bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthetic whole-slide image tile generation with gene expression profiles infused deep generative models
Authors: Carrillo-Perez Francisco , Pizurica Marija , Ozawa Michael G. , Vogel Hannes , West Robert B. , Kong Christina S. , Herrera Luis Javier , Shen Jeanne , Gevaert Olivier
Published: December 2022

The acquisition of multi-modal biological data for the same sample, such as RNA sequencing and whole slide imaging (WSI), has increased in recent years, enabling studying human biology from multiple angles. However, despite these emerging multi-modal efforts, for the majority of studies only one modality is typically available, mostly due to financial or logistical constraints. Given these difficulties, multi-modal data imputation and multi-modal synthetic data generation are appealing as a solution for the multi-modal data scarcity problem. Currently, most studies focus on generating a single modality (e.g. WSI), without leveraging the information provided by additional data modalities (e.g. gene expression profiles). In this work, we propose an approach to generate WSI tiles by using deep generative models infused with matched gene expression profiles. First, we train a variational autoencoder (VAE) that learns a latent, lower dimensional representation of multi-tissue gene expression profiles. Then, we use this representation to infuse generative adversarial networks (GAN) that generate lung and brain cortex tissue tiles, resulting in a new model that we call RNA-GAN. Tiles generated by RNA-GAN were preferred by expert pathologists in comparison to tiles generated using traditional GANs and in addition, RNA-GAN needs fewer training epochs to generate high-quality tiles. Finally, RNA-GAN was able to generalize to gene expression profiles outside of the training set, showing imputation capabilities. A web-based quiz is available for users to play a game distinguishing real and synthetic tiles:https://rna-gan.stanford.edu/and the code for RNA-GAN is available here:https://github.com/gevaertlab/RNA-GAN.
Evolution of seasonal plasticity in response to climate change differs between life-stages of a butterfly
Authors: Nielsen Matthew E. , Nylin Sören , Wiklund Christer , Gotthard Karl
Published: December 2022

Climate change alters seasonal environments without altering photoperiod, creating a cue-environment mismatch for organisms that rely on photoperiod as a cue for seasonal plasticity and phenology. Evolution can potentially correct for this mismatch by altering the photoperiodic reaction norm, but often phenology depends on multiple plastic decisions made at different life stages and times of year. We tested whether seasonal plasticity in different life stages evolves independently or in concert under climate change usingPararge aegeria(Speckled wood butterfly). This butterfly uses day length as a cue for life history plasticity in two different life stages: larval development time and pupal diapause. Photoperiodic reaction norms for plasticity in these traits were first measured over 30 years ago for two different Swedish populations. In this study, we replicated historic experiments that measured these reaction norms using the contemporary populations. We found evidence for evolution of the reaction norm for larval development time, but in opposite directions in the two populations. In contrast, we found no evidence for evolution of the reaction norm for pupal diapause. These results show that different life stages can evolve differently in response to climate change and only studying one part of the life cycle will not always be enough to fully understand how climate change impacts phenotypic plasticity and phenology.
Machine learning prediction of cancer cell metabolism from autofluorescence lifetime images
Authors: Hu Linghao , Wang Nianchao , Bryant Joshua D , Liu Lin , Xie Linglin , West A Phillip , Walsh Alex J.
Published: December 2022

Metabolic reprogramming at a cellular level contributes to many diseases including cancer, yet few assays are capable of measuring metabolic pathway usage by individual cells within living samples. Here, we combine autofluorescence lifetime imaging with single-cell segmentation and machine-learning models to predict the metabolic pathway usage of cancer cells. The metabolic activities of MCF7 breast cancer cells and HepG2 liver cancer cells were controlled by growing the cells in culture media with specific substrates and metabolic inhibitors. Fluorescence lifetime images of two endogenous metabolic coenzymes, reduced nicotinamide adenine dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD), were acquired by a multi-photon fluorescence lifetime microscope and analyzed at the cellular level. Quantitative changes of NADH and FAD lifetime components were observed for cells using glycolysis, oxidative phosphorylation, and glutaminolysis. Conventional machine learning models trained with the autofluorescence features classified cells as dependent on glycolytic or oxidative metabolism with 90 – 92% accuracy. Furthermore, adapting convolutional neural networks to predict cancer cell metabolic perturbations from the autofluorescence lifetime images provided improved performance, 95% accuracy, over traditional models trained via extracted features. In summary, autofluorescence lifetime imaging combined with machine learning models can detect metabolic perturbations between glycolysis and oxidative metabolism of living samples at a cellular level, providing a label-free technology to study cellular metabolism and metabolic heterogeneity.
Parallels and divergences in landscape genetic and metacommunity patterns in zooplankton inhabiting soda pans
Authors: Horváth Zsófia , Haileselasie Tsegazeabe Hadush , Vad Csaba F. , Ptacnik Robert , Meester Luc De
Published: December 2022

Ecological processes maintaining landscape genetic variation and metacommunity structure in natural landscapes have traditionally been studied in isolation. Their integrated study may hold important information as to what extent the effect of major ecological processes are species-or landscape-specific, resulting in a more coherent picture on the spatial organization of biodiversity. Here, we explicitly compared the relative importance of spatial and environmental drivers of both cladoceran metacommunity structure as well as landscape genetic structure of its most widespread member, the water fleaDaphnia magna, in soda pans of the Seewinkel region in Austria. This landscape of soda pans is characterized by strong environmental gradients and unidirectional wind acting as a key dispersal agent among these temporary habitats. Our study shows both parallels and divergences in the relative importance of local environmental sorting and spatial connectivity in determining landscape genetic versus metacommunity structure. The metacommunity is structured primarily by the environment, while in theD. magnametapopulation, the spatial signal is predominant. The much weaker environmental signal inDaphniacan be explained by the fact that the microsatellite markers are presumably neutral and was confirmed by a per-allele analysis. An important parallel between metacommunity and landscape genetic structure is the strong signal of the prevailing wind direction in determining the spatial pattern. This suggests that for both community assembly in cladocerans and population assembly inD. magna, wind plays an important role in determining connectivity among soda pans, thereby affecting dispersal and colonization rates, influencing both local species and genetic composition.
Genetic basis and selection of glyceollin induction in wild soybean
Authors: Yasmin Farida , Zhang Hengyou , Leamy Larry , Wang Baosheng , Winnike Jason , Reid Robert W. , Brouwer Cory R. , Song Bao-Hua
Published: December 2022

Glyceollins, a family of phytoalexin induced in legume species, play essential roles in responding to environmental stresses and in human health. However, little is known about the genetic basis and selection of glyceollin induction.

We employed a metabolite-based genome-wide association (mGWA) approach to identify candidate genes involved in glyceollin induction from genetically diverse and understudied wild soybeans subjected to soybean cyst nematode stress.

Eight SNPs on chromosomes 3, 9, 13, 15, and 20 showed significant association with glyceollin induction. Six genes close to one of the significant SNPs (ss715603454) on chromosome 9 fell into two clusters, and they encode enzymes in the glycosyltransferase class within the phenylpropanoid pathway. Transcription factors (TFs) genes, such asMYBandWRKYwere also found within the linkage disequilibrium of the significant SNPs on chromosome 9. Epistasis and a strong selection signal were detected on the four significant SNPs on chromosome 9.

Gene clusters and transcription factors may play important roles in regulating glyceollin induction in wild soybeans. Additionally, as major evolutionary factors, epistatic interactions and selection may influence glyceollin variation in natural populations.
The pan-genome and local adaptation ofArabidopsis thaliana
Authors: Kang Minghui , Wu Haolin , Liu Wenyu , Zhu Mingjia , Han Yu , Liu Wei , Chen Chunlin , Yin Kangqun , Zhao Yusen , Yan Zhen , Liu Huanhuan , Lou Shangling , Zan Yanjun , Liu Jianquan
Published: December 2022

Arabidopsis thalianahas been used as a model species for research in a diverse collection of plant species. However, previous studies based on single reference genomes and short-read sequencing data are restricted to detecting variable genes and large structural variation (SV) underlying local adaptation. Here wede novoassemble high-quality chromosomal genomes of 38A. thalianaecotypes (with 6 relict ones) using PacBio-HiFi long-read sequencing. From these newly assembled genomes, we annotate several thousand new genes through pan-genomic analysis in comparison to the previous reference genome. The identified variable genes are mainly enriched in and associated with ecological adaptation and this species substantially expands its gene repertoire for local adaptation. We construct a graph-based pan-genome and identify 62,525 SVs which overlap with 14,243 genes. These genes are enriched in multiple ecological adaptation functions, including secondary metabolic processes, enzyme regulation, and biotic/abiotic stimulus. For example, a 566 bp insertion in the promoter of the light-adaptationKNAT3gene was specific to the high-altitude relict Tibet-0 ecotype. This SV reduces the expression level ofKNAT3and promotesA. thalianaadaptation to habitats high in light radiation. In addition, compared with the SNPs, the SVs identified in this study captured the missing heritability and we detected novel SV associations with environmental variables in their native range, highlighting the value of SVs in environmental adaptation. The genome resources presented here will help pinpoint genetic changes that include both SVs and the ecotype-specific genes for local adaptation ofA. thalianaand increase our understanding of the molecular mechanisms in this model species to respond to varied habitats.
Regulatory changes associated with the head to trunk developmental transition
Authors: Duarte Patrícia , Correia Rion Brattig , Nóvoa Ana , Mallo Moisés
Published: December 2022

Development of vertebrate embryos is characterized by early formation of the anterior tissues followed by the sequential extension of the axis at their posterior end to build the trunk and tail structures, first by the activity of the primitive streak and then of the tail bud. Embryological, molecular and genetic data demonstrate that head and trunk development are significantly different, indicating that the transition into the trunk formation stage involves changes in regulatory gene networks, that might include the acquisition of cell competence to respond to key regulatory factors. Herein, we explored the regulatory changes involved in this developmental transition by assessing the transcriptome and chromatin accessibility profiles from the posterior epiblast region of mouse embryos at embryonic day (E)7.5 and E8.5. We observed changes in various cell processes, including signaling pathways, ubiquitination, ion dynamics and metabolic processes involving lipids that could contribute to the functional switch in the progenitor region of the embryo. Our data also led to the identification of novel mechanisms controlling the differential Wnt functional requirements during head and trunk development. Moreover, we found substantial changes in chromatin accessibility mostly mapping to intergenic regions, indicating a significant switch in the regulatory elements controlling either head or trunk development. In addition, we tested the functional relevance of potential enhancers ofWnt5aandNr2f2, identified in the accessibility assays, that reproduced the expression profiles of the target genes. Deletion of these regions by genome editing had limited effect on the expression of those genes, suggesting the existence of redundant enhancers that guarantee robust expression patterns. Overall, this study provides new insights on the regulatory mechanisms that change during the transition from head to trunk development.

Author Summary

Vertebrate main body axis is generated sequentially from head to tail. The developmental processes building head and trunk structures are significantly different, and the transition between these two stages requires substantial changes in functional gene regulatory networks. Herein, we explored such changes through genome wide analyses in developing mouse embryos. We observed significant differences in several signaling pathways and in the basic cell machinery, which may interact promoting a functional switch in the differentiating progenitor cells. We also found substantial changes in the accessibility of regulatory elements controlling either head or trunk formation, which conditioned the binding activity of key developmental transcription factors. Overall, our study gives relevant insights into the mechanisms regulating the head to trunk transition that, if disrupted, can lead to embryonic developmental arrest.
Polygenic Parkinson’s disease genetic risk score as risk modifier of parkinsonism in Gaucher disease
Authors: Blauwendraat Cornelis , Tayebi Nahid , Woo Elizabeth Geena , Lopez Grisel , Fierro Luca , Toffoli Marco , Limbachiya Naomi , Hughes Derralynn , Pitz Vanessa , Patel Dhairya , Vitale Dan , Koretsky Mathew J. , Hernandez Dena , Real Raquel , Alcalay Roy N. , Nalls Mike A , Morris Huw R , Schapira Anthony H. V. , Balwani Manisha , Sidransky Ellen
Published: December 2022

Background

Bi-allelic pathogenic variants inGBA1are the cause of Gaucher disease (GD1), a lysosomal storage disorder resulting from deficient glucocerebrosidase. HeterozygousGBA1variants are also a common genetic risk factor for Parkinson’s disease (PD). GD manifests with considerable clinical heterogeneity and is also associated with an increased risk of PD.

Objective

To investigate the contribution of PD risk variants to risk of PD in patients with GD1.

Methods

We studied 225 patients with GD1, including 199 without PD and 26 with PD. All cases were genotyped and the genetic data was imputed using common pipelines.

Results

On average, patients with GD1 with PD have a significantly higher PD genetic risk score than those without PD (P=0.021).

Conclusions

Our results indicate that variants included in the PD genetic risk score were more frequent in patients with GD1 who developed PD, suggesting that common risk variants may affect underlying biological pathways.

Supplemental datahere
Assessing the clinical application of deep-learning-derived CT volumetric measures in neurodegenerative disease diagnostics
Authors: Srikrishna Meera , Ashton Nicholas J. , Moscoso Alexis , Pereira Joana B. , Heckemann Rolf A. , van Westen Danielle , Volpe Giovanni , Simrén Joel , Zettergren Anna , Kern Silke , Wahlund Lars-Olof , Gyanwali Bibek , Hilal Saima , Ruifen Joyce Chong , Zetterberg Henrik , Blennow Kaj , Westman Eric , Chen Christopher , Skoog Ingmar , Schöll Michael
Published: December 2022

Background

Existing bio fluid and imaging biomarkers used in research and clinical diagnostics of neurodegenerative diseases are often expensive or invasive and are mainly available in specialised care centres. CT is an affordable and widely available imaging modality predominantly used to evaluate structural abnormalities, but not for the volumetric quantification of neurodegeneration. Previously, we developed a deep learning model trained on MRI segmentations from individuals with paired CT and MR scans, which achieved high accuracy and robust tissue classification based on brain CT images.

Purpose

To explore the diagnostic utility of deep-learning-derived CT-based atrophy measures and study their association with relevant cognitive, biochemical and other imaging markers of neurodegenerative diseases.

Materials and methods

In this retrospective study, we analysed 917 CT and 744 MR scans from cognitively healthy participants of the Gothenburg H70 Birth Cohort (70.4 ± 2.6 years) and 204 CT and 241 MR scans from participants of the Memory Clinic Cohort, Singapore (73 Alzheimer’s disease, 20 vascular dementia, 22 cognitively normal; 74.0 ± 8.2 years). We tested associations between six CT-derived volumetric measures with clinical diagnosis, fluid and imaging biomarkers and cognition.

Results

In the Memory Clinic Cohort, deep-learning-derived CT-based atrophy measures differentiated cognitively healthy individuals from Alzheimer’s disease (AUC 0.88; 95% CI: 0.79-0.96) and vascular dementia (AUC 0.91; 95% CI: 0.81-1.00) patients with high accuracy levels comparable to MR-derived measures. Additionally, CT-based measures distinguished early, prodromal Alzheimer’s disease (AUC= 0.73, 95% CI: 0.62, 0.85) and prodromal vascular dementia patients from healthy individuals (CT-GM: AUC= 0.7, 95% CI: 0.51, 0.81). CT-derived volumes were significantly associated with measures of cognition and biochemical markers of neurodegeneration, notably plasma-derived neurofilament light (ρ=-0.43, p<0.001, in the Memory Clinic Cohort).

Conclusion

Our findings provide strong evidence for the potential of deep-learning-derived CT-based atrophy measures in aiding neurodegenerative disease diagnostics in primary care settings.
The effect of the foreign language on cognitive reappraisal during exposure to a phobic stimulus
Authors: Ortigosa-Beltrán Isabel , Jaén Irene , Costumero Víctor , García-Palacios Azucena
Published: December 2022

The foreign language effect shows that emotional reactivity is reduced when we use a second language instead of our native one to address different situations. The present study aims to test whether the use of cognitive reappraisal could be influenced by the participant’s language (native/foreign). For this purpose, a sample of 60 participants with subclinical phobia to cockroaches was exposed to several phobic and neutral pictures while they used cognitive reappraisal in their native or in a foreign language. Physiological measures (pupil dilation and electrodermal activity) and self-reports of affective valence and arousal were collected. Results show an overall effectiveness of the strategy of reappraisal in both languages. Additionally, the use of a foreign language depicts a decrease in the affective negativity of the threat stimuli in terms of valence. The ratings of arousal also show a general higher arousal as an effect of the use of a foreign language. The present results suggest that using a foreign language could be advantageous to reduce negative emotionality by reappraisal. However, it could be a barrier for reappraising non-unpleasant pictures. Further studies should explore the foreign language effect in psychotherapy to open new ways of approaching different disorders.
Young people’s data governance preferences for their mental health data: MindKind Study findings from India, South Africa, and the United Kingdom
Authors: Sieberts Solveig K. , Marten Carly , Bampton Emily , Björling Elin A. , Burn Anne-Marie , Carey Emma Grace , Carlson Sonia , Fernandes Blossom , Kalha Jasmine , Lindani Simthembile , Masomera Hedwick , Neelakantan Lakshmi , Pasquale Lisa , Ranganathan Swetha , Scanlan Jo , Shah Himani , Sibisi Refiloe , Sumant Sushmita , Suver Christine , Thungana Yanga , Tummalacherla Meghasyam , Velloza Jennifer , Collins Pamela Y. , Fazel Mina , Ford Tamsin , Freeman Melvyn , Pathare Soumitra , Zingela Zukiswa ,   The MindKind Consortium, Doerr Megan
Published: December 2022

Mobile devices offer a scalable opportunity to collect longitudinal data that facilitate advances in mental health treatment to address the burden of mental health conditions in young people. Sharing these data with the research community is critical to gaining maximal value from rich data of this nature. However, the highly personal nature of the data necessitates understanding the conditions under which young people are willing to share them. To answer this question, we developed the MindKind Study, a multinational, mixed methods study that solicits young people’s preferences for how their data are governed and quantifies potential participants’ willingness to join under different conditions. We employed a community-based participatory approach, involving young people as stakeholders and co-researchers. At sites in India, South Africa, and the UK, we enrolled 3575 participants ages 16-24 in the mobile app-mediated quantitative study and 143 participants in the public deliberation-based qualitative study. We found that while youth participants have strong preferences for data governance, these preferences did not translate into (un)willingness to join the smartphone-based study. Participants grappled with the risks and benefits of participation as well as their desire that the “right people” access their data. Throughout the study, we recognized young people’s commitment to finding solutions and co-producing research architectures to allow for more open sharing of mental health data to accelerate and derive maximal benefit from research.
Processing negative autobiographical memories in a foreign language
Authors: Ortigosa-Beltrán Isabel , Jaén Irene , García-Palacios Azucena
Published: December 2022

The use of a foreign language has been introduced in the clinical setting as a form of emotional distance to help deal with negative experiences. However, its evidence of reducing emotionality during the emotional processing is still scarce. This study aims to test whether the description and processing of a traumatic or highly emotional event in a foreign language could modulate the strength of the connection between traumatic symptomatology and emotional reaction. For this purpose, a sample of 128 healthy participants completed a series of questionnaires via an online platform. Firstly, their levels of distress, arousal and valence were assessed in their native language. Secondly, they were assigned to either the native language or the foreign language group and described a negative childhood event in the assigned language, followed by five questions adapted from Foa and Rothbaum (1998) and related to the event. Next, their emotionality was assessed again in their native language. Finally, a questionnaire of traumatic stress symptoms and an avoidance scale were completed. Multivariate regression analyses showed that the relationship between traumatic symptomatology and emotionality was moderated by the language of processing the negative event. Traumatic symptomatology was more strongly associated with distress and arousal change when the task was performed in the native language. These findings suggest the influence of a foreign language on emotional reactivity when a negative experience is processed, which could be an essential tool in the treatment of disorders related to stress and trauma.
Curcumin combined with verapamil improve cardiovascular phenotype of a Williams-Beuren Syndrome mice model reducing oxidative stress
Authors: Abdalla Noura , Ortiz-Romero Paula , Rodriguez-Rovira Isaac , Pérez-Jurado Luis A. , Egea Gustavo , Campuzano Victoria
Published: December 2022

Williams-Beuren syndrome (WBS) is a rare neurodevelopmental disorder with hallmarks in the cardiovascular manifestations and no well-defined therapeutic strategies. We investigated the progression of cardiovascular phenotype present in CD (complete deletion) mice, a murine model of WBS, after chronic treatment with curcumin and verapamil, both compounds with positive effects on related pathologies. Treatment was administered orally dissolved in drinking water. After measuring “in vivo” systolic blood pressure, aortic and left ventricular myocardium were histological and molecular analysed to determine the effects of treatment and its underlying mechanism in CD mice. We observed upregulated xanthine oxidoreductase (XOR) expression in both aortic and left ventricular myocardium of CD mice. This overexpression is concomitant with increased levels of nitrated proteins as example of byproduct-mediated oxidative stress damage, indicating of XOR-generated oxidative stress impact on the pathophysiology of cardiovascular manifestations in WBS, and suggesting that the inhibition of XOR and/or oxidative stress damage could help to ameliorate the severe cardiovascular injuries presented in WBS.
Indole produced during dysbiosis mediates host–microorganism chemical communication
Authors: Yang Rui-Qiu , Chen Yong-Hong , Wu Qin-Yi , Tang Jie , Niu Shan-Zhuang , Zhao Qiu , Ma Yi-Cheng , Zou Cheng-Gang
Published: December 2022

An imbalance of the gut microbiota, termed dysbiosis, has a substantial impact on host physiology. However, the mechanism by which host deals with gut dysbiosis to maintain fitness remains largely unknown. InC. elegans,E. coli, which is its bacterial diets, proliferates in its intestinal lumen during aging. Here, we demonstrate that progressive intestinal proliferation ofE. coliactivates the transcription factor DAF-16, which is required for maintenance of longevity and organismal fitness in worms with age. DAF-16 up-regulates two lysozymeslys-7andlys-8, thus limiting the bacterial accumulation in the gut of worms during aging. During dysbiosis, the levels of indole produced byE. coliare increased in worms. Indole is involved in the activation of DAF-16 by TRPA-1 in neurons of worms. Our finding demonstrates that indole functions as a microbial signal of gut dysbiosis to promote fitness of the host.
Follicular fluid metabolomic analysis in women with Hashimoto’s thyroiditis
Authors: da Silva Bastos Diana Caroline , Chiamolera Maria Izabel , Costa da Silva Renata Elen , Borges De Souza Maria Do Carmo , De Azevedo Antunes Roberto , Marinho De Souza Marcelo , Allemand Mancebo Ana Cristina , Fernandes Arêas Patrícia Cristina , Reis Fernando M. , Lo Turco Edson Guimarães , Bloise Flavia Fonseca , Ortiga-Carvalho Tania Maria
Published: December 2022

Hashimoto’s thyroiditis is an autoimmune thyroid disease characterized by hypothyroidism and a high level of anti-thyroid autoantibodies. This disease has been linked to a negative impact on female fertility, but the mechanisms are unclear. Ovarian follicular fluid appears to be the key to understanding how Hashimoto’s thyroiditis can affect fertility. Therefore, we aimed to evaluate the follicular fluid metabolic profile and its relationship with anti-thyroid autoantibody levels. For this, we collected follicular fluid from a total of 61 patients undergoing in vitro fertilization treatment, comprising 34 women with thyroid autoantibody positivity and 18 negative controls. Follicular fluid samples were analysed using metabolomics and thyroid autoantibodies were measured. Follicular fluid samples from Hashimoto’s thyroiditis patients presented 15 metabolites with higher concentrations than those in controls, which indicates five possible affected pathways: the glycerophospholipid, arachidonic acid, linoleic acid, alpha-linolenic acid, and sphingolipid metabolism pathways. These pathways are known to regulate ovarian functions. In addition, anti-thyroglobulin antibody concentrations were more than tenfold higher in women with Hashimoto’s thyroiditis than in controls, in both serum and follicular fluid. Our data showed that Hashimoto’s thyroiditis can change the metabolic profile of follicular fluid, suggesting a potential mechanistic explanation for the association of this disease with female infertility.
Actl7b-deficiency leads to mislocalization of LC8 type dynein light chains and disruption of murine spermatogenesis
Authors: Merges Gina E. , Arévalo Lena , Lohanadan Keerthika , de Rooij Dirk G. , Jokwitz Melanie , Witke Walter , Schorle Hubert
Published: December 2022

Actin-related proteins (Arp) are classified according to their similarity to actin and are involved in diverse cellular processes.ACTL7Bis a testis-specific Arp and highly conserved in rodents and primates. ACTL7B is specifically expressed in round and elongating spermatids during spermiogenesis. Here, we have generated anActl7b-null allele in mice to unravel the role of ACTL7B in sperm formation. Male mice homozygous for theActl7b-null allele (Actl7b-/-) were infertile, while heterozygous males (Actl7b+/-) were fertile. Severe spermatid defects such as detached acrosomes, disrupted membranes and failed elongation of the axoneme start to appear at spermiogenesis step 9 inActl7b-/-mice, finally resulting in spermatogenic arrest. Abnormal spermatids, were degraded. Co-immunoprecipitation experiments identified interaction between ACTL7B and the LC8 dynein light chains DYNLL1 and DYNLL2, which are first detected in step 9 spermatids and mislocalized when ACTL7B is absent. Our data unequivocally establishes that mutations in ACTL7B are directly related to male infertility, pressing for additional research in men.

Summary statement

In this study, Actl7b-deficient mice were generated. Loss of Actl7b leads to spermatogenic arrest in mice. ACTL7B interacts in with DYNLL1/DYNLL2 and seems to function in spermatid cytoskeleton.
Engineering of the EndogenousHBDpromoter increases HbA2
Authors: Boontanrart Mandy Y. , Mächler Elia , Ponta Simone , Nelis Jan C. , Preiano Viviana G. , Corn Jacob E.
Published: December 2022

The β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, are one of the most common genetic diseases worldwide and are caused by mutations affecting the structure or production of β-globin subunits in adult hemoglobin. Many gene editing efforts to treat the β-hemoglobinopathies attempt to correct β-globin mutations or increase γ-globin for fetal hemoglobin production. δ-globin, the subunit of adult hemoglobin A2, has high homology to β-globin and is already pan-cellularly expressed at low levels in adult red blood cells. However, upregulation of δ-globin is a relatively unexplored avenue to increase the amount of functional hemoglobin. Here, we use CRISPR-Cas9 to repair non-functional transcriptional elements in the endogenous promoter region of δ-globin to increase overall expression of adult hemoglobin 2 (HbA2). We find that insertion of a KLF1 site alone is insufficient to upregulate δ-globin. Instead, multiple transcription factor elements are necessary for robust upregulation of δ-globin from the endogenous locus. Promoter edited HUDEP-2 immortalized erythroid progenitor cells exhibit striking increases ofHBDtranscript, from less than 5% to over 20% of total β-like globins. Edited CD34+ hematopoietic stem and progenitors (HSPCs) differentiated to primary human erythroblasts express up to 35%HBD. These findings add mechanistic insight to globin gene regulation and offer a new therapeutic avenue to treat β-hemoglobinopathies.
Exploiting effector - host interactions using TurboID-based proximity labeling
Authors: Shi Wei , Stolze Sara C , Nakagami Hirofumi , Misas Villamil Johana C. , Saur Isabel ML , Doehlemann Gunther
Published: December 2022

Plant pathogens secrete effectors, which target host proteins to facilitate infection. TheUstilago maydiseffector UmSee1 is required for tumor formation in the leaf during infection of maize. UmSee1 interacts with maize SGT1 and blocks its phosphorylationin-vivo. In the absence of UmSee1,U. maydiscannot trigger tumor formation in the bundle sheath. However, it remains unclear which host processes are manipulated by UmSee1 and the UmSee1-SGT1 interaction to cause the observed phenotype. Proximity-dependent protein labeling involving the turbo biotin ligase tag (TurboID) for proximal labeling of proteins is a powerful tool for identifying the protein interactome. We have generated transgenicU. maydisthat secretes biotin ligase-fused See1 effector (UmSee1-TurboID-3HA) directly into maize cells. This approach, in combination with conventional co-immunoprecipitation allowed to identify additional UmSee1 interactors in maize cells. Collectively, our data identified three ubiquitin-proteasome pathway-related proteins (ZmSIP1, ZmSIP2, ZmSIP3) that either interact with or are close to UmSee1 during host infection of maize withU. maydis.ZmSIP3 represents a cell cycle regulator which degradation appears to be promoted in the presence of UmSee1. Our data provide a possible explanation for the requirement of UmSee1 in tumor formation duringU. maydis-Zea maysinteraction.
High genetic load without purging in a diverse species-at-risk
Authors: Taylor Rebecca S. , Manseau Micheline , Keobouasone Sonesinh , Liu Peng , Mastromonaco Gabriela , Solmundson Kirsten , Kelly Allicia , Larter Nicholas C. , Gamberg Mary , Schwantje Helen , Thacker Caeley , Polfus Jean , Andrew Leon , Hervieux Dave , Simmons Deborah , Wilson Paul J.
Published: December 2022

High intra-specific genetic diversity is associated with adaptive potential which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, unless purged, thereby increasing the risk of inbreeding depression if population sizes decrease rapidly. Purging of deleterious variation has now been demonstrated in some threatened species. However, less is known about the costs of population declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that have or are expected to undergo rapid population declines. Caribou is a species of ecological and cultural significance in North America with a continental-wide distribution supporting extensive phenotypic variation, but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We also found highly divergent levels of inbreeding across individuals including the loss of alleles by drift (genetic erosion) but not purging, likely due to rapid population declines not allowing time for purging of deleterious alleles. As a result, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the ‘double-edged sword’ of genetic diversity that may be representative of other species-at-risk affected by anthropogenic activities.
Combining modelling and experimental approaches to assess the feasibility of developing rice-oil palm agroforestry system
Authors: Perez Raphaël P.A , Vezy Rémi , Bordon Romain , Laisné Thomas , Roques Sandrine , Rebolledo Maria-Camila , Rouan Lauriane , Fabre Denis , Gibert Olivier , De Raissac Marcel
Published: December 2022

Climatic hazards affecting the main rice producing regions of Indonesia increase the risk of annual production loss and encourage the development of innovative strategies to maintain stable production. Conversion of oil palm monocultures to rice-based intercropping systems is a strategy to be considered, but relies on the existence of suitable planting management that optimizes both palm productivity while providing enough light for undergrowth rice varieties tolerant to shady conditions. This paper proposes to couple a model of light interception on virtual canopies with indoor experiments to evaluate the feasibility of developing rice-oil palm agroforestry systems. We first selected a planting design that optimized the transmitted light available for rice using a functional-structural plant model (FSPM) of oil palm. Secondly, we reproduced the light regime simulated with specific changes in the intensity and the daily fluctuation of light in controlled conditions. Three light treatments were designed to test independently the effect of daily light quantity and the effect of diurnal fluctuation on contrasted rice subpopulations.

Light quantity was the main factor driving changes in plant morphology and architecture, while light fluctuation only appeared to explain variations in yield components and phenology. This study highlighted the importance of light fluctuation in the grain filling process and resource reallocation. The conservation of relative change among varieties between treatments suggests that varietal responses to low light are likely to be heritable, and that varietal screening under full light can provide clue on varietal behavior under low light. However, the identification of specific traits such as a limited expansion of leaf area and a conservation of leaf senescence under shade and high light fluctuation paves the way for selecting varieties dedicated to agroforestry systems. Further investigations including light quality and larger genotypic population to screen are discussed.
DNMT3B PWWP mutations cause hypermethylation of heterochromatin
Authors: Taglini Francesca , Kafetzopoulos Ioannis , Musialik Kamila Irena , Lee Heng Yang , Zhang Yujie , Marenda Mattia , Kerr Lyndsay , Finan Hannah , Rubio-Ramon Cristina , Wapenaar Hannah , Davidson-Smith Hazel , Wills Jimi , Murphy Laura C. , Wheeler Ann , Wilson Marcus D. , Sproul Duncan
Published: December 2022

The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved largely by thede novoDNA methyltransferases DNMT3A and DNMT3B. Mutations in DNMT3B can cause immunodeficiency-centromeric instability-facial anomalies type 1 (ICF1) syndrome which is characterised by hypomethylated heterochromatin. However, in the genome, DNMT3B primarily localises to actively transcribing gene bodies through the interaction of its PWWP domain with the histone modification H3K36me3 and it is unclear how it is recruited to heterochromatin. Here we show that in DNMT3B knockout cells, loss of DNA methylation predominantly occurs in heterochromatic domains marked by H3K9me3. We also find that PWWP domain mutations which disrupt DNMT3B’s interaction with H3K36me3 result in striking increases of DNA methylation in H3K9me3-marked heterochromatin. Gains of methylation are also observed when the PWWP domain of DNMT3B is deleted. In contrast, we find that the ICF1 syndrome-causing PWWP mutation, S270P, does not result in hypermethylation of heterochromatin and destabilises the protein. We also show that removal of the N-terminus region of DNMT3B affects its recruitment to chromatin and ability to methylate H3K9me3 marked regions. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent manner and that this recruitment is facilitated by the protein’s N-terminus. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in ICF syndrome, cancer and aging.
Cuticle architecture and mechanical properties: a functional relationship delineated through correlated multimodal imaging
Authors: Reynoud Nicolas , Geneix Nathalie , D’Orlando Angelina , Petit Johann , Mathurin Jeremie , Deniset-Besseau Ariane , Marion Didier , Rothan Christophe , Lahaye Marc , Bakan Bénédicte
Published: December 2022

Cuticle are multifunctional hydrophobic biocomposites that protect aerial organs of plants. Along plant development, plant cuticle must accommodate different mechanical constraints combining extensibility and stiffness, the corresponding structure-function relationships are unknown. Recent data showed a fine architectural tuning of the cuticle architecture and the corresponding chemical clusters along fruit development which raise the question of their impact on the mechanical properties of the cuticle.

We investigated the in-depth nanomechanical properties of tomato fruit cuticle from early development to ripening, in relation to chemical and structural heterogeneities by developing a correlative multimodal imaging approach.

Unprecedented sharps heterogeneities were evidenced with the highlighting of an in-depth mechanical gradient and a ‘soft’ central furrow that were maintained throughout the plant development despite the overall increase in elastic modulus. In addition, we demonstrated that these local mechanical areas are correlated to chemical and structural gradients.

This study shed light on a fine tuning of mechanical properties of cuticle through the modulation of their architecture, providing new insight for our understanding of structure-function relationships of plant cuticle and for the design of biosinpired material.
Species interactions promote parallel evolution of global transcriptional regulators in a widespreadStaphylococcusspecies
Authors: Cosetta Casey , Niccum Brittany , Kamkari Nick , Dente Michael , Podniesinski Matthew , Wolfe Benjamin E.
Published: December 2022

Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacteriumStaphylococcus xylosus. We evolvedS. xylosusfor 450 generations alone or in co-culture with one of three microbes: the yeastDebaryomyces hansenii, the bacteriumBrevibacterium aurantiacum, and the moldPenicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution after 15 weeks of the evolution. The yeastD. hanseniistrongly promoted diversification ofS. xylosus; by the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations ofS. xylosusgrown alone, withBrevibacterium, or withPenicilliumdid not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments revealed numerous unique mutations in the operons for the SigB, Agr, and WalKR global regulators, but only in theD. hanseniitreatment. Phenotyping and RNA-seq experiments demonstrated that these mutations altered pigment and biofilm production, spreading, stress tolerance, and metabolism ofS. xylosus. Fitness experiments revealed trade-offs of these mutations across biotic environments caused by antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeastDebaryomyceshad strong negative fitness effects in other biotic environments.

IMPORTANCE

Substantial phenotypic and genomic variation exists within microbial species, but the ecological factors that shape this strain diversity are poorly characterized. We demonstrate that the biotic context of a widespreadStaphylococcusspecies can impact the evolution of strain diversity. This work demonstrates the potential for microbes in food production environments to rapidly evolve to novel substrates and biotic environments. Our findings may also help understand how otherStaphylococcusspecies may evolve in multispecies microbiomes.
Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon
Authors: Mimpen Jolet Y. , Ramos-Mucci Lorenzo , Paul Claudia , Kurjan Alina , Hulley Phillipa , Ikwuanusi Chinemerem , Gwilym Steve , Baldwin Mathew J. , Cribbs Adam P. , Snelling Sarah J.B.
Published: December 2022

The molecular and cellular basis of health in human tendons remains poorly understood. Amongst human tendons, the hamstrings are the least likely to be injured or degenerate, providing a prototypic healthy tendon reference. The aim of this study was to define the transcriptome and location of all cell types in healthy hamstring tendon. We profiled the transcriptomes of 10,533 nuclei from 4 healthy donors using single-nucleus RNA sequencing (snRNA-seq) and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and revealed the presence of cell types previously unreported for tendon sites, including different skeletal muscle cell types, satellite cells, adipocytes, and nerve cells, which are undefined nervous system cells. Location of these cell types within tendon was defined using spatial transcriptomics and imaging, and transcriptional networks and cell-cell interactions were identified. We demonstrate that fibroblasts have a high number of potential cell-cell interactions, are present throughout the whole tendon tissue, and play an important role in the production and organisation of extracellular matrix, thus confirming their role as key regulators of hamstring tendon tissue homeostasis. Overall, our findings highlight the highly complex cellular networks underpinning tendon function and underpins the importance of fibroblasts as key regulators of hamstring tendon tissue homeostasis.
Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane
Authors: Yadav Seema , Ross Elizabeth M. , Wei Xianming , Powell Owen , Hivert Valentin , Hickey Lee T. , Atkin Felicity , Deomano Emily , Aitken Karen S. , Voss-Fels Kai P. , Hayes Ben J.
Published: December 2022

Mate-allocation in breeding programs can improve progeny performance by exploiting non-additive effects. Breeding decisions in the mate-allocation approach are based on predicted progeny merit rather than parental breeding value. This is particularly attractive when non-additive effects are significant, and the best-predicted progeny can be clonally propagated, for example sugarcane. We compared mate-allocation strategies that leverage non-additive and heterozygosity effects to maximise sugarcane clonal performance to schemes that use only additive effects to maximise breeding value. We used phenotypes and genotypes from a population of 2,909 clones phenotyped in Australia’s sugarcane breeding program’s final assessment trials for three traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fibre. The clones from the last generation of this data set were used as parents to simulate families from all possible crosses (1,225), each with 50 progenies. The breeding and clonal values of progeny were predicted using GBLUP (considering only additive effects) and the e-GBLUP model (incorporating additive, non-additive and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among the selected parents. Compared to the breeding value, the predicted progeny value of allocated crossing pairs based on clonal performance (e-GBLUP) increased by 57%, 12%, and 16% for TCH, CCS, and fibre, respectively. In our study, the mate-allocation strategy exploiting non-additive and heterozygosity effects resulted in better clonal performance. However, there was a noticeable decline in additive gain, particularly for TCH, which might have been caused by the presence of large epistatic effects. When crosses were chosen based on clonal performance for TCH, progenies’ inbreeding coefficients were found significantly lower than for random mating, indicating that utilising non-additive and heterozygosity effects has advantages for controlling inbreeding depression. Therefore, mate-allocation is recommended in clonal crops to improve clonal performance and reduce inbreeding.