bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleoside-modified mRNA-based influenza vaccines circumvent problems associated with H3N2 vaccine strain egg-adaptation
Authors: Gouma Sigrid , Parkhouse Kaela , Weirick Madison , Muramatsu Hiromi , Pardi Norbert , Fan Steven H.Y. , Weissman Drew , Hensley Scott E.
Published: July 2022

Most human influenza vaccine antigens are produced in fertilized chicken eggs. Recent H3N2 egg-based vaccine antigens have limited effectiveness, partially due to egg-adaptive substitutions that alter the antigenicity of the hemagglutinin (HA) protein. The nucleoside-modified messenger RNA encapsulated in lipid nanoparticle (mRNA-LNP) vaccine platform is a promising alternative for egg-based influenza vaccines because mRNA-LNP-derived antigens are not subject to adaptive pressures that arise during the production of antigens in chicken eggs. Here, we compared H3N2-specific antibody responses in mice vaccinated with either 3c.2A H3-encoded mRNA-LNP or a conventional egg-based Fluzone vaccine (which included an egg-adapted 3c.2A antigen) supplemented with an MF59-like adjuvant. We tested mRNA-LNP encoding wild-type and egg-adapted 3c.2A H3 antigens. We found that mRNA-LNP encoding wild-type 3c.2A H3 elicited antibodies that neutralized the wild-type 3c.2A H3N2 virus more effectively relative to antibodies elicited by mRNA-LNP encoding egg-adapted 3c2.A H3 or the egg-based Fluzone vaccine. mRNA-LNP expressing either wild-type or egg-adapted 3c2.A H3 protected mice against infection with the wild-type 3c2.A H3N2, whereas the egg-based Fluzone vaccine did not. We found that both mRNA-LNP vaccines elicited high levels of group 2 HA stalk-reactive antibodies that likely contributed to protection in vivo. Our studies indicate that nucleoside-modified mRNA-LNP-based vaccines can circumvent problems associated with egg-adaptations with recent 3c2.A H3N2 viruses.

This study shows that the nucleoside-modified messenger RNA encapsulated in lipid nanoparticle (mRNA-LNP) vaccine platform is a promising alternative for egg-based influenza vaccines. We show that mRNA-LNP expressing H3 antigens elicit high levels of antibodies in mice and protect against H3N2 influenza virus infection.
The associations of chronotype and shift work with rheumatoid arthritis
Authors: Butler TD , Maidstone RJ , Rutter MK , McLaughlin J , Ray DW , Gibbs JE
Published: July 2022

Introduction

The circadian clock regulates multiple aspects of human physiology including immunity. People have a circadian preference termed chronotype. Those with an evening preference may be better suited to shift work, but also carry higher risk of adverse health. Shift work leads to misalignment of circadian rhythms and is associated with increased risk of inflammatory disease such as asthma and cancer. Here, we investigate the association between chronotype, shift work and rheumatoid arthritis (RA).

Methods

The associations between exposures of shift work and chronotype on risk of RA were studied in up to 444,210 UK Biobank participants. Multivariate logistic regression models were adjusted for covariates including age, sex, alcohol intake, smoking history and BMI.

Results

After adjusting for covariates, individuals with a morning chronotype had lower odds of having RA (OR 0.93, 95% CI 0.88 to 0.99) when compared to intermediate chronotypes. The association between morning chronotype and lower odds of RA persisted with a more stringent RA case definition (Covariate-adjusted OR 0.89, 95% CI 0.81 to 0.97). Shift workers had a higher odds of RA (OR 1.22, 95% CI 1.1 – 1.36), that attenuated to the null after covariate adjustment.

Conclusions

These data implicate circadian rhythms in RA pathogenesis. Further studies are required to determine the mechanisms underlying this association and understand the potential impact of shift work on chronic inflammatory disease and its mediating factors.

KEY MESSAGES

What is already known about this subject?

Chronotype impacts a person’s ability to adapt to shift work, which contributes to circadian misalignment and is associated with adverse health outcomes including asthma, diabetes and cancer

What does this study add?

People with morning chronotype have a lower likelihood of RA, compared to intermediate chronotypes

Shift workers have higher likelihood of RA, compared to day workers, but this relationship may be mediated or confounded by factors such as smoking and BMI

How might this impact on clinical practice or future developments?

Chronotype is easy to assess and could be combined with other factors to determine an individual’s risk of developing RA and influence decisions about undertaking shift work

Growing evidence that common chronic inflammatory disorders are affected by circadian misalignment generates further need to investigate the impact of chronotype and shift work on immune function
Racial Disparities in Hesitancy and Utilization of Monoclonal Antibody Infusion Treatment of COVID-19
Authors: Shaikh Yahya , Gupta Ishaan , Purekal Sophia , Vaeth Mary Jane E. , Foyez Maisha , Callahan Charles D. , Elhabashy Maryam , Ficke James R. , Wu Albert W. , Auwaerter Paul G. , Kantsiper Melinda E. , Siddiqui Zishan K.
Published: July 2022

Background and Methods

We conducted a single center cross-sectional study to investigate racial disparities in the hesitancy and utilization of monoclonal antibody (mAb) treatment of COVID-19 among treatment eligible patients who were referred to the infusion center between January 4, 2021 and May 14, 2021.

Results

Among the 2,406 eligible participants, African Americans were significantly more likely to underutilize mAb treatment (OR 1.8; 95% CI 1.5-2.1) and miss treatment opportunities due to monoclonal hesitancy (OR 1.7, 95% CI 1.3-2.1).

Conclusion

Addressing racial disparities in mAb delivery is an opportunity to bridge the racial inequities in COVID-19 care.
Ecological models predict narrow potential distribution for Trioza erytreae, vector of the citrus greening disease
Authors: Godefroid Martin
Published: July 2022

The African citrus psyllid, Trioza erytreae (Hemiptera: Triozidae), is a vector of citrus greening disease (Huanglonbing - HLB) caused by the bacterium Candidatus liberibacter. Native from Africa, T. erytreae was detected in northwestern Spain in 2014, and since then it has established along Atlantic coastal areas of the Iberian Peninsula. Given the severe bio-economic impact of HLB, an accurate assessment of the risk of potential spread of African citrus psyllid to citrus-growing regions of the Mediterranean area and the rest of the world, is urgently needed to design effective control strategies and anticipate economic losses. Therefore, I calibrated species distribution models to understand the bioclimatic characteristics that shape the distribution of T. erytreae and to assess the climatic suitability of the world’s major citrus-growing regions for this species under current and future climate conditions. The models identify mild summer and winter temperatures and high levels of precipitation as optimal conditions for long-term psyllid establishment. It is noteworthy that the models trained without the available occurrences in continental Europe, predict only the Atlantic coastal regions of the Iberian Peninsula as highly climatically suitable in Europe, which corresponds perfectly with the area currently invaded by the psyllid. This striking predictive accuracy lends great credibility to the model predictions. Most economically important citrus production areas in the world are predicted to be of low or moderate climatic suitability for T. erytreae. This research is crucial for assessing the global risk of HLB and is particularly timely for Europe where the African citrus psyllid has recently been detected.
svCapture: Efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing
Authors: Wilson Thomas E. , Ahmed Samreen , Higgins Jake , Salk Jesse J. , Glover Thomas W.
Published: July 2022

Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to strategies for comparable detection of rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from cell samples with known SV properties, we demonstrate that Duplex Sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple source molecules. In contrast, tagmentation libraries coupled with data filtering based on strand family size greatly reduced both artifact classes and enabled efficient and specific detection of even single-molecule SV junctions. The throughput of SV capture sequencing (svCapture) and the high base-level accuracy of DuplexSeq provided detailed views of the microhomology profile and limited occurrence of de novo SNVs near the junctions of hundreds of sub-clonal and newly created SVs, suggesting end joining as a predominant formation mechanism. The open source svCapture pipeline enables rare SV detection as a routine addition to SNVs/indels in properly prepared capture sequencing libraries.
Drivers of polar bear behavior, and the possible effects of prey availability on foraging strategy
Authors: Togunov Ron R. , Derocher Andrew E. , Lunn Nicholas J. , Auger-Méthé Marie
Published: July 2022

1

Change in behavior is one of the earliest measurable responses to variation in habitat suitability, making the study of factors that promote behaviors particularly important in areas undergoing environmental change. We applied hidden Markov models to movement data of 14 polar bears, Ursus maritimus, from Western Hudson Bay, Canada between 2011 and 2021 during the foraging season (January–June) when bears inhabit the sea ice. The model incorporated bear movement and orientation relative to wind to classify three behaviors (stationary/drifting, area-restricted search, and olfactory search), and investigated 11 factors to identify conditions that may promote these behaviors. In contrast to other polar bear populations, we found high levels of evening activity, with active behaviors peaking around 20:00. We identified an increase in activity as the ice-covered season progressed. This apparent shift in foraging strategy from still-hunting to active search corresponds to a shift in prey availability (i.e., increase in haul-out behavior during winter to the spring pupping and molting seasons). Last, we described spatial patterns of distribution with respect to season and ice concentration that may be indicative of variation in habitat quality and segregation by bear age that may reflect competitive exclusion. Our observations were generally consistent with predictions of the marginal value theorem, and differences between our findings compared to other populations could be explained by variation in regional or temporal variation in resource abundance or distribution. Our findings and novel methodology can help identify periods, locations, and environmental conditions representing critical habitat.
Deep proteomic analysis of microglia reveals fundamental biological differences between model systems
Authors: Lloyd Amy F , Martinez-Muriana Anna , Davis Emma , Daniels Michael JD , Hou Pengfei , Mancuso Renzo , Brenes Alejandro J , Geric Ivana , Snellinx An , Craessaerts Katleen , Theys Tom , Fiers Mark , De Strooper Bart , Howden Andrew JM
Published: July 2022

Using high resolution quantitative mass spectrometry, we have generated the most comprehensive human and mouse microglia proteomic datasets to date, consisting of over 11,000 proteins across all six microglia groups. Microglia from different sources share a core protein signature of over 5600 proteins, yet fundamental differences are observed between species and culture conditions, indicating limitations for human disease modelling in mouse or inin vitrocultures of microglia. Mouseex vivomicroglia show important differences at the proteome level such as differential expression of inflammation and Alzheimer’s Disease associated proteins. We identify a tenfold difference in the protein content ofex vivoandin vitrocells and significant proteome differences associated with protein synthesis, metabolism, microglia marker expression and environmental sensors. Culturing microglia induces rapidly increased growth, protein content and inflammatory protein expression. These changes can be restored by engraftingin vitrocells into the brain, with xenografted hESC-derived microglia closely resembling microglia from human brain. This data provides an important resource for the field and highlights important considerations needed when using model systems to study human physiology and pathology of microglia.
Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
Authors: Barrera-Redondo Josué , Lotharukpong Jaruwatana Sodai , Drost Hajk-Georg , Coelho Susana M.
Published: July 2022

The emergence of new genes is an important driver of evolutionary novelty. Yet, we lack a conceptual and computational approach that accurately traces gene-family founder events and effectively associates them with trait innovation and major radiation events. Here, we present GenEra, a DIAMOND-fuelled gene-family founder inference framework that addresses previously raised limitations and biases of founder gene detection in genomic phylostratigraphy by accounting for homology detection failure (HDF). We demonstrate how GenEra can accelerate gene-family founder computations from several months to a few days for any query genome of interest. We analyzed 30 genomes to explore the emergence of new gene families during the major evolutionary transitions in plants, animals and fungi. The detection of highly conserved protein domains in these gene families indicates that neofunctionalization of preexisting protein domains is a richer source of gene-family founder events compared withde novogene birth. We report vastly different patterns of gene-family founder events in animal and fungi before and after accounting for HDF. Only plants exhibit a consistent pattern of founder gene emergence after accounting for HDF, suggesting they are more likely to evolve novelty through the emergence of new genes compared to opisthokonts. Finally, we show that gene-family founder bursts are associated with the transition to multicellularity in streptophytes, the terrestrialization of land plants and the origin of angiosperms, as well as with the evolution of bilateral symmetry in animals.
Annexin A2 modulates phospholipid membrane composition upstream of Arp2 to control angiogenic sprout initiation
Authors: Sveeggen Timothy M. , Abbey Colette A. , Smith Rebecca L. , Bayless Kayla J.
Published: July 2022

The intersection of protein and lipid biology is of growing importance for understanding how cells address structural challenges during adhesion and migration. While protein complexes engaged with the cytoskeleton play a vital role, support from the phospholipid membrane is crucial for directing localization and assembly of key protein complexes. During angiogenesis, it is well observed that dramatic cellular remodeling is necessary for endothelial cells to shift from a stable monolayer to invasive structures. However, the molecular dynamics between lipids and proteins during endothelial invasion are not defined. Here, we utilized cell culture, immunofluorescence, and lipidomic analyses to identify a novel role for the membrane binding protein Annexin A2 (ANXA2) in modulating the composition of specific membrane lipids necessary for cortical F-actin organization and adherens junction stabilization. In the absence of ANXA2, there is disorganized cortical F-actin, reduced junctional Arp2, excess sprout initiation, and ultimately failed sprout maturation. Further, we observed reduced filipin III labeling of membrane cholesterol in cells with reduced ANXA2, suggesting there is an alteration in phospholipid membrane dynamics. Lipidomic analyses reveal that 42 lipid species are altered with loss of ANXA2, including an accumulation of phosphatidylcholine (16:0_16:0). We find that supplementation of phosphatidylcholine (16:0_16:0) in wild-type endothelial cells mimics the ANXA2 knock-down phenotype, indicating that ANXA2 regulates the phospholipid membrane upstream of Arp2 recruitment and organization of cortical F-actin. Altogether these data indicate a novel role for ANXA2, and show that proper lipid modulation is a critical component of endothelial sprouting.

Summary Statement

Annexin A2 modulates composition of select phospholipid species in endothelial cells needed for F-actin organization and Arp2 recruitment to endothelial adherens junctions. These events simultaneously temper sprout initiation and support sprout maturation to maintain the integrity of sprouting structures during angiogenesis
Multimodal Prediction of Breast Cancer Recurrence Assays and Risk of Recurrence
Authors: Howard Frederick M. , Dolezal James , Kochanny Sara , Khramtsova Galina , Vickery Jasmine , Srisuwananukorn Andrew , Woodard Anna , Chen Nan , Nanda Rita , Perou Charles M. , Olopade Olufunmilayo I. , Huo Dezheng , Pearson Alexander T.
Published: July 2022

Gene expression-based recurrence assays are strongly recommended to guide the use of chemotherapy in hormone receptor-positive, HER2-negative breast cancer, but such testing is expensive, can contribute to delays in care, and may not be available in low-resource settings. Here, we describe the training and independent validation of a deep learning model that predicts recurrence assay result and risk of recurrence using both digital histology and clinical risk factors. We demonstrate that this approach outperforms an established clinical nomogram (area under the receiver operating characteristic curve of 0.833 versus 0.765 in an external validation cohort, p = 0.003), and can identify a subset of patients with excellent prognoses who may not need further genomic testing.
Machine learning analysis reveals the dynamics of mode transition in dendritic cell migration
Authors: Song Taegeun , Choi Youngjun , Jeon Jae-Hyung , Cho Yoon-Kyoung
Published: July 2022

Dendritic cells (DCs) patrol the body as immunological sentinels and search for pathogens. Upon stimulation, immature DCs (imDCs) become mature DCs (mDCs), which migrate to the lymph nodes and present antigens to T cells. The migratory behavior is crucial for initiating and controlling immune responses; however, the properties of the highly heterogeneous and dynamic motility phenotype are not fully understood. Here, we established an unsupervised machine learning (ML) strategy to investigate spatiotemporal motility patterns in long-term, two-dimensional cell migration trajectories, and determined the number of motility patterns and how these are related to the maturation status. We identified three distinct migratory modes independent of the cell state: slow-diffusive (SD), slow-persistent (SP), and fast-persistent (FP). We found that maturation-dependent motility changes are emergent properties of the distribution and dynamic transitions of these three modes. Remarkably, imDCs changed their migration modes more frequently, and predominantly followed the SD→FP→SP→SD unicyclic transition, indicating that imDCs rapidly increase their speed during the shift from diffusive to persistent motility; however, persistence progressively declines when switching back to diffusive motility. In contrast, mDCs show no transition directionality. Our ML-promoted motility pattern analysis and history-dependent mode transition investigation may provide new insights into the complex process of biological motility.
Putting the F in FBD analyses: tree constraints or morphological data ?
Authors: Barido-Sottani Joëlle , Pohle Alexander , De Baets Kenneth , Murdock Duncan , Warnock Rachel C. M.
Published: July 2022

1

The fossilized birth-death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils (with or without character data) are directly considered as part of the tree. This leads to a statistically coherent prior on divergence times, where the variance associated with node ages reflects uncertainty in the placement of fossil taxa in the phylogeny. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. Previously, this information has been provided in two different forms: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or so-called total-evidence analyses, which use a morphological data matrix with data for both fossil and extant specimens in addition to the molecular alignment. In this work, we use simulations to evaluate these different approaches to handling fossil placement in FBD analyses, both in ideal conditions and in datasets including uncertainty or even errors. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. These results are consistent with expectations: in FBD inferences, divergence times are mostly informed by fossil ages, so variations in the position of fossils strongly impact these estimates. On the other hand, the placement of extant taxa in the phylogeny is driven primarily by the molecular alignment. We see similar patterns in datasets which include rate variation, however one notable difference is that relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non-FBD (i.e., non-time calibrated) inference. This result holds even with the use of erroneous fossil constraints and model misspecification under the FBD. Overall, our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process.
Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS
Authors: Hatano Yuya , Ishihara Tomohiko , Onodera Osamu
Published: July 2022

Background

In the sporadic form of amyotrophic lateral sclerosis (ALS), the pathogenicity of rare variants in the causative genes characterizing the familial form remains largely unknown. To predict the pathogenicity of such variants, in silico analysis is commonly used. In some cases of ALS, the gene mutations are concentrated in specific regions, and the resulting alterations in protein structure are thought to significantly affect pathogenicity. However, existing methods have not taken this issue into account. To address this, we have developed a technique termed MOVA (method for evaluating the pathogenicity of missense variants using AlphaFold2), which applies positional information for structural variants predicted by AlphaFold2. Here we examined the utility of MOVA for analysis of several causative genes of ALS.

Methods

We analyzed variants of six ALS-related genes (TARDBP, FUS, SETX, TBK1, OPTN, and SOD1) and classified them as pathogenic or neutral. For each gene, the features of the variants, including their positions in the 3D structure predicted by AlphaFold2, were entered into a random forest algorithm and evaluated by leave-one-out cross-validation. We compared how accurately MOVA was able to classify the pathogenic and neutral mutation variants.

Results

MOVA yielded useful results (AUC ≥0.70 for 3 (TARDBP 0.755, FUS 0.844, and SOD1 0.787) of the 6 genes) and was particularly useful for genes where pathogenic mutations were concentrated at specific sites (TARDBP, FUS).

Conclusions

MOVA is useful for predicting the virulence of rare variants of ALS-causing genes in which mutations are concentrated at specific structural sites.
Modulating the proliferative and cytotoxic properties of human TIL by a synthetic immune niche of immobilized CCL21 and ICAM1
Authors: Yunger Sharon , Geiger Benjamin , Friedman Nir , Besser Michal J , Adutler-Lieber Shimrit
Published: July 2022

The major challenge in developing an effective adoptive cancer immunotherapy, is theex-vivogeneration of tumor-reactive cells, in sufficient numbers and with enhanced cytotoxic potential. It was recently demonstrated, that culturing of activated murine CD8+ T-cells on a “Synthetic Immune Niche” (SIN), consisting of immobilized CCL21 and ICAM-1, enhances T-cell expansion, increases cytotoxicity against cultured cancer cells and suppresses tumor growthin vivo[1, 2]. In the study reported here, we have tested the effect of the CCL21+ICAM1 SIN, on the expansion and cytotoxic phenotype of Tumor Infiltrating Lymphocytes (TIL), following activation with immobilized anti-CD3/CD28 stimulation, or commercial activation beads. The majority of TIL tested, displayed higher expansion when cultured on the coated SIN compared to cells incubated on uncoated substrate. Comparable enhancement of TIL proliferation was obtained by the CCL21+ICAM1 SIN, in a clinical setting that includes a 14-day rapid expansion procedure (REP), initiated with feeder cells, anti CD3 and IL-2. Co-incubation of post-REP TIL with matching target cancerous cells, demonstrated increased IFNγ secretion beyond baseline in most of the TILs and a significant increase in granzyme B levels following activation on SIN. The SIN did not significantly alter the relative frequency of CD8/CD4 populations, as well as the expression of CD28, CD25 and several exhaustion markers. These results demonstrate the potential capacity of the CCL21+ICAM1 SIN to reinforce TIL-based immunotherapy.
Antibody-mediated prevention of vaginal HIV transmission is dictated by IgG subclass in humanized mice
Authors: Brady Jacqueline M. , Phelps Meredith , MacDonald Scott W. , Lam Evan C. , Nitido Adam , Parsons Dylan , Boutros Christine L. , Deal Cailin E. , Tanno Serah , Natarajan Harini , Ackerman Margaret E. , Vrbanac Vladimir D. , Balazs Alejandro B.
Published: July 2022

HIV broadly neutralizing antibodies (bNAbs) are capable of both blocking viral entry and recruiting innate immunity to HIV-infected cells through their fragment crystallizable (Fc) region. Vaccination or productive infection results in a polyclonal mixture of class-switched IgG antibodies comprised of four subclasses, each encoding distinct Fc regions that differentially engage innate immune functions. Despite evidence that innate immunity contributes to protection, the relative contribution of individual IgG subclasses is unknown. Here we use vectored immunoprophylaxis (VIP) in humanized mice to interrogate the efficacy of individual IgG subclasses during prevention of vaginal HIV transmission by VRC07, a potent CD4-binding site directed bNAb. We find that VRC07-IgG2, which lacks Fc-mediated functionality, exhibits significantly reduced protection in vivo relative to other subclasses. However, even low concentrations of highly functional VRC07-IgG1 yields substantial protection against vaginal challenge, suggesting that interventions capable of eliciting modest titers of functional subclasses may provide meaningful benefit against infection.
Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD
Authors: Gauto Diego F. , Lebedenko Olga O. , Becker Lea Marie , Ayala Isabel , Lichtenecker Roman , Skrynnikov Nikolai R. , Schanda Paul
Published: July 2022

Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear are remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 is broadened in all crystals, presumably due to μs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
Growth of brown trout in the wild predicted by embryo stress reaction in the laboratory
Authors: Bylemans Jonas , Marques da Cunha Lucas , Wilkins Laetitia G. E. , Nusbaumer David , Uppal Anshu , Wedekind Claus
Published: July 2022

Laboratory studies on embryos of salmonids, such as the brown trout (Salmo trutta), have been extensively used to study environmental stress and how responses vary within and between natural populations. These studies are based on the implicit assumption that early life-history traits are relevant for stress tolerance in the wild. Here we test this assumption by combining two datasets from studies on the same 60 full-sib families. These families had been experimentally produced from wild breeders to determine, in separate samples, (i) stress tolerances of singly kept embryos in the laboratory and (ii) growth of juveniles during 6 months in the wild. We found that growth in the wild was well predicted by larval size of their full sibs in the laboratory, especially if these siblings had been experimentally exposed to a pathogen. Exposure to the pathogen had not caused elevated mortality among the embryos but induced early hatching. The strength of this stress-induced change of life history was a significant predictor of juvenile growth in the wild: the stronger the response in the laboratory, the slower the growth in the wild. We conclude that embryo performance in controlled environments can be useful predictors of juvenile performance in the wild.
An amino-terminal fragment of apolipoprotein E4 leads to behavioral deficits, increased PHF-1 immunoreactivity, and mortality in zebrafish
Authors: McCarthy Madyson M. , Hardy Makenna J. , Leising Saylor E. , LaFollette Alex , Stewart Erica S. , Cogan Amelia S. , Sanghal Tanya , Matteo Katie , Oxford Julia T.T. , Rohn Troy T.
Published: July 2022

Although the increased risk of developing sporadic Alzheimer’s disease (AD) associated with the inheritance of the apolipoprotein E4 (APOE4) allele is well characterized, the molecular underpinnings of how ApoE4 imparts risk remains unknown. Enhanced proteolysis of the ApoE4 protein with a toxic-gain of function has been suggested and a 17 kDa amino-terminal ApoE4 fragment (nApoE41-151) has been identified in post-mortem human AD frontal cortex sections. Recently, we demonstrated in vitro, exogenous treatment of nApoE41-151 in BV2 microglial cells leads to uptake, trafficking to the nucleus and increased expression of genes associated with cell toxicity and inflammation. In the present study, we extend these findings to zebrafish (Danio rerio), which is an emerging in vivo model system to study AD. Exogenous treatment of nApoE41-151 to 24-hour post-fertilization for 24 hours resulted in significant mortality. In addition, developmental abnormalities were observed following treatment with nApoE41-151 including improper folding of the hindbrain, delay in ear development, deformed yolk sac, enlarged cardiac cavity, and significantly lower heart rates. Decreased presence of pigmentation was noted for nApoE41-151 treated fish compared with controls. Behaviorally, touch-evoked responses to stimulus were negatively impacted by treatment with nApoE41-151. A similar nApoE31-151 fragment that differs by a single amino acid change (C>R) at position 112 had no effects on these parameters under identical treatment conditions. Additionally, triple-labeling confocal microscopy not only confirmed the nuclear localization of the nApoE41-151 fragment within neuronal populations following exogenous treatment, but also identified the presence of tau pathology, one of the hallmark features of AD. Collectively, these in vivo data demonstrating toxicity as well as sublethal effects on organ and tissue development support a novel pathophysiological function of this AD associated-risk factor.
Genetic diversity in global populations of the Critically Endangered addax (Addax nasomaculatus) and its implications for conservation
Authors: Dicks Kara L , Ball Alex D , Banfield Lisa , Barrios Violeta , Boufaroua Mohamed , Chetoui Abdelkader , Chuven Justin , Craig Mark , Al Faqeer Mohammed Yousef , Mallam Garba Hamissou Halilou , Guedara Hela , Harouna Abdoulaye , Ivy Jamie , Najjar Chawki , Petretto Marie , Pusey Ricardo , Rabeil Thomas , Riordan Philip , Senn Helen V , Taghouti Ezzedine , Wacher Tim , Woodfine Tim , Gilbert Tania
Published: July 2022

Threatened species are frequently patchily distributed across small wild populations,ex situpopulations managed with varying levels of intensity, and reintroduced populations. Best practice advocates for integrated management acrossin situandex situpopulations. Wild addax (Addax nasomaculatus) now number fewer than 100 individuals, yet thousands of addax remain inex situpopulations, which can provide addax for reintroductions, as has been the case in Tunisia in the mid-1980s. However, integrated management requires genetic data to ascertain the relationships between wild andex situpopulations that have incomplete knowledge of founder origins, management histories and pedigrees. We undertook a global assessment of genetic diversity across wild,ex situ, and reintroduced populations in Tunisia to assist conservation planning for this Critically Endangered species. We show that the remnant wild populations retain more mitochondrial haplotypes which are more evolutionarily diverse than the entirety of theex situpopulations across Europe, North America and the United Arab Emirates, and the reintroduced Tunisian population. Additionally, 1704 SNPs revealed that whilst population structure within theex situpopulation is minimal, each population carries unique diversity. Finally, we show that careful selection of founders and subsequent genetic management is vital to ensure genetic diversity is provided to, and minimise drift and inbreeding within, reintroductions. Our results highlight a vital need to conserve the last remaining wild addax population, and we provide a genetic foundation for determining integrated conservation strategies to prevent extinction and optimise future reintroductions.
Experimental introgression inDrosophila: asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome
Authors: Poikela N. , Laetsch D. R. , Kankare M. , Hoikkala A. , Lohse K.
Published: July 2022

Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatricDrosophila virilisgroup species,D. flavomontanaandD. montana. We backcrossed F1hybrid females from a cross betweenD. flavomontanafemale andD. montanamale with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal 2ndgeneration backcross (BC2mon and BC2fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC2female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC2mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towardsD. montana. In contrast, the BC2fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). This observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.
lncRNA H19/Let7b/EZH2 axis regulates somatic cell senescence
Authors: Potnis Manali , Do Justin , Naggar Olivia El , Noguchi Eishi , Sell Christian
Published: July 2022

Long non-coding RNAs (lncRNAs) regulate diverse cellular processes and are associated with many age-associated diseases. However, the function of lncRNAs in cellular senescence remains largely unknown. Here we characterize the role of lncRNA H19 in senescence. We show that H19 levels decline as cells undergo senescence, and depletion of H19 results in premature senescence. We find that repression of H19 is triggered by the loss of CTCF and prolonged activation of p53 as part of the senescence pathway. Mechanistically, the loss of H19 drives senescence via increased let7b mediated targeting of EZH2. We further demonstrate that H19 is required for senescence inhibition by the mTOR inhibitor rapamycin, where it maintains lncRNA H19 levels throughout the cellular lifespan and thus prevents the reduction of EZH2 that would otherwise lead to cellular senescence. Therefore, lncRNA H19 is crucial in maintaining the balance between sustained cell growth and the onset of senescence.
Demographic variation and demographic niches of trees species in the Barro Colorado Forest
Authors: Condit Richard , Rüger Nadja
Published: July 2022

One goal for the 50-ha plot on Barro Colorado Island since its inception has been to understand demographic variability across the entire community of tree species. Early papers classified demographic response of many species to canopy gaps, culminating over the last decade with improved statistical methods that could quantify the response of growth, survival, and recruitment rates to increasing light for the entire community. We compile results from recent studies to illustrate the demographic trade-off between fast growth in high light and long life in deep shade. Growth and recruitment in high light are significantly correlated with mortality across species, and this trade-off is the primary demographic differentiation in the community. Here we add a new analysis of expected adult lifespan of 31 dominant canopy species spanning the growth-mortality axis. Using analytical solutions to matrices describing the lifetable, we demonstrate that the trade-off between high growth and long lifespan is not equalizing. The expected adult lifespan of a newly-recruited sapling is shorter in fast-growing pioneers than in long-lived shade-tolerant species: elevated growth rates of pioneers is insufficient to overcome their high death rates. If reproductive output were equal across the demographic axis, pioneer species could not persist. This suggests pioneers out-reproduce shade-tolerant species. The next goal is incorporating seed and seedling production into the demographic analysis to test the trade-off using lifetables having reproductive output included.
Integrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction
Authors: Zhu Yi-Heng , Zhang Chengxin , Yu Dong-Jun , Zhang Yang
Published: July 2022

Accurate identification of protein function is critical to elucidate life mechanism and design new drugs. We proposed a novel deep-learning method, ATGO, to predict Gene Ontology (GO) attributes of proteins through a triplet neural-network architecture embedded with pre-trained self-attention transformer models. The method was systematically tested on 1068 non-redundant benchmarking proteins and 3328 targets from the third Critical Assessment of Protein Function Annotation (CAFA) challenge. Experimental results showed that ATGO achieved a significant increase of the GO prediction accuracy compared to the state-of-the-art approaches in all aspects of molecular function, biological process, and cellular component. Detailed data analyses showed that the major advantage of ATGO lies in the utilization of attention transformer models which can extract discriminative functional pattern from the feature embeddings. Meanwhile, the proposed triplet network helps enhance the association of functional similarity with feature similarity in the sequence embedding space. In addition, it was found that the combination of the network scores with the complementary homology-based inferences could further improve the accuracy and coverage of the predicted models. These results demonstrated a new avenue for high-accuracy deep-learning function prediction that is applicable to large-scale protein function annotations from sequence alone.

Availability

The benchmark dataset, standalone package, and online server for ATGO are available at https://zhanggroup.org/ATGO/.

Author Summary

In the post-genome sequencing era, a major challenge in computational molecular biology is to annotate the biological functions of all gene and gene products, which have been classified, in the context of the widely used Gene Ontology (GO), into three aspects of molecular function, biological process, and cellular component. In this work, we proposed a new open-source deep-learning architecture, ATGO, to deduce GO terms of proteins from the primary amino acid sequence, through the integration of the triplet neural-network with attention transformer models. Large benchmark tests showed that, when powered with a pre-trained self-attention transformer model, ATGO achieved a significantly improved performance than other state-of-the-art approaches in all the GO aspect predictions. Following the rapid progress of self-attention neural network techniques, which have demonstrated remarkable impacts on language processing and multi-sensory data process, and most recently on protein structure prediction, this study showed the significant potential of attention transformer models on protein function annotations.
The inceptionist’s guide to base editing – de novo PAM generation to reach initially inaccessible target-sites
Authors: Pakari Kaisa , Wittbrodt Joachim , Thumberger Thomas
Published: July 2022

Base editing by CRISPR crucially depends on the presence of a PAM in proper distance to the editing-site. Here we present and validate an efficient one-shot approach termed “inception”, relaxing these constraints. This is achieved by sequential, combinatorial base editing: de novo generated synonymous, non-synonymous or intronic PAM-sites facilitate subsequent base editing at nucleotide positions inaccessible before, increasing the targeting range of highly precise editing approaches.
The thermodynamic state of aerobic glycolytic flux plays a critical role in stabilizing aerobic glycolytic flux of cancer cells
Authors: Jin Chengmeng , Hu Wei , Wang Yuqi , Wu Hao , Zeng Siying , Ying Minfeng , Hu Xun
Published: July 2022

Inhibition of aerobic glycolysis (AG) is a strategy for cancer treatment, but its clinical translation has not been successful, suggesting that the mechanism underlying the inhibition of AG is not completely understood. We introduce thermodynamic state of AG (TSAG) into AG flux control, which refers the actual change of Gibbs free energy (ΔG) of reactions along the pathway. By using PKM2 knockdown and knockout models, we found that TSAG is resistant to PKM2 perturbation and it can effectively counteract the inhibitory effect of PKM2 perturbation on AG flux. Moreover, we deciphered the interrelationship between TSAG, AG rate, intermediate concentrations, and PK activity, revealed that TSAG is a system property of AG independent of cancer cells’ pathophysiological features and it plays important roles in stabilizing AG flux responding to perturbation. We propose that both inhibition of glycolytic enzyme and disruption of TSAG are required for effective AG inhibition.
Rescue of alveolar wall liquid secretion blocks fatal lung injury by influenza-staphylococcal coinfection
Authors: Tang Stephanie , De Jesus Ana Cassandra , Chavez Deebly , Suthakaran Sayahi , Moore Sarah K. L. , Rathnasinghe Raveen , Schotsaert Michael , Bhattacharya Jahar , Hook Jaime L.
Published: July 2022

Secondary lung infection by inhaled Staphylococcus aureus (SA) is a common and lethal event in individuals infected with influenza A virus (IAV). It is unclear how IAV disrupts host defense to promote SA infection in lung alveoli, where fatal lung injury occurs. We addressed this issue using the first real-time determinations of alveolar responses to IAV in live, intact, perfused lungs. Our findings show IAV infection blocked defensive alveolar wall liquid (AWL) secretion and induced airspace liquid absorption, thereby reversing normal alveolar liquid dynamics and inhibiting alveolar clearance of inhaled bacteria. Loss of AWL secretion resulted from dephosphorylation, hence inhibition of the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel in alveolar epithelium, and airspace liquid absorption was caused by alveolar epithelial stimulation of the epithelial Na+ channel (ENaC). Loss of AWL secretion promoted alveolar stabilization by SA and alveolar damage by the secreted SA toxin, alpha hemolysin, but rescue of AWL secretion protected against fatal SA-induced lung injury in IAV-infected mice. These findings reveal a central role for AWL secretion in alveolar defense against inhaled bacteria and identify AWL inhibition as a critical mechanism of IAV lung pathogenesis. AWL rescue may represent a new therapeutic approach for IAV-SA coinfection.

GRAPHICAL ABSTRACT
Age-associated changes in knee osteoarthritis, pain-related behaviors, and dorsal root ganglia immunophenotyping of male and female mice
Authors: Geraghty Terese , Obeidat Alia M. , Ishihara Shingo , Wood Matthew J. , Li Jun , Lopes Erika Barboza Prado , Scanzello Carla R. , Griffin Timothy M. , Malfait Anne-Marie , Miller Rachel E.
Published: July 2022

Objective

Osteoarthritis (OA) is a leading cause of chronic pain, yet OA pain management remains poor. Age is the strongest predictor of OA development, and mechanisms driving OA pain are unclear. While injury-induced OA models are useful, only a subset of OA is linked to traumatic injury. Here, we aimed to characterize age-associated joint damage, mechanical sensitization, and dorsal root ganglia (DRG) immune phenotypes in mice of both sexes.

Methods

Male or female mice aged 6- or 20-months old were evaluated for histopathologic knee OA, pain-related behaviors, and L3-L5 dorsal root ganglia (DRG) immune characterization via flow cytometry. DRG gene expression in aged mice and humans was also examined.

Results

Twenty-month old male mice had worse cartilage degeneration than 6-month old mice. Older female knees showed increased cartilage degeneration, but to a lesser degree than males. Older mice of both sexes had worse mechanical allodynia, knee hyperalgesia, and grip strength compared to younger mice. For both sexes, DRGs from older mice showed decreased CD45+ cells, and a significant increase in F4/80+ macrophages and CD11c+ dendritic cells. Older male DRGs showed increased expression of Ccl2 and Ccl5 and older female DRGs showed increased Cxcr4 and Ccl3 compared to 6-month DRGs, among other differentially expresssed genes. Human DRG analysis from six individuals >80 years old revealed elevated CCL2 in male DRGs compared to females, whereas CCL3 was higher in female DRGs.

Conclusions

Here we show that aging in male and female mice is accompanied by mild knee OA, mechanical sensitization, and changes to immune cell populations in the DRG, suggesting novel avenues for development of analgesic therapies.