphericity (Lc.Sr). These were then compared against each other and also with previously measured tissue morphometries including: bone volume density (BV/TV), trabecular separation (Tb.Sp), trabecular number (Tb.N), and trabecular thickness (Tb.Th), structure model index (SMI), cortical porosity (Ct.Po) and cortical pore spacing (Ct.Sp). We detected no differences in lacunar morphology between the IOP, ILBMD and healthy premenopausal women. In contrast, we did find significant differences between lacunar morphologies in cortical and trabecular regions within all three groups, which was consistent with our previous findings on a subgroup of the healthy group. Furthermore, we discovered strong correlations between Lc.Sr from both trabecular and cortical regions with the measured BV/TV. The findings and comprehensive lacunar dataset we present here will be a crucial foundation for future investigations of the relationship between osteocyte lacunar morphology and disease.
A Fast Lasso-Based Method for Inferring Higher-Order Interactions
Authors: Elmes Kieran , Heywood Astra , Huang Zhiyi , Gavryushkin Alex
Published: December 2021

Abstract

Large-scale genotype-phenotype screens provide a wealth of data for identifying molecular alterations associated with a phenotype. Epistatic effects play an important role in such association studies. For example, siRNA perturbation screens can be used to identify combinatorial gene-silencing effects. In bacteria, epistasis has practical consequences in determining antimicrobial resistance as the genetic background of a strain plays an important role in determining resistance. Recently developed tools scale to human exome-wide screens for pairwise interactions, but none to date have included the possibility of three-way interactions. Expanding upon recent state-of-the art methods, we make a number of improvements to the performance on large-scale data, making consideration of three-way interactions possible. We demonstrate our proposed method, Pint, on both simulated and real data sets, including antibiotic resistance testing and siRNA perturbation screens. Pint outperforms known methods in simulated data, and identifies a number of biologically plausible gene effects in both the antibiotic and siRNA models. For example, we have identified a combination of known tumor suppressor genes that is predicted (using Pint) to cause a significant increase in cell proliferation.

Author Summary

In recent years, large-scale genetic datasets have become available for analysis. These large datasets often stretch the limits of classic computational methods, requiring too much memory or simply taking a prohibitively long time to run. Due to the enormous number of potential interactions, each gene or variation in the data is often modeled on its own, without considering interactions between them. Recently, methods have been developed to solve regression problems that include these interacting effects. Even the fastest of these cannot include threeway interactions, however. We improve upon one such method, developing an approach that is significantly faster than the current state of the art. Moreover, our method scales to three-way interactions among thousands of genes, while avoiding a number of the limitations of previous approaches. We analyse large-scale simulated data, antibiotic resistance, and gene-silencing datasets to demonstrate the accuracy and performance of our approach.
Spatially distributed computation in cortical circuits
Authors: Gepshtein Sergei , Pawar Ambarish , Kwon Sunwoo , Savel’ev Sergey , Albright Thomas D.
Published: December 2021

The traditional view of neural computation in the cerebral cortex holds that sensory neurons are specialized, i.e., selective for certain dimensions of sensory stimuli. This view was challenged by evidence of contextual interactions between stimulus dimensions in which a neuron’s response to one dimension strongly depends on other dimensions. Here we use methods of mathematical modeling, psychophysics, and electrophysiology to address shortcomings of the traditional view. Using a model of a generic cortical circuit, we begin with the simple demonstration that cortical responses are always distributed among neurons, forming characteristic waveforms, which we call neural waves. When stimulated by patterned stimuli, circuit responses arise by interference of neural waves. Resulting patterns of interference depend on interaction between stimulus dimensions. Comparison of these modeled responses with responses of biological vision makes it clear that the framework of neural wave interference provides a useful alternative to the standard concept of neural computation.

Teaser

Investigating interference of neural waves helps to overcome limitations of the traditional view of cortical computation.
Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta
Authors: Ahern Darcy T. , Bansal Prakhar , Faustino Isaac , Kondaveeti Yuvabharath , Glatt-Deeley Heather R. , Banda Erin C. , Pinter Stefan F.
Published: December 2021

SUMMARY/ABSTRACT

Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the male Y and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y-pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants of these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development.

Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely-used model for the human syncytiotrophoblast. While these isogenic panels trigger a GATA2/3 and TFAP2A/C -driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes, and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene co-expression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition, and that the pseudoautosomal region likely plays a key role in these changes, which may facilitate prioritization of haploinsufficient drivers of 45,X extra-embryonic phenotypes.
Predicting the effects of multiple global change drivers on microbial communities remains challenging
Authors: Suleiman Marcel , Daugaard Uriah , Choffat Yves , Zheng Xue , Petchey Owen L
Published: December 2021

Microbial communities in many ecosystems are facing a broad range of global change drivers, such as nutrient enrichment, chemical pollution, and temperature change. These drivers can cause changes in the abundance of taxa, the composition of communities, and the properties of ecosystems. While the influence of single drivers is already described in numerous studies, the effect and predictability of multiple drivers changing simultaneously is still poorly understood. In this study, we used 240 highly replicable oxic/anoxic aquatic lab microcosms and four drivers (fertilizer, glyphosate, metal pollution, antibiotics) in all possible combinations at three different temperatures (20 °C, 24 °C, and 28 °C) to shed light into consequences of multiple drivers on different levels of organization, ranging from species abundance to community and ecosystem parameters. We found (i) that at all levels of ecological organisation, combinations of drivers can change the biological consequence and direction of effect compared to single drivers (ii), that effects of combinations are further modified by temperature, (iii) that a larger number of drivers occurring simultaneously is often quite closely related to their effect size, and (iv) that there is little evidence that any of these effects are associated with the level of ecological organisation of the state variable. These findings suggest that, at least in this experimental ecosystem approximating a stratified aquatic ecosystem, there may be relatively little scope for predicting the effects of combinations of drivers from the effects of individual drivers, or by accounting for the level of ecological organisation in question, though there may be some scope for prediction based on the number of drivers that are occurring simultaneous. A priority, though also a considerable challenge, is to extend such research to consider continuous variation in the magnitude of multiple drivers acting together.
A neuron, microglia, and astrocyte triple coculture model to study Alzheimer disease
Authors: Luchena Celia , Zuazo-Ibarra Jone , Valero Jorge , Matute Carlos , Alberdi Elena , Capetillo-Zarate Estibaliz
Published: December 2021

Glial cells are essential to understand Alzheimer’s disease (AD) progression, given their role in neuroinflammation and neurodegeneration. There is a need for reliable and easy to manipulate models that allow studying the mechanisms behind neuron and glia communication. Currently available models such as cocultures require complex methodologies and/or might not be affordable for all laboratories. With this in mind, we aimed to establish a straightforward in vitro setting with neurons and glial cells to study AD.

We generated a triple co-culture with neurons, microglia and astrocytes. Immunofluorescence, western blot and ELISA techniques were used to characterize the effects of oligomeric Aβ (oAβ) in this model.

We found that, in the triple co-culture, microglia increased the expression of anti-inflammatory markers Arginase I and TGF-β1, and reduced pro-inflammatory iNOS and IL-1β, compared with microglia alone. Astrocytes reduced expression of pro-inflammatory A1 markers AMIGO2 and C3, and displayed a ramified morphology resembling physiological conditions. Lastly, neurons increased post-synaptic markers, and developed more and longer branches than in individual primary cultures. Addition of oAβ in the triple coculture reduced synaptic markers and increased microglial activation, which are hallmarks of AD.

Consequently, we developed a reliable model, where cells better resemble physiological conditions: microglia are less inflammatory, astrocytes are less reactive and neurons display a more mature morphology than in individual primary cultures. Moreover, we were able to recapitulate Aβ-induced synaptic loss and inflammation. This model emerges as a powerful tool to study neurodegeneration and inflammation in the context of AD and other neurodegenerative diseases.

Table of content image

Main points

In our model, microglia and astrocytes are less reactive, and neurons have a more mature morphology than in primary cultures.

oAβ reduced synaptic markers and increased microglial activation.

This triple co-culture is a reliable tool to study neurodegeneration and gliosis in vitro.
Ecology drives the degree of convergence in the gene expression of extremophile fishes
Authors: Tobler Michael , Greenway Ryan , Kelley Joanna L.
Published: December 2021

Convergent evolution, where independent lineages evolve similar traits when adapting to similar habitats, is a common phenomenon and testament to the repeatability of evolutionary processes. Still, non-convergence is also common, and a major question is whether apparently idiosyncratic, lineage-specific evolutionary changes are reflective of chance events inherent to evolutionary processes, or whether they are also influenced by deterministic genetic or ecological factors. To address this question, we quantified the degree of convergence in genome-wide patterns of gene expression across lineages of livebearing fishes (family Poeciliidae) that span 40 million years of evolution and have colonized extreme environments in the form of toxic, hydrogen-sulfide-rich springs. We specifically asked whether the degree of convergence across lineage pairs was related to their phylogenetic relatedness or the ecological similarity of the habitats they inhabit. Using phylogenetic comparative analyses, we showed that the degree of convergence was highly variable across lineage pairs residing in sulfide springs. While closely related lineages did not exhibit higher degrees of convergence than distantly related ones, we uncovered a strong relationship between degree of convergence and ecological similarity. Our results indicate that variation in the degree of convergence is not merely noise associated with evolutionary contingency. Rather, cryptic environmental variation that is frequently ignored when we employ reductionist approaches can significantly contribute to adaptive evolution. This study highlights the importance of multivariate approaches that capture the complexities of both selective regimes and organismal design when assessing the roles of determinism and contingency in evolution.

Significance Statement

When different species adapt to similar environmental conditions, we frequently observe a mix between shared (convergent) and lineage-specific (nonconvergent) evolutionary changes. Shared changes provide evidence for the repeatability and predictability of evolution. However, it remains unclear whether lineage-specific changes are caused by random forces that limit the predictability of evolution, or whether they reflect deterministic processes shaped by unidentified genetic and environmental factors. By analyzing patterns of gene expression across fishes in extreme environments, we show that the degree of convergence between lineages is related to ecology, indicating that lineage-specific evolutionary changes are not just noise caused by random processes. Thus, acknowledging the complexity of nature in empirical research is critical if we want to predict evolution.
Artificial selection of communities drives the emergence of structured interactions
Authors: Fraboul Jules , Biroli Giulio , De Monte Silvia
Published: December 2021

Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level functions of interest. These experiments typically involve selection acting on populations of communities, each of which is composed of multiple species. Numerical simulations explored the evolutionary dynamics of this complex, multi-scale system. However, a comprehensive theoretical understanding of the process of artificial selection of communities is still lacking. Here, we propose a general model for the evolutionary dynamics of communities composed of a large number of interacting species, described by disordered generalized Lotka-Volterra equations. Our analytical and numerical results reveal that selection for total community abundance leads to increased levels of mutualism and interaction diversity. Correspondingly, the interaction matrix acquires a specific structure that is generic for selection of collective functions. Our approach moreover allows to disentangle the role of different control parameters in determining the efficiency of the selection process, and can thus be used as a guidance in optimizing artificial selection protocols.
Enriching for orthologs increases support for Xenacoelomorpha and Ambulacraria sister relationship
Authors: Mulhair Peter O , McCarthy Charley GP , Siu-Ting Karen , Creevey Christopher J , O’Connell Mary J
Published: December 2021

Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum, or within Deuterostomia, sister to Ambulacraria. While their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral Bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. More recently, further studies have brought into question whether Deuterostomia should be considered monophyletic at all. Hidden paralogy presents a major challenge for reconstructing species phylogenies. Here we assess whether hidden paralogy has contributed to the conflict over the placement of Xenacoelomorpha. Our approach assesses previously published datasets, enriching for orthogroups whose gene trees support well resolved clans elsewhere in the animal tree of life. We find that the majority of constituent genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy is rife at this depth. We demonstrate that enrichment for genes with orthologous signal alters the final topology that is inferred, whilst simultaneously improving fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our orthology enriched set of genes. At a time when we are steadily progressing towards sequencing all of life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modelled adequately.
Variability in mosquito community composition associated with estuarine wetlands in Northern NSW, Australia
Authors: Webb Cameron Ewart , Hanford Jayne , Bald Michael , Roberts Scott
Published: December 2021

The Northern Rivers region of NSW, Australia, is well documented as being impacted by nuisance-biting mosquitoes and mosquito-borne disease. Mosquitoes of greatest concern are those associated with estuarine and brackish water habitats associated with coastal wetlands and understanding the spatial variability in abundance and diversity will assist the assessment of risk and inform surveillance and control programs. Adult mosquito populations were sampled, using carbon dioxide baited traps, at four locations within the Richmond River estuary at Ballina, NSW, Australia, during January and February 2021. Concomitant sampling of habitats for immature mosquitoes was also undertaken. A total of 16,467 mosquitoes was collected at all sites across two sampling periods with the most abundant mosquitoes, Verrallina funerea, Aedes vigilax, and Culex sitiens, those typically associated with estuarine environments. Culex annulirostris, a mosquito associated with freshwater habitats, and Aedes notoscriptus, a mosquito associated with water-holding containers, were also commonly collected. The mosquito communities differed, in relative abundance and species richness, between the four locations. The result highlighted the need for authorities to understand the variability in productivity of potential mosquito habitats, beyond those determinants associated with vegetation communities alone, when assessing suitable locations of mosquito surveillance and integrated mosquito management.
Validated Determination of NRG1 Ig-like Domain Structure by Mass Spectrometry Coupled with Computational Modeling
Authors: Khaje Niloofar Abolhasani , Eletsky Alexander , Biehn Sarah E. , Mobley Charles K. , Rogals Monique J. , Kim Yoonkyoo , Mishra Sushil K. , Doerksen Robert J. , Lindert Steffen , Prestegard James , Sharp Joshua S.
Published: December 2021

High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally-informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure leaving questions of unintentional bias and applicability to unknown structures unresolved. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 Å. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure.
Broad misappropriation of developmental splicing profile by cancer in multiple organs
Authors: Singh Arashdeep , Rajeevan Arati , Gopalan Vishaka , Agrawal Piyush , Day Chi-Ping , Hannenhalli Sridhar
Published: December 2021

Oncogenesis mimics key aspects of embryonic development. However, the underlying molecular determinants are not completely understood. Leveraging temporal transcriptomic data during development in multiple human organs, we demonstrate that the ‘embryonic positive (EP)’ alternative splicing events, specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. EP events are associated with key oncogenic processes and their reactivation predicts proliferation rates in cancer cell lines as well as patient survival. EP exons are significantly enriched for nitrosylation and transmembrane domains coordinately regulating splicing in multiple genes involved in intracellular transport and N-linked glycosylation respectively, known critical players in cancer. We infer critical splicing factors (CSF) potentially regulating these EP events and show that CSFs exhibit copy number amplifications in cancer and are upregulated specifically in malignant cells in the tumor microenvironment. Mutational inactivation of CSFs results in decreased EP splicing, further supporting their causal role. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of CSFs in brain and liver, which can be potentially targeted using FDA approved drugs. Our study provides the first comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest novel targets including splicing events, splicing factors, and transcription factors.
Proximity-assisted photoactivation (PAPA): Detecting molecular interactions in live-cell single-molecule imaging
Authors: Graham Thomas G.W. , Ferrie John J. , Dailey Gina M. , Tjian Robert , Darzacq Xavier
Published: December 2021

Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the “sender”) can reactivate a second fluorophore (the “receiver”) from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a sub-population of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.
GZMKhigh CD8+ T effector memory cells are associated with CD15high neutrophil abundance in early-stage colorectal tumors and predict poor clinical outcome
Authors: Tiberti Silvia , Catozzi Carlotta , Scirgolea Caterina , Croci Ottavio , Ballerini Mattia , Cagnina Danilo , Soriani Chiara , Nava Lauson Carina B. , Macandog Angeli D. , Bertalot Giovanni , Petz Wanda L. , Ravenda Simona P. , Licursi Valerio , Paci Paola , Rasponi Marco , Fazio Nicola , Ren Guangwen , Fumagalli-Romario Uberto , Shaefer Martin H. , Campaner Stefano , Lugli Enrico , Nezi Luigi , Manzo Teresa
Published: December 2021

Tumor contexture has emerged as a major prognostic determinant and tumor infiltrating CD8+ T cells have been associated with a better prognosis in several solid tumors, including early-stage colorectal cancer (CRC). However, the tumor immune infiltrate is highly heterogeneous and understanding how the interplay between different immune cell compartments impacts on the clinical outcome is still in its infancy.

Here, we describe in a prospective cohort a novel CD8+ T effector memory population, which is characterized by high levels of Granzyme K (GZMKhigh CD8+ TEM) and is correlated with CD15high tumor infiltrating neutrophils. We provide both in vitro and in vivo evidence of the role of stromal cell-derived factor 1 (CXCL12/SDF-1) in driving functional changes on neutrophils at the tumor site, promoting their retention and increasing the crosstalk with CD8+ T cells. Mechanistically, as a consequence of the interaction with neutrophils, CD8+ T cells are skewed towards a CD8+ TEM phenotype and produce high levels of GZMK, which in turn decreases E-cadherin pathway. The correlations of GZMKhigh CD8+ TEM and neutrophils with both tumor progression in mice and early relapse in CRC patients demonstrate the role of GZMKhigh CD8+ TEM in promoting malignancy. Indeed, a gene signature defining GZMKhigh CD8+ TEM was associated with worse prognosis on a larger independent cohort of CRC patients and a similar analysis was extended to lung cancer (TCGA).

Overall, our results highlight the emergence of GZMKhigh CD8+ TEM in early-stage CRC tumors as a hallmark driven by the interaction with neutrophils, which could implement current patient stratification and be targeted by novel therapeutics.
Sex-specific topology of the nociceptive circuit shapes dimorphic behavior in C. elegans
Authors: Pechuk Vladyslava , Salzberg Yehuda , Goldman Gal , Chaubey Aditi H. , Bola R. Aaron , Hoffman Jonathon R. , Endreson Morgan L. , Miller Renee M. , Reger Noah J. , Portman Douglas S. , Ferkey Denise M. , Schneidman Elad , Oren-Suissa Meital
Published: December 2021

How sexually dimorphic behavior is encoded in the nervous system is poorly understood. Here, we characterize the dimorphic nociceptive behavior in C. elegans and study the underlying circuits, which are composed of the same neurons but are wired differently. We show that while sensory transduction is similar in the two sexes, the downstream network topology markedly shapes behavior. We fit a network model that replicates the observed dimorphic behavior in response to external stimuli, and use it to predict simple network rewirings that would switch the behavior between the sexes. We then show experimentally that these subtle synaptic rewirings indeed flip behavior. Strikingly, when presented with aversive cues, rewired males were compromised in finding mating partners, suggesting that network topologies that enable efficient avoidance of noxious cues have a reproductive “cost”. Our results present a deconstruction of the design of a neural circuit that controls sexual behavior, and how to reprogram it.
LRRFIP2 modulates the response to hypoxia during embryonic cardiogenesis
Authors: Driss Laura Ben , Houbron Christophe , Britto Florian , Schmitt Alain , Gall Morgane Le , Daubas Philippe , Maire Pascal
Published: December 2021

Oxygen is crucial for appropriate embryonic and fetal development, including cardiogenesis. The heart is the first organ formed in the embryo and is required to provide oxygen and nutrients to all cells in the body. Embryonic cardiogenesis is a complex process finely regulated and prone to congenital malformations. It takes place in a hypoxic environment that activates the HIF-1α signaling pathway which mediates cellular and systemic adaptations to low oxygen levels. Since inhibition or overactivation of the HIF-1α signaling pathway in the myocardium lead to severe cardiac malformations and embryonic lethality, it is important that the cellular response to hypoxia be precisely regulated. While many gene regulatory networks involved in embryonic cardiogenesis have been characterized in detail, the modulation of the response of cardiomyocytes (CM) to hypoxia has remained less studied. We identified LRRFIP2 as a new negative cofactor of HIF-1α. Indeed, we have shown that the absence of Lrrfip2 expression in a mouse KI model led to an enhance of many HIF-1α target genes including Igfbp3, Bnip3 and Ndufa4l2 in embryonic CM during development. As results, the absence of Lrrfip2 led to the inhibition of the PI3K/Akt survival pathway, growth defects, mitochondrial dysfunction and to a precocious maturation of the embryonic CMs. Altogether, these defects led to the formation of a smaller heart unable to provide sufficient oxygen to the embryo and finally to a severe hypoxia and a precocious lethality.

Graphical abstract

Highlights

LRRFIP2 regulates negatively the HIF-1α activity

Lrrfip2 deletion leads to an embryonic lethality between E11.5 and E13.5

LRRFIP2 controls ROS production and CM maturation
Novel inhibitors designing against the potential drug target of Plasmodium falciparum M17 Leucyl Aminopeptidase – PfM17LAP
Authors: Dabburu Govinda Rao , Kumar Manish , Subbarao Naidu
Published: December 2021

Malaria is one of the major disease of concern worldwide especially in the African regions. According to the recent WHO reports, African regions share 95% of the total deaths worldwide that occurs due to malaria. Plasmodium falciparum M17 Leucyl Aminopeptidase (PfM17LAP) plays an important role in the regulation of amino acids release and for the survival of the parasite. We performed molecular docking and simulation studies to find the potential inhibitors against PfM17LAP using ChEMBL antimalarial library. Molecular docking studies and post-docking analysis revealed that molecules CHEMBL369831 and CHEMBL176888 showed better binding than the reference molecule BESTATIN. LibDock and X-SCORES of molecules BES, CHEMBL369831 and CHEMBL176888 are 130.071, 230.38, 223.56 and -8.75 Kcal/mol, -10.90 Kcal/mol, -11.05 Kcal/mol respectively. ADMET profiling of the top ten ranked molecules was done by using the Discovery Studio. Molecular dynamic studies revealed that the complex PfM17LAP-CHEMBL369831 is stable throughout the simulation. Finally, we have reported novel inhibitors which possess more binding affinity towards PfM17LAP.
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion
Authors: Zaremba Mindaugas , Dakineviciene Donata , Golovinas Edvardas , Zagorskaitė Evelina , Stankunas Edvinas , Lopatina Anna , Sorek Rotem , Manakova Elena , Ruksenaite Audrone , Silanskas Arunas , Asmontas Simonas , Grybauskas Algirdas , Tylenyte Ugne , Jurgelaitis Edvinas , Grigaitis Rokas , Timinskas Kęstutis , Venclovas Česlovas , Siksnys Virginijus
Published: December 2021

Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID, and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprised of only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here, we show that Geobacter sulfurreducens short pAgo and the NAD+-bound Sir2-protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD+ depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD+ depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD+ to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids and underscores the diversity of mechanisms of prokaryotic Agos.
The effects of social environment and the metapleural gland on disease resistance in acorn ants
Authors: Scavetta Joseph T. , Senula Sarah F. , Crowell Daniel R. , Siddique Farzana , Segrest Jennifer F. , Dairo Olseun A. , Nguyen Lindsey U. , Pekora Mathew S. , Kruse Svjetlana Vojvodic
Published: December 2021

Eusocial species differ in living conditions when compared to solitary species primarily due to the dense living conditions of genetically related individuals. Consequently, these crowded conditions can induce a high rate of pathogen transmission and pathogen susceptibility. To resist an epidemic, individuals rely on sets of behaviors, known as social immunity, to decrease pathogen transmission among nestmates. Alongside social immunity, ants have a pair of secretory metapleural glands (MG), thought to secrete antimicrobial compounds important for antisepsis, that are believed to be transferred among nestmates by social immune behaviors such as grooming. To investigate the effects of social immunity on pathogen resistance, we performed a series of experiments by inoculating acorn ants Temnothorax curvispinosus with a lethal spore concentration of the entomopathogenic fungus Metarhizium brunneum. After inoculation ant survival was monitored in two environments: solitary and in groups. Additionally, the MG role in pathogen resistance was evaluated for both solitary and grouped living ants, by sealing the MG prior to inoculations. Individuals within a group environment had a higher survival compared to those in a solitary environment, and individuals with sealed glands had significantly decreased survival than ants with non-sealed-MG in both solitary and social environments. We observed the lowest survival for solitary-sealed-MG individuals. Although sealing the MG reduced survival probability, sealing the MG did not remove the benefits of grouped living. We show here that social living plays a crucial role in pathogen resistance and that the MG has an important role in pathogen resistance of individual T. curvispinosus ants. Although important for an individual’s pathogen resistance, our data show that the MG does not play a strong role in social immunity as previously believed. Overall, this study provides insights into mechanisms of social immunity and the role of MG in disease resistance.