bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Abdominal Subcutaneous-Derived Active Beige Adipocytes CarryingFTOrs1421085 Obesity-Risk Alleles Exert Lower Thermogenic Capacity
Authors: Vámos Attila , Arianti Rini , Vinnai Boglárka Ágnes , Alrifai Rahaf , Shaw Abhirup , Póliska Szilárd , Guba Andrea , Csősz Éva , Csomós István , Mocsár Gábor , Lányi Cecilia , Balajthy Zoltán , Fésüs László , Kristóf Endre
Published: February 2023

White adipocytes store lipids, have a large lipid droplet and few mitochondria. Brown and beige adipocytes, which produce heat, are characterized by high expression of uncoupling protein (UCP) 1, multilocular lipid droplets, and large amounts of mitochondria. The rs1421085 T-to-C single-nucleotide polymorphism (SNP) of the humanFTOgene interrupts a conserved motif for ARID5B repressor, resulting in adipocyte type shift from beige to white. We obtained abdominal subcutaneous adipose tissue from donors carryingFTOrs1421085 TT (risk-free) or CC (obesity-risk) genotypes, isolated and differentiated their preadipocytes into beige adipocytes (driven by the PPARγ agonist rosiglitazone for 14 days), and activated them with dibutyryl-cAMP for 4 hours. Then, either the same culture conditions were applied for additional 14 days (active beige adipocytes) or it was replaced by a white differentiation medium (inactive beige adipocytes). White adipocytes were differentiated by their medium for 28 days. RNA-sequencing was performed to investigate the gene expression pattern of adipocytes carrying differentFTOalleles and found that active beige adipocytes had higher brown adipocyte content and browning capacity compared to white or inactive beige ones when the cells were obtained from risk-free TT but not from obesity-risk CC genotype carriers. Active beige adipocytes carryingFTOCC had lower thermogenic gene (e.g.,UCP1, PM20D1, CIDEA) expression and thermogenesis measured by proton leak respiration as compared to TT carriers. In addition, active beige adipocytes with CC alleles exerted lower expression of ASC1 neutral amino acid transporter (encoded bySLC7A10) and less consumption of Ala, Ser, Cys, and Gly as compared to risk-free carriers. We did not observe any influence of theFTOrs1421085 SNP on white and inactive beige adipocytes highlighting its exclusive and critical effect when adipocytes were activated for thermogenesis.
Delayed normalization model captures disparate nonlinear neural dynamics measured with different techniques in macaque and human V1
Authors: Zhou Jingyang , Whitmire Matt , Chen Yuzhi , Seidemann Eyal
Published: February 2023

Neuronal representations throughout the primate visual system display a wide range of nonlinear dynamics in response to static visual stimuli. To understand the neural basis of visual perception, it is important to quantify these nonlinearities and to develop general models that allow one to predict response dynamics to visual stimuli with arbitrary temporal waveform.

Voltage-sensitive dye imaging (VSDI) is a powerful method for measuring neural population responses from the cortex of awake, behaving, subjects. Here we used VSDI to measure the dynamics of neural population responses in macaque V1 to visual stimuli with a wide range of time courses.

We found that beyond clear nonlinearities for briefly presented visual stimuli, stimulus-evoked VSDI responses are surprisingly near additive in time. These results are qualitatively different from neural dynamics to similar stimuli previously measured in human visual cortex using fMRI and electrocorticography (ECoG), which show strong sub-additivity in time.

To test whether this discrepancy is specific to VSDI, a signal dominated by subthreshold neural activity, we repeated our measurements using a genetically encoded calcium indicator (GCaMP), a signal dominated by spiking activity. We found that GCaMP signals in macaque V1 are also near-additive. Therefore, the discrepancies in the degree of additivity between these different measurements are not attributed to the difference between sub- and supra-threshold neural response.

Finally, we show that a simple yet flexible delayed normalization model can capture the dynamics of all of these measurements, suggesting that dynamic gain-control is an important mechanism contributing to neural processing in the brain.
Chemical defences indicate distinct colour patterns with reduced variability in aposematic nudibranchs
Authors: van den Berg Cedric P. , Santon Matteo , Endler John A. , Drummond Leon , Dawson Bethany R. , Santiago Carl , Weber Nathalie , Cheney Karen L.
Published: February 2023

The selective factors that shape phenotypic diversity in prey communities with aposematic animals are diverse and coincide with similar diversity in the strength of underlying secondary defences. However, quantitative assessments of colour pattern variation and the strength of chemical defences in assemblages of aposematic species are lacking. We quantified colour pattern diversity using Quantitative Colour Pattern Analysis (QCPA) in 13 Dorid nudibranch species (Infraorder: Doridoidei) that varied in the strength of their chemical defences. We accounted for the physiological properties of a potential predator’s visual system (a triggerfish,Rhinecanthus aculeatus) and modelled the appearance of nudibranchs from multiple viewing distances (2cm and 10cm). We identified distinct colour pattern properties associated with the presence and strength of chemical defences. Colour patterns were also less variable among species with chemical defences when compared to undefended species. This confirms correlations between secondary defences and diverse, bold colouration while showing that chemical defences coincide with decreased colour pattern variability among species. Our study suggests that complex spatiochromatic properties of colour patterns perceived by potential predators can be used to make inferences on the presence and strength of chemical defences.
Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages
Authors: Chen Heidi I. , Turakhia Yatish , Bejerano Gill , Kingsley David M.
Published: February 2023

Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm thatPelA, aPitx1enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform,syngnathid, and synbranchid species with caudal fin reduction, and which alters caudal fin development when targeted by genome editing. Our study illustrates a general strategy for mapping phenotypes to genotypes across a tree of vertebrate species, and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes during 100 million years of fish evolution.
TheOrshinarhythm in a colonial urochordate: recurrent aging/rejuvenation sequels
Authors: Ben-Hamo Oshrat , Izhaki Ido , Ben-Shlomo Rachel , Rinkevich Baruch
Published: February 2023

When it comes to aging, some colonial invertebrates present disparate patterns from the customary aging phenomenon in unitary organisms, where a single senescence phenomenon along ontogeny culminates in their inevitable deaths. Here we studied aging processes in 81 colonies of the marine urochordateBotryllus schlosserieach followed from birth to death (over 720 days). The colonies were divided between three life history strategies, each distinct from the others based on the existence/absence of colonial fission: NF (no fission), FA (fission develops after the colony reaches maximal size), and FB (fission develops before the colony reaches maximal size). Results revealed that sexual reproductive statuses (hermaphroditism and male only settings), colonial vigorousness and sizes, represent coinciding and repeated rhythms of one or more emerged life/death ‘astogenic segments’ on the whole-genet level, each is termed asOrshina, and the sum of all segments as theOrshinarhythm. EachOrshinasegment lasts about three months (containing ca. 13 blastogenic cycles), ends by either the colonial death or rejuvenation, and manipulated by absence/existing of fission events in NF/FA/FB strategies. These findings indicate that reproduction, life span, death, rejuvenation and fission events are important scheduled biological components in the constructedOrshinarhythm, a novel aging phenomenon.
Generation time and seasonal migration explain variation in spatial population synchrony across European bird species
Authors: Martin Ellen C. , Hansen Brage Bremset , Lee Aline Magdalena , Herfindal Ivar
Published: February 2023

Spatial population synchrony is common among populations of the same species and is an important predictor of extinction risk. Despite the potential consequences for metapopulation persistence, we still largely lack understanding of what makes one species more likely to be synchronized than another given the same environmental conditions.

Generally, environmental conditions on a shared environment or a species’ sensitivity to the environment can explain the extent of synchrony. Populations that are closer together experience more similar fluctuations in their environments than those populations that are further apart and are therefore more synchronized. The relative importance of environmental and demographic stochasticity for population dynamics is strongly linked to species’ life history traits, such as pace of life, why may impact population synchrony. For populations that migrate, there may be multiple environmental conditions at different locations driving synchrony. However, the importance of life history and migration strategies in determining patterns of spatial population synchrony have rarely been explored empirically. We therefore hypothesize that generation time, a proxy for pace of life, and migration play an important role in determining spatial population synchrony.

We used population abundance data on breeding birds from four countries to investigate patterns of spatial population synchrony in growth rate and abundance. We investigated differences in synchrony across a gradient of generation times in resident, short-distance migrant, and long-distance migrant bird species.

Species with shorter generation times were more synchronized than species with longer generation times. Short-distance migrants were more synchronized than long-distance migrants and resident birds.

Our results provide novel empirical links between spatial population synchrony and species traits known to be of key importance for population dynamics, generation time and migration characteristics. We show how these different mechanisms can be combined to understand species-specific causes of spatial population synchrony. Understanding these specific drivers of spatial population synchrony is important in the face of increasingly severe threats to biodiversity and could be key for successful future conservation outcomes.
USP8 inhibition promotes Parkin-independent mitophagy in theDrosophilabrain and in human neurons
Authors: Mauri Sofia , Bernardo Greta , Martinez Aitor , Favaro Mariavittoria , Trevisan Marta , Cobraiville Gael , Fillet Marienne , Caicci Federico , Whitworth Alexander J. , Ziviani Elena
Published: February 2023

Stress-induced mitophagy, a tightly regulated process that targets dysfunctional mitochondria for autophagy-dependent degradation, mainly relays on two proteins, PINK1 and Parkin, which genes are mutated in some forms of familiar Parkinson’s Disease (PD). Upon mitochondrial damage, the protein kinase PINK1 accumulates on the organelle surface where it controls the recruitment of the E3-ubiquitin ligase Parkin. On mitochondria, Parkin ubiquitinates a subset of mitochondrial resident proteins located on the outer mitochondrial membrane, leading to the recruitment of downstream cytosolic autophagic adaptors, and subsequent autophagosome formation.

Importantly, PINK1/Parkin-independent mitophagy pathways also exist that can be counteracted by specific deubiquitinating enzymes (DUBs). Downregulation of these specific DUBs can presumably enhances basal mitophagy, and be beneficial in models in which accumulation of defective mitochondria is implicated. Among these DUBs, USP8 is an interesting target because of its role in the endosomal pathway and autophagy, and its beneficial effects, when inhibited, in models of neurodegeneration. Based on this, we evaluated autophagy and mitophagy levels when USP8 activity is altered. We used genetic approaches inD. melanogasterto measure autophagy and mitophagyin vivo, and complementaryin vitroapproaches to investigate the molecular pathway that regulates mitophagy via USP8.

We found an inverse correlation between basal mitophagy and USP8 levels, in that inhibition of USP8 correlates with increased Parkin-independent mitophagy. These results suggest the existence of a yet uncharacterized mitophagic pathway that is inhibited by USP8.
Quantifying invasive pest dynamics through inference of a two-node epidemic network model
Authors: Wadkin Laura E , Golightly Andrew , Branson Julia , Hoppit Andrew , Parker Nick G , Baggaley Andrew W
Published: February 2023

Invasive woodland pests are having a substantial ecological, economic and social impact, harming biodiversity and ecosystem services. Mathematical modelling informed by Bayesian inference can deepen our understanding of the fundamental behaviours of invasive pests and provide predictive tools for forecasting the future spread. A key invasive pest of concern in the UK is the oak processionary moth (OPM). OPM was established in the UK in 2006, is harmful to both oak trees and humans, and its infestation area is continually expanding. Here, we use a computational inference scheme to estimate the parameters for a two-node network epidemic model to describe the temporal dynamics of OPM in two geographically neighbouring parks (Bushy Park and Richmond Park, London). We show the applicability of such a network model to describing invasive pest dynamics and our results suggest that the infestation within Richmond Park has largely driven the infestation within Bushy Park.
Tropical invertebrate community assembly processes are robust to a gradient of land use intensity
Authors: Granville Natasha R. , Barclay Maxwell V. L. , Boyle Michael J. W. , Chung Arthur Y. C. , Fayle Tom M. , Hah Huai En , Hardwick Jane L. , Kinneen Lois , Kitching Roger L. , Maunsell Sarah C. , Miller Jeremy A. , Sharp Adam C. , Stork Nigel E. , Wai Leona , Yusah Kalsum M. , Ewers Robert M.
Published: February 2023

Understanding how community assembly processes drive biodiversity patterns is a central goal of community ecology. While it is generally accepted that ecological communities are assembled by both stochastic and deterministic processes, quantifying their relative importance remains challenging. Few studies have investigated how the relative importance of stochastic and deterministic community assembly processes vary among taxa and along gradients of habitat degradation. Using data on 1,645 arthropod species across seven taxonomic groups in Malaysian Borneo, we quantified the importance of ecological stochasticity and of a suite of community assembly processes across a gradient of logging intensity. The relationship between logging and community assembly varied depending on the specific combination of taxa and stochasticity metric used, but, in general, the processes that govern invertebrate community assembly were remarkably robust to changes in land use intensity.
Uncovering the consequences of batch effect associated missing values in omics data analysis
Authors: Hui Harvard Wai Hann , Goh Wilson Wen Bin
Published: February 2023

Statistical analyses in high-dimensional omics data are often hampered by the presence of batch effects (BEs) and missing values (MVs), but the interaction between these two issues is not well-studied nor understood. MVs may manifest as a BE when their proportions differ across batches. These are termed as Batch-Effect Associated Missing values (BEAMs). We hypothesized that BEAMs in data may introduce bias which can impede the performance of missing value imputation (MVI). To test this, we simulated data with two batches, then introduced over 100 iterations, either 20% and 40% MVs in each batch (BEAMs) or 30% in both (control). K-nearest neighbours (KNN) was then used to perform MVI, in a typical global approach (M1) and a supposed superior batch-sensitized approach (M2). BEs were then corrected using ComBat. The effectiveness of the MVI was evaluated by its imputation accuracy and true and false positive rates. Notably, when BEAMs existed, M2 was generally undesirable as the differing application of MV filtering in M1 and M2 strategies resulted in an overall coverage deficiency. Additionally, both M1 and M2 strategies suffered in the presence of BEAMs, highlighting the need for a novel approach to handle MVI in data with BEAMs.

Author summary

Data in high-throughput omics data are often combined from different sources (batches), which creates batch effects in the data. Missing values are a common occurrence in these data, and their proportions are assumed to be equal across batches. However, instances exist when these proportions vary between batches, such as one batch having more missing values than another, resulting in batch effect associated missing values. Missing values are often dealt with through missing value imputation, but whether the variation in missing value proportions across batches affects imputation outcomes is unknown. In this paper, we investigate the consequence of performing imputation when this issue persists. We simulated data with equal and unequal missing value proportions, then assessed the performance of k-nearest neighbours imputation by its imputation accuracy and downstream analysis outcomes. This revealed that unequal missing value proportions worsens imputation and establishes the need for smarter imputation strategies to handle this complication.
UTRGAN: Learning to Generate 5’ UTR Sequences for Optimized Translation Efficiency and Gene Expression
Authors: Barazandeh Sina , Ozden Furkan , Hincer Ahmet , Seker Urartu Ozgur Safak , Cicek A. Ercument
Published: February 2023

The 5’ untranslated region (5’ UTR) of mRNA is crucial for the molecule’s translatability and stability, making it essential for designing synthetic biological circuits for high and stable protein expression. Several UTR sequences are patented and widely used in laboratories. This paper presents UTRGAN, a Generative Adversarial Network (GAN)-based model for generating 5’ UTR sequences, coupled with an optimization procedure to ensure high expression for target gene sequences or high ribosome load and translation efficiency. The model generates sequences mimicking various properties of natural UTR sequences and optimizes them to achieve (i) up to 5-fold higher average expression on target genes, (ii) up to 2-fold higher mean ribosome load, and (iii) a 34-fold higher average translation efficiency compared to initial UTR sequences. UTRGAN-generated sequences also exhibit higher similarity to known regulatory motifs in regions such as internal ribosome entry sites, upstream open reading frames, G-quadruplexes, and Kozak and initiation start codon regions. In-vitro experiments show that the UTR sequences designed by UTRGAN result in a higher translation rate for the human TNF-αprotein compared to the human Beta Globin 5’ UTR, a UTR with high production capacity.
Trade-offs between immunity and competitive ability in fighting ant males
Authors: Metzler Sina , Kirchner Jessica , Grasse Anna V , Cremer Sylvia
Published: February 2023

Background

Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogenMetarhizium robertsiiinterfered with fighting success inCardiocondyla obscuriorant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.

Results

We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.

Conclusions

Males of the antC. obscuriorhave evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk.
Input-specific synaptic depression shapes temporal integration in mouse visual cortex
Authors: Li Jennifer Y. , Glickfeld Lindsey L.
Published: February 2023

Efficient sensory processing requires the nervous system to adjust to ongoing features of the environment. In primary visual cortex (V1), neuronal activity strongly depends on recent stimulus history. Existing models can explain effects of prolonged stimulus presentation, but remain insufficient for explaining effects observed after shorter durations commonly encountered under natural conditions. We investigated the mechanisms driving adaptation in response to brief (100 ms) stimuli in L2/3 V1 neurons by performingin vivowhole-cell recordings to measure membrane potential and synaptic inputs. We find that rapid adaptation is generated by stimulus-specific suppression of excitatory and inhibitory synaptic inputs. Targeted optogenetic experiments reveal that these synaptic effects are due to input-specific short-term depression of transmission between layers 4 and 2/3. Thus, distinct mechanisms are engaged following brief and prolonged stimulus presentation and together enable flexible control of sensory encoding across a wide range of time scales.
Epitenon-derived cells comprise a distinct progenitor population that contributes to both tendon fibrosis and regeneration following acute injury
Authors: Nichols Anne E.C. , Wagner Nicholas W. , Ketonis Constantinos , Loiselle Alayna E.
Published: February 2023

Flexor tendon injuries are common and heal poorly owing to both the deposition of function- limiting peritendinous scar tissue and insufficient healing of the tendon itself. Therapeutic options are limited due to a lack of understanding of the cell populations that contribute to these processes. Here, we identified a bi-fated progenitor cell population that originates from the epitenon and goes on to contribute to both peritendinous fibrosis and regenerative tendon healing following acute tendon injury. Using a combination of genetic lineage tracing and single cell RNA-sequencing (scRNA-seq), we profiled the behavior and contributions of each cell fate to the healing process in a spatio-temporal manner. Branched pseudotime trajectory analysis identified distinct transcription factors responsible for regulation of each fate. Finally, integrated scRNA-seq analysis of mouse healing with human peritendinous scar tissue revealed remarkable transcriptional similarity between mouse epitenon- derived cells and fibroblasts present in human peritendinous scar tissue, which was further validated by immunofluorescent staining for conserved markers. Combined, these results clearly identify the epitenon as the cellular origin of an important progenitor cell population that could be leveraged to improve tendon healing.
Association between the magnitude of melatonin circadian rhythm and personality in the threespine stickleback
Authors: Philippe Morgane Anita , Aubin-Horth Nadia
Published: February 2023

Melatonin secretion follows a circadian pattern with a maximum level at night in many species. However, in zebrafish (Danio rerio, a diurnal fish species) large inter-individual variations in daily rhythmicity of melatonin levels are present and are associated with variation in behaviour. Melatonin secretion rhythm of proactive individuals that are more active and exploratory are of larger amplitude compared to reactive individuals. In threespine sticklebacks (Gasterosteus aculeatus), a nocturnal species, inter-individual variability of behaviour is well described. However, inter-individual variation of melatonin rhythm and its association with variation in behaviour has never been measured in this species, which would allow to test if patterns found in zebrafish can be generalized for diurnal and nocturnal species. We measured large inter-individual variation in melatonin levels and found that activity was positively correlated with plasma melatonin concentration measured at night. We did not observe any significant difference in nigh-day variation in melatonin concentration between very active and less active groups. However, we found that individuals classified as reactive based on their propensity to wall-hugging, a measure of anxiety in fish, showed large variation in melatonin between night and day, while this rhythm was not seen in proactive individuals that frequently used the centre of the aquarium. Overall, our study suggests that melatonin may directly modulate specific behaviours in wild sticklebacks, and that while interindividual variation in melatonin rhythm may be widespread in fish, different patterns of association with behaviours should be expected.
Four-color fluorescence cross-correlation spectroscopy with one laser and one camera
Authors: Gandhi Sonali A. , Sanders Matthew A. , Granneman James G. , Kelly Christopher V.
Published: February 2023

The diffusion and reorganization of phospholipids and membrane-associated proteins are fundamental for cellular function. Fluorescence cross-correlation spectroscopy (FCCS) measures the diffusion and molecular interactions at nanomolar concentration in biological systems. We have developed a novel, economical method to simultaneously monitor diffusion and oligomerization with the use of super-continuum laser and spectral deconvolution from a single detector. Customizable excitation wavelengths were chosen from the wide-band source and spectral fitting of the emitted light revealed the interactions for up to four spectrally overlapping fluorophores simultaneously. This method was applied to perform four-color FCCS, as demonstrated with polystyrene nanoparticles, lipid vesicles, and membrane-bound molecules. Up to four individually customizable excitation channels were selected from the broad-spectrum fiber laser to excite the diffusers within a diffraction-limited spot. The fluorescence emission passed through a cleanup filter and a dispersive prism prior to being collected by a sCMOS or EMCCD camera with up to 10 kHz frame rates. The emission intensity versus time of each fluorophore was extracted through a linear least-square fitting of each camera frame and temporally correlated via custom software. Auto- and cross-correlation functions enabled the measurement of the diffusion rates and binding partners. We have measured the induced aggregation of nanobeads and lipid vesicles in solution upon increasing the buffer salinity. Because of the adaptability of investigating four fluorophores simultaneously with a cost-effective method, this technique will have wide application for examining complex homo- and heterooligomerization in model and living systems.
A hypothalamic node for the cyclical control of female sexual rejection
Authors: Gutierrez-Castellanos Nicolas , Husain Basma Fatima Anwar , Dias Inês C. , Nomoto Kensaku , Duarte Margarida A. , Ferreira Liliana , Lacoste Bertrand , Lima Susana Q.
Published: February 2023

Internal state-dependent behavioral responses, such as the switch between rejection and acceptance of sexual advances depending on a female’s reproductive capacity, are fundamental to maintain social interactions and wellbeing. Here we characterize a dedicated circuit for the cyclical control of rejection behavior in the mouse, located in the anterior ventrolateral ventromedial hypothalamus (aVMHvl).In vivorecordings reveal that progesterone receptor expressing neurons of the aVMHvl (aVMHvlPr+) are active during rejection but silent when females accept the male. Moreover, we show that aVMHvlPr+neurons receive reduced excitatory to inhibitory synaptic input balance during the receptive phase of the reproductive cycle. Finally, optogenetic activation of aVMHvlPr+neurons in receptive females is sufficient to increase rejection behavior, disrupting the probability of copulation, without affecting other male-directed interactions. This population of aVMHvlPr+ neurons is thus a key neural substrate controlling female sexual behavior, providing an additional barrier to mating when fertilization is not possible.
Fundamentals of biofilm formation in soil: From functionalized self-assembled monolayers to rewilding
Authors: Hendiani Saghar , Hansen Mads Frederik , Kontopoulos Ioannis , Verma Taru , Pucetaite Milda , Burmølle Mette , Ramstedt Madeleine , Svenninggaard Sand Karina Krarup
Published: February 2023

Surface energy and surface charges play crucial roles in bacterial adhesion and biofilm formation, however the mechanisms underlying the bacteria-surface interaction, particularly on the formation of soil biofilms, remain unclear. In spite of considering the spatiotemporal dynamics of biofilm formation on different soil surfaces, we compared the impact of four different substrates on bacterial attachment and biofilm formation. The substrates were constituted of gold layer covered by NH2+, CH3, COO-and OH-terminated self-assembled monolayers (SAMS). Two soil habitat bacteria with different Gram barriers,Bacillus subtilisandAcinetobacter baylyi, were grown with incubation times of 6-72 h on each type of surfaces. Bacterial attachment and biofilm formation was assessed using metabolic activity of the cells adhered to the surfaces. The spatial distribution of adhere bacteria was visualized by scanning electron microscopy and confocal laser scanning microscopy. We also investigated whether the surface impacts the biofilm matrix composition. A general view of our results suggests a major influence of the surface chemistry on bacterial potential to form biofilms. The hydrophobic or positively charged substrates attract bacteria while a lack of attachment and biofilm formation on hydrophilic and negatively charged surfaces. This work points out the potential of surface treatments in the environment where it is intended to either repel or attract bacteria.
Single cell DNA methylation ageing in mouse blood
Authors: Bonder Marc Jan , Clark Stephen J. , Krueger Felix , Luo Siyuan , de Sousa João Agostinho , Hashtroud Aida M. , Stubbs Thomas M. , Stark Anne-Katrien , Rulands Steffen , Stegle Oliver , Reik Wolf , von Meyenn Ferdinand
Published: February 2023

Ageing is the accumulation of changes and overall decline of the function of cells, organs and organisms over time. At the molecular and cellular level, the concept of biological age has been established and biomarkers of biological age have been identified, notably epigenetic DNA-methylation based clocks. With the emergence of single-cell DNA methylation profiling methods, the possibility to study biological age of individual cells has been proposed, and a first proof-of-concept study, based on limited single cell datasets mostly from early developmental origin, indicated the feasibility and relevance of this approach to better understand organismal changes and cellular ageing heterogeneity.

Here we generated a large single-cell DNA methylation and matched transcriptome dataset from mouse peripheral blood samples, spanning a broad range of ages (10-101 weeks of age). We observed that the number of genes expressed increased at older ages, but gene specific changes were small. We next developed a robust single cell DNA methylation age predictor (scEpiAge), which can accurately predict age in a broad range of publicly available datasets, including very sparse data and it also predicts age in single cells. Interestingly, the DNA methylation age distribution is wider than technically expected in 19% of single cells, suggesting that epigenetic age heterogeneity is presentin vivoand may relate to functional differences between cells. In addition, we observe differences in epigenetic ageing between the major blood cell types. Our work provides a foundation for better single-cell and sparse data epigenetic age predictors and highlights the significance of cellular heterogeneity during ageing.

Highlights

- Model to estimate DNA methylation age in single cells

- Large multi-omics dataset of single cells from murine blood

- Epigenetic age deviations from chronological age are greater than technical expected from technical variability

- Number of genes expressed increases with chronological and epigenetic age
Rewiring of the host cell metabolome and lipidome during lytic gammaherpesvirus infection is essential for infectious virus production
Authors: Clark Sarah A. , Vazquez Angie , Furiya Kelsey , Splattstoesser Madeleine K. , Bashmail Abdullah K. , Schwartz Haleigh , Russell Makaiya , Bhark Shun-Je , Moreno Osvaldo K. , McGovern Morgan , Owsley Eric R. , Nelson Timothy A. , Sanchez Erica , Delgado Tracie
Published: February 2023

Oncogenic virus infections are estimated to cause ∼15% of all cancers. Two prevalent human oncogenic viruses are members of the gammaherpesvirus family: Epstein Barr Virus (EBV) and Kaposi’s Sarcoma Herpesvirus (KSHV). We use murine herpesvirus 68 (MHV-68), which shares significant homology with KSHV and EBV, as a model system to study gammaherpesvirus lytic replication. Viruses implement distinct metabolic programs to support their life cycle, such as increasing the supply of lipids, amino acids, and nucleotide materials necessary to replicate. Our data define the global changes in the host cell metabolome and lipidome during gammaherpesvirus lytic replication. Our metabolomics analysis found that MHV-68 lytic infection induces glycolysis, glutaminolysis, lipid metabolism, and nucleotide metabolism. We additionally observed an increase in glutamine consumption and glutamine dehydrogenase protein expression. While both glucose and glutamine starvation of host cells decreased viral titers, glutamine starvation led to a greater loss in virion production. Our lipidomics analysis revealed a peak in triacylglycerides early during infection and an increase in free fatty acids and diacylglyceride later in the viral life cycle. Furthermore, we observed an increase in the protein expression of multiple lipogenic enzymes during infection. Interestingly, pharmacological inhibitors of glycolysis or lipogenesis resulted in decreased infectious virus production. Taken together, these results illustrate the global alterations in host cell metabolism during lytic gammaherpesvirus infection, establish essential pathways for viral production, and recommend targeted mechanisms to block viral spread and treat viral induced tumors.

IMPORTANCE

Viruses are intracellular parasites which lack their own metabolism, so they must hijack host cell metabolic machinery in order to increase the production of energy, proteins, fats, and genetic material necessary to replicate. Using murine herpesvirus 68 (MHV-68) as a model system to understand how similar human gammaherpesviruses cause cancer, we profiled the metabolic changes that occur during lytic MHV-68 infection and replication. We found MHV-68 infection of host cells increases glucose, glutamine, lipid, and nucleotide metabolic pathways. We also showed inhibition or starvation of glucose, glutamine or lipid metabolic pathways results in an inhibition of virus production. Ultimately, targeting changes in host cell metabolism due to viral infection can be used to treat gammaherpesvirus induced cancers and infections in humans.
Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism
Authors: Fanunza Elisa , Cheng Adam Z. , Auerbach Ashley A. , Stefanovska Bojana , Moraes Sofia N. , Lokensgard James R. , Biolatti Matteo , Dell’Oste Valentina , Bierle Craig J. , Bresnahan Wade A. , Harris Reuben S.
Published: February 2023

The APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses EBV and KSHV and the alpha-herpesviruses HSV-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting involvement of an immediate early or early (IE-E) viral protein. In support of this mechanism, cycloheximide treatment of HCMV-infected cells prevents the expression of viral proteins and simultaneously blocks APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which is a viral DNA synthesis inhibitor affecting late protein expression, still permits A3B relocalization. These results combine to show that the beta-herpesvirus HCMV uses a fundamentally different, RNR-independent molecular mechanism to antagonize APOBEC3B.

Importance

Human cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses in order to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
Human ovarian ageing is characterized by oxidative damage and mitochondrial dysfunction
Authors: Smits Myrthe A.J. , Schomakers Bauke V. , van Weeghel Michel , Wever Eric J.M. , Wüst Rob C.I. , Dijk Frederike , Janssens Georges E. , Goddijn Mariëtte , Mastenbroek Sebastiaan , Houtkooper Riekelt H. , Hamer Geert
Published: February 2023

Human ovarian ageing encompasses the age-related decline in female fertility. Oxidative stress and mitochondrial dysfunction in oocytes are suggested as causal, but corroborating evidence is limited. Using immunofluorescence imaging on human ovarian tissue, we found oxidative damage by protein and lipid (per)oxidation at the primordial follicle stage. Additionally, using comprehensive metabolomics and lipidomics, a cohort of 150 human germinal vesicles and metaphase I oocytes and 15 corresponding cumulus cell samples displayed a shift in glutathione to oxiglutathione ratio and depletion of phospholipids. Age-related changes in polar metabolites suggested a decrease in mitochondrial function, as demonstrated by NAD+, purine and pyrimidine depletion, while glycolysis substrates and glutamine accumulated with age. Oocytes of advanced maternal age likely used alternative energy sources like glycolysis and the adenosine salvage pathway, and possibly increased ATP production in cumulus cells. These findings indicate that oocytes of advanced maternal age suffer from oxidative damage and mitochondrial dysfunction.

Graphical abstract
Perforin-2 is a pore-forming effector of endocytic escape in cross-presenting dendritic cells
Authors: Rodríguez-Silvestre Pablo , Laub Marco , Davies Alexandra K. , Schessner Julia P. , Krawczyk Patrycja A. , Tuck Benjamin J. , McEwan William A. , Borner Georg H.H. , Kozik Patrycja
Published: February 2023

During initiation of antiviral and antitumour T cell-mediated immune responses, dendritic cells (DCs) cross-present exogenous antigens on MHC class I. Cross-presentation relies on the unique ‘leakiness’ of endocytic compartments in DCs, whereby internalised proteins escape into the cytosol for proteasome-mediated generation of MHC I-binding peptides. Given that type 1 conventional DCs excel at cross-presentation, we searched for cell-type specific effectors of endocytic escape. We devised an escape assay suitable for genetic screening and identified a pore-forming protein, perforin-2, as a dedicated effector exclusive to cross-presenting cells. Perforin-2 is recruited to antigen-containing compartments, where it undergoes maturation, releasing its pore-forming domain.Mpeg1-/-mice fail to efficiently prime CD8+T cells to cell-associated antigens, revealing an important role of perforin-2 in cytosolic entry of antigens during cross-presentation.

One-Sentence Summary

Pore-forming protein perforin-2 is a dedicated effector of endocytic escape specific to cross-presenting cells
Spatial and compositional variations in fruit characteristics of papaya (Carica papayacv. Tainung No. 2) during ripening
Authors: Chung Sun Woo , Kim Seolah , Kim Seong Cheol
Published: February 2023

Papaya fruit (Carica papaya) has different degrees of ripening within a fruit, affecting its commercial market value. The fruit characteristics of ‘Tainung No. 2’ papaya was investigated at the stem-end, middle, and calyx-end parts at three ripening stages and categorized based on fruit skin coloration: unripe at ca. 16 weeks after anthesis (WAA), half-ripe at ca. 18 WAA, and full-ripe at ca. 20 WAA. The fruits maintained an elliptical shape during ripening with 2.36 of the ratios of the length to the width. The peel and pulp color changed from green to white to yellow during ripening, regardless of the fruit three parts. In the pulp, soluble solid content increased to about 320% and firmness decreased to about 99% during ripening but did not differ among fruit three parts. Individual nutrient contents, including primary and secondary metabolites, and minerals, changed dynamically between the ripening stages and fruit parts. Total carbohydrates and proteins, N, and K, were more accumulated at the stem-end during ripening, meanwhile fructose, glucose, Mg, and Mn were at the calyx-end. In the principal component analysis, ripening stages and fruit parts were distinctly determined by the first and second principal components, respectively. These results provide fundamental information for improving ripening during papaya cultivation.
Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution
Authors: Feng Xuehuan , Zheng Jinfang , Irisarri Iker , Yu Huihui , Zheng Bo , Ali Zahin , de Vries Sophie , Keller Jean , Fürst-Jansen Janine M.R. , Dadras Armin , Zegers Jaccoline M.S. , Rieseberg Tim P. , Ashok Amra Dhabalia , Darienko Tatyana , Bierenbroodspot Maaike J. , Gramzow Lydia , Petroll Romy , Haas Fabian B. , Fernandez-Pozo Noe , Nousias Orestis , Li Tang , Fitzek Elisabeth , Grayburn W. Scott , Rittmeier Nina , Permann Charlotte , Rümpler Florian , Archibald John M. , Theißen Günter , Mower Jeffrey P. , Lorenz Maike , Buschmann Henrik , von Schwartzenberg Klaus , Boston Lori , Hayes Richard D. , Daum Chris , Barry Kerrie , Grigoriev Igor V. , Wang Xiyin , Li Fay-Wei , Rensing Stefan A. , Ari Julius Ben , Keren Noa , Mosquna Assaf , Holzinger Andreas , Delaux Pierre-Marc , Zhang Chi , Huang Jinling , Mutwil Marek , de Vries Jan , Yin Yanbin
Published: February 2023

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains ofZygnema circumcarinatumand one strain ofZ. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model systemZ. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

HIGHLIGHTS

Genomes of four filamentous algae (Zygnema) sisters to land plants

Zygnemaare rich in genes for multicellular growth and environmental acclimation: signaling, lipid modification, and transport

Cell wall innovations: diversification of hexameric rosette cellulose synthase in Zygnematophyceae

Co-expression networks reveal conserved modules for balancing growth and acclimation