bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms
Authors: Méndez Laura , Barratt Christopher D. , Durka Walter , Kissling W. Daniel , Eiserhardt Wolf L. , Baker William J. , Randrianasolo Vonona , Onstein Renske E.
Published: January 2023

Seed dispersal is a key process in the generation and maintenance of genetic diversity and genetic differentiation of plant populations in tropical ecosystems. During the Last Quaternary, most seed-dispersing megafauna was lost globally, but whether this has caused dispersal limitation, loss of genetic diversity, and increased genetic differentiation between plant populations with large, ‘megafaunal’ fruits (i.e., > 4 cm - megafruits) remains unclear.

Here, we assessed whether megafrugivore extinctions in Madagascar (e.g., giant lemurs, elephant birds) have affected the genetic diversity and genetic differentiation of four animal-dispersed Malagasy palm (Arecaceae) species with large (Borassus madagascariensis), medium-sized (Hyphaene coriacea, Bismarckia nobilis), and small (Chrysalidocarpus madagascariensis) fruits. We integrated double-digest restriction-site-associated DNA sequencing (ddRAD) of 167 individuals from 25 populations with (past) distribution ranges for extinct and extant seed-dispersing animal species, climate and human impact data, and applied linear mixed-effects models to explore the drivers of variation in genetic diversity and genetic differentiation across Malagasy palm populations.

We detected higher genetic diversity in species with megafruits than in the species with small fruits, and genetic differentiation was lowest for the human-used medium-sized megafruit species. Furthermore, we found that a higher number of shared extinct megafrugivore species between palm population pairs was associated with less genetic differentiation, indicating higher gene flow, whereas no relationship with extant frugivores – that are not able to swallow and disperse the seeds – was found. Finally, genetic diversity decreased with road density, whereas genetic differentiation decreased with increasing human population density, but only for populations with megafruits.

Our results suggest that the legacy of megafrugivores regularly achieving long dispersal distances is still reflected in the genetic diversity and genetic differentiation of palms that were formerly dispersed by such large animals. Furthermore, high genetic diversity and low genetic differentiation were possibly maintained after the megafauna extinctions through human-mediated dispersal, long generation times, and long lifespans of these palms. Our study illustrates how integrating genetics with ecological data on species interactions, climate, and human impact, provides novel insights into the consequences of megafauna extinctions for plants with megafruits.
Measuring the long arm of childhood in real-time: Epigenetic predictors of BMI and social determinants of health across childhood and adolescence
Authors: Raffington Laurel , Schneper Lisa , Mallard Travis , Fisher Jonah , Vinnik Liza , Hollis-Hansen Kelseanna , Notterman Daniel A. , Tucker-Drob Elliot M. , Mitchell Colter , Harden Kathryn P.
Published: January 2023

Children who are socioeconomically disadvantaged are at increased risk for high body mass index (BMI) and multiple diseases in adulthood. The developmental origins of health and disease hypothesis proposes that early life conditions affect later-life health in a manner that is only partially modifiable by later-life experiences. Epigenetic mechanisms may regulate the influence of early life conditions on later life health. Recent epigenetic studies of adult blood samples have identified DNA-methylation sites associated with higher BMI and worse health (epigenetic-BMI).

Here, we used longitudinal and twin study designs to examine whether epigenetic predictors of BMI developed in adults are valid biomarkers of child BMI and are sensitive to early life social determinants of health. Salivary epigenetic-BMI was calculated from two samples: (1) N=1,183 8-to-19-year-olds (609 female,meanage=13.4) from the Texas Twin Project (TTP), and (2) N=2,020 children (1,011 female) measured at 9 and 15 years from the Future of Families and Child Well-Being Study (FFCWS).

We found that salivary epigenetic-BMI is robustly associated with children’s BMI (r=0.36 tor=0.50). Longitudinal analysis suggested that epigenetic-BMI is highly stable across adolescence, but remains both a leading and lagging indicator of BMI change. Twin analyses showed that epigenetic-BMI captures differences in BMI between monozygotic twins. Moreover, children from more disadvantaged socioeconomic status (SES) and marginalized race/ethnic groups had higher epigenetic-BMI, even when controlling for concurrent BMI, pubertal development, and tobacco exposure. SES at birth relative to concurrent SES best predicted epigenetic-BMI in childhood and adolescence.

We show for the first time that epigenetic predictors of BMI calculated from pediatric saliva samples are valid biomarkers of childhood BMI that are sensitive to social inequalities. Our findings are in line with the hypothesis that early life conditions are especially important factors in epigenetic regulation of later life health. Research showing that health later in life is linked to early life conditions have important implications for the development of early-life interventions that could significantly extend healthy life span.
Effects of assisted gene flow on the flowering onset of the annual legumeLupinus angustifoliusL.: from phenotype to genotype
Authors: Sacristán-Bajo Sandra , Lara-Romero Carlos , García-Fernández Alfredo , Prieto-Benítez Samuel , Morente-López Javier , Rubio Teso María Luisa , Torres Elena , Iriondo José María
Published: January 2023

Current climate change may impede species to evolutionary adapt quickly enough to environmental changes, threatening their survival. In keystone populations, it may be necessary to consider the introduction of adaptive alleles through assisted gene flow. Considering that flowering time is a crucial trait in plant response to global warming, the objective of our study was to test the potential benefits and limitations of assisted gene flow for enhancing the evolutionary potential ofLupinus angustifoliusL. (Fabaceae) populations through the advancement of flowering time in the context of global warming. Previous studies have shown that southern populations ofL. angustifoliusflower earlier than northern populations. We collected seeds from four populations in Spain from two different latitudes, and we established them in a common garden environment. To advance the flowering onset of northern populations, we used pollen from southern individuals to pollinate plants from northern populations, creating an F1 gene flow line. In the following season, the F1 gene flow line was self-pollinated to create an F2 self-pollination line. In parallel, individuals from the F1 gene flow line were pollinated again with pollen from northern plants, thus creating a backcross line. We also included a control line resulting from a random selection of individuals in each population in the first generation and their descendants from self-crosses in the second generation. We measured flowering onset, reproductive success and other plant traits in all individuals resulting from these lines. To characterize the effects of the assisted gene flow line at the genomic level, we carried out a gene capture analysis to sequence genes related to reproduction, growth, stress, nitrogen, and alkaloids in individuals from the F1 gene flow line and the control line in the first generation. All gene flow-derived lines flowered significantly earlier than the control line. Furthermore, plants from the F1 gene flow line produced heavier seeds and had a lower shoot growth than the control line. Genomic analyses identified 36 SNPs outliers that were associated to flowering onset, seed weight, and shoot growth. These results highlight that assisted gene flow can increase the evolutionary potential of populations by modifying the values of a specific trait. However, the modification of one trait may affect the values of other plant traits. The characteristics of the populations will have a fundamental effect on the results of assisted gene flow. Therefore, the selection of the donor population is a critical step in this process.
A machine learning approach to quantify individual gait responses to ankle exoskeletons
Authors: Ebers Megan R. , Rosenberg Michael C. , Kutz J. Nathan , Steele Katherine M.
Published: January 2023

We currently lack a theoretical framework capable of characterizing heterogeneous responses to exoskeleton interventions. Predicting an individual’s response to an exoskeleton and understanding what data are needed to characterize responses has been a persistent challenge. In this study, we leverage a neural network-based discrepancy modeling framework to quantify complex changes in gait in response to passive ankle exoskeletons in nondisabled adults. Discrepancy modeling aims to resolve dynamical inconsistencies between model predictions and real-world measurements. Neural networks identified models of (i)Nominalgait, (ii)Exoskeleton(Exo) gait, and (iii) theDiscrepancy(i.e., response) between them. If anAugmented(Nominal+Discrepancy) model captured exoskeleton responses, its predictions should account for comparable amounts of variance inExogait data as theExomodel. Discrepancy modeling successfully quantified individuals’ exoskeleton responses without requiring knowledge about physiological structure or motor control: a model ofNominalgait augmented with aDiscrepancymodel of response accounted for significantly more variance inExogait (medianR2for kinematics (0.928 – 0.963) and electromyography (0.665 – 0.788), (p< 0.042)) than theNominalmodel (medianR2for kinematics (0.863 – 0.939) and electromyography (0.516 – 0.664)). However, additional measurement modalities and/or improved resolution are needed to characterizeExogait, as the discrepancy may not comprehensively capture response due to unexplained variance inExogait (medianR2for kinematics (0.954 – 0.977) and electromyography (0.724 – 0.815)). These techniques can be used to accelerate the discovery of individual-specific mechanisms driving exoskeleton responses, thus enabling personalized rehabilitation.
Mutual antagonism between glucocorticoid and canonical Wnt signaling pathways in B-cell acute lymphoblastic leukemia
Authors: Bergeron Brennan P. , Barnett Kelly R. , Bhattarai Kashi Raj , Mobley Robert J. , Hansen Baranda S. , Brown Anthony , Kodali Kiran , High Anthony A. , Jeha Sima , Pui Ching-Hon , Peng Junmin , Pruett-Miller Shondra M. , Savic Daniel
Published: January 2023

Glucocorticoids (GCs; i.e., steroids) are important chemotherapeutic agents in the treatment of B-cell precursor acute lymphoblastic leukemia (B-ALL) andde novoGC resistance predicts relapse and poor clinical outcome in patients. Glucocorticoids induce B-ALL cell apoptosis through activation of glucocorticoid receptor (GR), a ligand-induced nuclear receptor transcription factor (TF). We previously identified disruptions to glucocorticoid receptor (GR)-boundcis-regulatory elements controllingTLE1expression in GC-resistant primary B-ALL cells from patients.TLE1is a GC-response gene up-regulated by steroids and functions as a canonical Wnt signaling repressor. To better understand the mechanistic relationship between GC signaling and canonical Wnt signaling, we performed diverse functional analyses that identified extensive crosstalk and mutual antagonism between these two signaling pathways in B-ALL. We determined that crosstalk and antagonism was driven by the binding of GR and the canonical Wnt signaling TFs LEF1 and TCF7L2 to overlapping sets ofcis-regulatory elements associated with genes impacting cell death and cell proliferation, and was further accompanied by overlapping and opposing transcriptional programs. Our data additionally suggest thatcis-regulatory disruptions atTLE1are linked to GC resistance through a dampening of the GC response and GC-mediated apoptosis via enhanced canonical Wnt signaling. As a result of the extensive genomic and gene regulatory connectivity between these two signaling pathways, our data supports the importance of canonical Wnt signaling in mediating GC resistance in B-ALL.
Spatial transcriptomic brain imaging reveals the effects of immunomodulation therapy upon specific regional brain cells in mouse dementia model
Authors: Lee Eun Ji , Bae Sungwoo , Suh Minseok , Choi Hongyoon , Choi Yoori , Hwang Do Won , Lee Dong Soo
Published: January 2023

Increasing evidence of brain-immune crosstalk raises expectations for the efficacy of novel immunotherapies in Alzheimer’s disease (AD), but the lack of methods to understand brain tissues make it difficult to examine therapeutics. Here, we investigated the changes of spatial transcriptomic signatures and brain cell type using the 10x Genomics Visium platform in immune modulated AD models by various treatments. To proceed with an analysis suitable for a single spot-based transcriptomics, we first organized a workflow for segmentation of neuroanatomical regions, establishment of appropriate gene combinations, and comprehensive review of altered brain cell signatures. Ultimately, we investigated spatial transcriptomic changes following administration of immunomodulators, NK cell supplements and anti-CD4 antibody, that ameliorate behavior impairment, and designated brain cells and regions showing probable associations with behavior changes. We provided the customized analytic pipeline into an application named STquantool. Thus, we anticipate that our approach can help researchers to interpret real action of drug candidate by simultaneously investigating the dynamics of all transcripts for development of novel AD therapeutics.
Sample size calculation for a NanoString GeoMx spatial transcriptomics experiment to study predictors of fibrosis progression in non-alcoholic fatty liver disease
Authors: Ryaboshapkina Maria , Azzu Vian
Published: January 2023

Sample size calculation for spatial transcriptomics is a novel and understudied research topic. Prior publications focused on powering spatial transcriptomics studies to detect specific cell populations or spatially variable expression patterns on tissue slides. However, power calculations for translational or clinical studies often relate to the difference between patient groups, and this is poorly described in the literature. Here, we present a stepwise process for sample size calculation to identify predictors of fibrosis progression in non-alcoholic fatty liver disease as a case study. We illustrate how to infer study hypothesis from prior bulk RNA-sequencing data, gather input requirements and perform a simulation study to estimate required sample size to evaluate gene expression differences between patients with stable fibrosis and fibrosis progressors with NanoString GeoMx Whole Transcriptome Atlas assay.

Key points

Spatial transcriptomics is predominantly used in unpowered exploratory research.

We demonstrate that spatial transcriptomics studies with NanoString GeoMx Whole Transcriptome Atlas can be powered to address differences between patient groups and illustrate the sample size calculation using fibrosis progression in non-alcoholic fatty liver disease as an example.

We note that established software implementing negative binomial mixed effect models lme4 and GLMMadaptive yield more similar fold change estimates to simulated data than the recently published software GeoDiff.
No trade-off between the use of space and time for working memory
Authors: de Vries Eelke , Fejer George , van Ede Freek
Published: January 2023

Space and time can each act as scaffolds for the individuation and selection of visual objects in working memory. Here we ask whether there is a trade-off between the use of space and time for visual working memory: whether observers will rely less on space, when memoranda can additionally be individuated through time. We tracked the use of space through directional biases in microsaccades after attention was directed to memory contents that had been encoded simultaneously or sequentially to the left and right of fixation. We found that spatial gaze biases were preserved when participants could (Experiment 1) and even when they had to (Experiment 2) additionally rely on time for object individuation. Thus, space remains a profound organizing medium for working memory even when other organizing sources are available and utilised, with no evidence for a trade-off between the use of space and time.

SIGNIFICANCE STATEMENT

Space and time provide two foundational dimensions that govern not only our sensations and actions, but also the organisation of internal representations in working memory. Space and time have each been shown to provide an automatic organising principle – or scaffold – for memory retention. We uniquely address whether there is a trade-off between the use of space and time for working memory. We show that the profound and automatic reliance on memorised space is preserved not only when time can, but even when time has to be used for individuation and selection of memory contents. This shows there is no trade-off between spatial and temporal codes available for memory organisation, advancing our understanding of the spatial-temporal architecture of mind.
Landscape of IGH germline genes of Chiroptera and the pattern ofRhinolophus affinisbat IGH CDR3 repertoire
Authors: Ma Long , Liu Longyu , Li Jun , Zhou Hao , Xiao Jiaping , Ma Qingqing , Yao Xinsheng
Published: January 2023

The emergence and re-emergence of a number of viruses from bats that impact human and animal health has resulted in a resurgence of interest in bat immunology. Characterizing the immune receptor repertoire is critical to understanding how bats coexist with viruses in the absence of disease and developing new therapeutics to target viruses in humans and susceptible livestock. We annotated IGH germline genes ofRhinolophus ferrumequinum(RF),Phyllostomus discolor(RD) andPipistrellus pipistrellus(PP), and investigated the evolutionary relationship between bat germline genes and that of human, mouse, cow, and dog. The IGH repertoire characteristics ofRhinolophus affinisbat (RA) were also analyzed. The V gene families of all three bat species can be classified into three Clan, although PD is special with the abnormal length of IGH locus and 22 reverse V genes. Moreover, the bats germline genes are quite differed from those of human, mouse, cow, and dog in evolution, but the three bat species have high homology. The CDR3 repertoire of RA are unique in many aspects including CDR3 subclass, V/J genes access and pairing, CDR3 clones and somatic high-frequency mutation compared with that of human and mouse, which may be the immunologic basis for the asymptomatic nature of viral infection in bats. This study provide immune genome information and extensive reference for the basic research of bat and virus infection mechanism.
Comparison of force fields to study the zinc-finger containing protein NPL4, a target for Antabuse in cancer therapy
Authors: Scrima Simone , Tiberti Matteo , Ryde Ulf , Lambrughi Matteo , Papaleo Elena
Published: January 2023

All-atom molecular dynamics (MD) simulations are a powerful approach to study the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging for MD simulations. Over one-third of known protein structures bind metal ions and have various cellular functions, such as structural stability, catalysis, and regulation. NPL4 is a zinc-binding protein and works as a cofactor for p97, and together they regulate protein homeostasis. NPL4 is also of biomedical importance and has been proposed as the target of Antabuse, a drug recently repurposed for cancer treatment. Recent experimental studies have proposed that the Antabuse metabolites, bis- (diethyldithiocarbamate)-copper (CuET) and cupric ions released from CuET, induce NPL4 misfolding and consequent aggregation. However, the molecular details of the mechanisms of interactions of Antabuse metabolites with NPL4 and the consequent structural effects are still elusive. In this context, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper or Antabuse metabolites the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. We first examined different sets of non-bonded parameters, because we want to study the misfolding mechanism and cannot rule out that the zinc ion may detach from the protein structure during the process and copper replaces it in the metal binding site. We investigated the force-field ability to model the coordination geometry of the metal ions by comparing the results from MD simulations with optimized geometries from quantum mechanics (QM) calculations using model systems of the zinc coordination site for NPL4. Furthermore, we investigated the performance of a MD force field including bonded parameters to treat copper ions and metal-coordinating atoms in NPL4 that we obtained based on QM calculations.
Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans
Authors: Yaakub Siti N. , White Tristan A. , Roberts Jamie , Verhagen Lennart , Stagg Charlotte J. , Hall Stephen , Fouragnan Elsa F.
Published: January 2023

Low-intensity transcranial ultrasound stimulation (TUS) is an emerging non-invasive technique for focally modulating human brain function. The mechanisms and neurochemical substrates underlying TUS neuromodulation in humans and how these relate to excitation and inhibition are still poorly understood. In 24 healthy controls, we separately stimulated two deep cortical regions and investigated the effects of theta-burst TUS, a protocol shown to increase corticospinal excitability, on the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) and functional connectivity. We show for the first time in humans that theta-burst TUS selectively reduces GABA levels in the posterior cingulate, but not the dorsal anterior cingulate cortex. Functional connectivity increased following TUS in both regions. Our findings suggest that TUS changes overall excitability by reducing GABAergic inhibition, that changes in TUS-mediated neuroplasticity last at least 50 minutes after stimulation, and that these effects may be state-dependent – a mechanism increasingly recognized to influence the brain’s response to neuromodulation.
The effects of aging and hearing impairment on listening in noise
Authors: Boncz Ádám , Szalárdy Orsolya , Velősy Péter Kristóf , Béres Luca , Winkler István , Tóth Brigitta
Published: January 2023

Listening in a noisy environment (e.g., speech in noise) relies on the fundamental ability to extract coherence from the variable sensory input. This allows the detection active sound sources and their segregation of them from the rest of the scene (figure-ground segregation). Peripheral and central causes of age-related decline of listening in noise were assessed by a tone-cloud-based figure detection task. In two conditions differing in the amount of noise, figure detection performance was equalized between young, normal-hearing, and hearing-impaired elderly listeners by adapting the stimulation separately to the abilities of each person. Based on behavioral measures and event-related brain potentials (ERP), in the absence of cognitive deficits, aging alone does not appear to significantly deteriorate the ability to detect sound sources in noise, although ERPs show delayed perceptual processes and some expected deterioration in attention and/or executive functions. However, even mild hearing impairment substantially reduces the ability to segregate individual sound sources within a complex auditory scene, and susceptibility to masking noise increases together with the severity of the hearing deficit.

Significance Statement

This work provides new information about the contributions of central and peripheral causes to the typical age-related decline of listening in a noisy environment. Behavioral and neurophysiological data collected in a well-controlled model of listening in noise suggest that aging alone does not significantly reduce the ability to detect sound sources in a complex auditory scene. However, even mild hearing impairment significantly reduces this ability. The stimulus paradigm used appears to be quite sensitive to hearing loss, making it potentially useful for the early detection of hearing problems.
Accurate age prediction from blood using of small set of DNA methylation sites and a cohort-based machine learning algorithm
Authors: Varshavsky Miri , Harari Gil , Glaser Benjamin , Dor Yuval , Shemer Ruth , Kaplan Tommy
Published: January 2023

Chronological age prediction from DNA methylation sheds light on human aging, indicates poor health and predicts lifespan. Current clocks are mostly based on linear models from hundreds of methylation sites, and are not suitable for sequencing-based data.

We present GP-age, an epigenetic clock for blood, that uses a non-linear cohort-based model of 11,910 blood methylomes. Using 30 CpG sites alone, GP-age outperforms state-of-the-art models, with a median accuracy of ~2 years on held-out blood samples, for both array and sequencing-based data. We show that aging-related changes occur at multiple neighboring CpGs, with far-reaching implications on aging research at the cellular level. By training three independent clocks, we show consistent deviations between predicted and actual age, suggesting individual rates of biological aging.

Overall, we provide a compact yet accurate alternative to array-based clocks for blood, with future applications in longitudinal aging research, forensic profiling, and monitoring epigenetic processes in transplantation medicine and cancer.

Graphical abstract

Machine learning analysis of a large cohort (~12K) of DNA methylomes from blood

A 30-CpG regression model achieves a 2.1-year median error in predicting age

Improved accuracy (≥1.75 years) from sequencing data, using neighboring CpGs

Paves the way for easy and accurate age prediction from blood, using NGS data

Motivation

Epigenetic clocks that predict age from DNA methylation are a valuable tool in the research of human aging, with additional applications in forensic profiling, disease monitoring, and lifespan prediction. Most existing epigenetic clocks are based on linear models and require hundreds of methylation sites. Here, we present a compact epigenetic clock for blood, which outperforms state-of-the-art models using only 30 CpG sites. Finally, we demonstrate the applicability of our clock to sequencing-based data, with far reaching implications for a better understanding of epigenetic aging.
Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems
Authors: Paul Raegan , Rogers Timothy J. , Fullerton Kate M. , Selci Matteo , Cascone Martina , Stokes Murray H. , Steen Andrew D. , de Moor J. Maarten , Chiodi Agostina , Stefánsson Andri , Halldórsson Sæmundur A. , Ramirez Carlos J. , Jessen Gerdhard L. , Barry Peter H. , Cordone Angelina , Giovannelli Donato , Lloyd Karen G.
Published: January 2023

Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80°C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80°C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.
HumanVDACpseudogenes: an emerging role forVDAC1P8pseudogene in acute myeloid leukemia
Authors: Pappalardo Xena Giada , Risiglione Pierpaolo , Zinghirino Federica , Ostuni Angela , Luciano Daniela , Bisaccia Faustino , De Pinto Vito , Guarino Francesca , Messina Angela
Published: January 2023

Background

Voltage-dependent anion selective channels (VDACs) are the most abundant mitochondrial outer membrane proteins, encoded in mammals by three genes,VDAC1,2and3, mostly ubiquitously expressed. As ‘mitochondrial gatekeepers’,VDACscontrol organelle and cell metabolism and are involved in many diseases. Despite the presence of numerousVDACpseudogenes in the human genome, their significance and possible role in VDAC protein expression has not yet been considered.

Results

We investigated the relevance of processed pseudogenes of humanVDACgenes, both in physiological and in pathological contexts. Using high-throughput tools and querying many genomic and transcriptomic databases, we show that someVDACpseudogenes are transcribed in specific tissues and pathological contexts. The obtained experimental data confirm an association of theVDAC1P8pseudogene with acute myeloid leukemia (AML).

Conclusions

Ourin-silicocomparative analysis between theVDAC1gene and itsVDAC1P8pseudogene, together with experimental data produced in AML cellular models, indicate a specific over-expression of theVDAC1P8pseudogene in AML, correlated with a downregulation of the parentalVDAC1gene.
Identification of novel sex determination loci in Japanese weedy melon
Authors: Nashiki Akito , Matsuo Hiroki , Takano Kota , Fitriyah Fauziatul , Isobe Sachiko , Shirasawa Kenta , Yoshioka Yosuke
Published: January 2023

Sex expression contributes to fruit quality and yield in the Cucurbitaceae. In melon, orchestrated regulation by sex determination genes explains the mechanism of sex expression, resulting in a great variety of sexual morphologies. In this study, we examined the Japanese weedy melon UT1, which does not follow the reported model of sex expression. We conducted QTL analysis using F2plants for flower sex on the main stem and the lateral branch and mapped a “femaleness” locus on Chr. 3 (Fem3.1) and a “type of flower femaleness” (female or bisexual) locus on Chr. 8 (tff8.1).Fem3.1included the known sex determination geneCmACS11. Sequence comparison ofCmACS11between parental lines revealed three nonsynonymous SNPs. A CAPS marker developed from one of the SNPs was closely linked to femaleness in two F2populations with different genetic backgrounds. The femaleness allele was dominant in F1lines from crosses between UT1 and diverse cultivars and breeding lines. This study suggests that the identity oftff8.1isCmCPR5, a recently reported bisexual flower control gene. We found that the Japanese weedy melon UT1 does not follow the conventional sex expression model because of the interaction of the lociFem3.1andtff8.1with the previously reported sex determination genes. The results of this study provide new insights into the molecular mechanisms of sex determination in melons and considerations for the application of femaleness in melon breeding.

Key message

Japanese weedy melon exhibits unique sex expression with interactions between previously reported sex determination genes and two novel loci.
Improved Isolation of Extracellular Vesicles by Removal of Both Free Proteins and Lipoproteins
Authors: Ter-Ovanesyan Dmitry , Gilboa Tal , Budnik Bogdan , Nikitina Adele , Whiteman Sara , Lazarovits Roey , Trieu Wendy , Kalish David , Church George M , Walt David R
Published: January 2023

Extracellular vesicles (EVs) are released by all cells into biofluids such as plasma. The separation of EVs from highly abundant free proteins and similarly-sized lipoproteins remains technically challenging. We developed a digital ELISA assay based on Single Molecule Array (Simoa) technology for ApoB-100, the protein component of several lipoproteins. Combining this ApoB-100 assay with previously developed Simoa assays for albumin and three tetraspanin proteins found on EVs (Ter-Ovanesyan*, Norman* et al., 2021), we were able to measure the separation of EVs from both lipoproteins and free proteins. We used these five assays to compare EV separation from lipoproteins using size exclusion chromatography (SEC) with resins containing different pore sizes. We also developed improved methods for EV isolation based on combining several types of chromatography resins in the same column. We present a simple approach to quantitatively measure the main contaminants of EV isolation in plasma and apply this approach to develop novel methods for isolating highly-pure EVs from human plasma. These methods will enable applications where high purity EVs are required to both understand EV biology and profile EVs for biomarker discovery.
Effect of caffeine and other xanthines on liver sinusoidal endothelial cell ultrastructure
Authors: Mao Hong , Szafranska Karolina , Kruse Larissa , Holte Christopher , Wolfson Deanna L. , Ahluwalia Balpreet Singh , Whitchurch Cynthia B. , Cole Louise , Lockwood Glen P. , Diekmann Robin , Le Couteur David , Cogger Victoria C. , McCourt Peter A.G.
Published: January 2023

Xanthines such as caffeine and theobromine are among the most consumed psychoactive stimulants in the world, either as natural components of coffee, tea and chocolate, or as food additives. The present study assessed if xanthines affect liver sinusoidal endothelial cells (LSEC). Cultured primary rat LSEC were challenged with xanthines at concentrations typically obtained from normal consumption of xanthine-containing beverages, food or medicines; and at higher concentrations below thein vitrotoxic limit. The fenestrated morphology of LSEC were examined with scanning electron and structured illumination microscopy. All xanthine challenges had no toxic effects on LSEC ultrastructure as judged by LSEC fenestration morphology, or function as determined by endocytosis studies. All xanthines in high concentrations (150 μg/mL) increased fenestration frequency but at physiologically relevant concentrations, only theobromine (8 μg/mL) showed an effect. LSEC porosity was influenced only by high caffeine doses which also shifted the fenestration distribution towards smaller pores. Moreover, a dose-dependent increase in fenestration number was observed after caffeine treatment. If these compounds induce similar changesin vivo, age-related reduction of LSEC porosity can be reversed by oral treatment with theobromine or with other xanthines using targeted delivery.
mRNA decay can be uncoupled from deadenylation during stress response
Authors: Czarnocka-Cieciura Agnieszka , Turtola Matti , Tomecki Rafał , Krawczyk Paweł , Mroczek Seweryn , Orzeł Wiktora , Saha Upasana , Jensen Torben Heick , Dziembowski Andrzej , Tudek Agnieszka
Published: January 2023

The polyadenosine tail (pA-tail) regulates mRNA nuclear export, stability, and translatability. Based on reporter constructs, the prevailing model suggests that pA-tail removal mediated by Ccr4-NOT or PAN2/3 deadenylases is required for mRNA decapping and degradation. Here, we use direct RNA sequencing to track mRNA deadenylation and decay at steady-state and in stress conditions to show a global correlation between deadenylation and decay. Interestingly, codon optimality, previously postulated to dictate mRNA stability, only strongly affects decay of conserved and abundant transcripts, such as coding for ribosomal protein subunits. Degradation of those mRNAs is also accelerated in response to stress. Still, the in-depth analysis revealed that deadenylation is a factor that contributes to degradation but is not indispensable for decapping. We further demonstrate that deadenylation is the fastest for newly made tails depending on polyA-binding protein Pab1. Unexpectedly, decapping initiates on mRNAs of pA-tails of 20-35 adenosines presumably bound by Pab1.
TCGAnalyzeR: a web application for integrative visualization of molecular and clinical data of cancer patients for cohort and associated gene discovery
Authors: Zengin Talip , Masud Başak Abak , Önal-Süzek Tuğba
Published: January 2023

Motivation

The vast size and complexity of The Cancer Genome Atlas (TCGA) database with multidimensional molecular and clinical data of ~11,000 cancer patients of 33 cancer types challenge the effective utilization of this valuable resource. Therefore, we built a web application named TCGAnalyzeR with the main idea of presenting an integrative visualization of mutations, transcriptome profile, copy number variation and clinical data allowing researchers to facilitate the identification of customized patient cohorts and gene sets for better decision-making for oncologists and cancer researchers.

Results

We present TCGAnalyzeR for integrative visualization of pre-analyzed TCGA data with the several novel modules: (i) Simple nucleotide variations with driver prediction; (ii) Recurrent copy number alterations; (iii) Differential expression in tumor versus normal, with pathway enrichment and the survival analysis; (iii) TCGA clinical data and survival analysis; (iv) External subcohorts from literature, curatedTCGAData and BiocOncoTK R packages; (v) Internal patient clusters determined using iClusterPlus R package or signature-based expression analysis. TCGAnalyzeR provides clinical oncologists and cancer researchers interactive and integrative representations of these multi-omic, pan-cancer TCGA data with availability of subcohort analysis and visualization. TCGAnalyzeR can be used to create their own custom gene sets for pan-cancer comparisons, to create custom patient subcohorts comparing external subcohorts (MSI, Immune, PAM50, Triple Negative, IDH1, miRNA, etc) along with our internal patient clusters, to visualize cohort-centric or gene-centric results along with pathway enrichment and survival analysis graphically on an interactive web tool.

Availability

TCGAnalyzeR is freely available on the web athttp://tcganalyzer.mu.edu.tr.

Contact

tugbasuzek@mu.edu.tr

Supplementary information

Supplementary data are available atBioinformaticsonline.
Variable effects ofWolbachiaon alphavirus infection inAedes aegypti
Authors: Dodson Brittany L. , Pujhari Sujit , Brustolin Marco , Metz Hillery C. , Rasgon Jason L.
Published: January 2023

2.

Wolbachia pipientis(=Wolbachia) has promise as a tool to suppress virus transmission byAedes aegyptimosquitoes. However,Wolbachiacan have variable effects on mosquito-borne viruses. This variation remains poorly characterized, yet the multimodal effects ofWolbachiaon diverse pathogens could have important implications for public health. Here, we examine the effects of somatic infection with two strains ofWolbachia(wAlbB andwMel) on the alphaviruses Sindbis virus (SINV), O’nyong-nyong virus (ONNV), and Mayaro virus (MAYV) inAe. aegypti. We found variable effects ofWolbachiaincluding enhancement and suppression of viral infections, with some effects depending onWolbachiastrain. BothwAlbB- andwMel-infected mosquitoes showed enhancement of SINV infection rates one week post-infection, withwAlbB-infected mosquitoes also having higher viral titers than controls. Infection rates with ONNV were low across all treatments and no significant effects ofWolbachiawere observed. The effects ofWolbachiaon MAYV infections were strikingly strain-specific;wMel strongly blocked MAYV infections and suppressed viral titers, whilewAlbB did not influence MAYV infection. The variable effects ofWolbachiaon vector competence underscore the importance of further research into how this bacterium impacts the virome of wild mosquitoes including the emergent human pathogens they transmit.

Impact statement

In recent years, wild populations ofAedes aegyptimosquitoes have been deliberately infected withWolbachia—a bacterium that helps to curb the spread of some pathogens including dengue virus. But how doesWolbachiaaffect the ability of mosquitoes to become infected with and spread the many different viruses they encounter in nature? Here, we characterize the effects ofWolbachiaon three alphaviruses that cause illness in humans— Sindbis virus, O’nyong-nyong virus, and Mayaro virus. We findWolbachiahas variable effects on these pathogens, including significant enhancement of Sindbis virus infections. Our research has important implications for the design of vector control strategies, and suggests further research is needed to understand howWolbachiashapes the replication and transmission of diverse viruses.

3.

Data Summary

All data in the study are available in the Figures and supplementary material.
Microglia Proliferation Underlies Synaptic Dysfunction in the Prefrontal Cortex: Implications for the Pathogenesis of HIV-1-Associated Neurocognitive and Affective Alterations
Authors: Li Hailong , McLaurin Kristen A. , Mactutus Charles F. , Booze Rosemarie M.
Published: January 2023

Microglia, which are productively infected by HIV-1, are critical for brain development and maturation, as well as synaptic plasticity. The pathophysiology of HIV-infected microglia and their role in the pathogenesis of HIV-1-associated neurocognitive and affective alterations, however, remains understudied. Three complementary aims were undertaken to critically address this knowledge gap. First, the predominant cell type expressing HIV-1 mRNA in the dorsolateral prefrontal cortex of postmortem HIV-1 seropositive individuals with HAND was investigated. Utilization of a combined RNAscope multiplex fluorescent and immunostaining assay revealed prominent HIV-1 mRNA in microglia of postmortem HIV-1 seropositive individuals with HAND. Second, measures of microglia proliferation and neuronal damage were evaluated in chimeric HIV (EcoHIV) rats. Eight weeks after EcoHIV innoculation, enhanced microglial proliferation was observed in the medial prefrontal cortex (mPFC) of EcoHIV rats, evidenced by an increased number of cells co-localized with both Iba1+ and Ki67+ relative to control animals. Neuronal damage in EcoHIV infected rats was evidenced by pronounced decreases in both synaptophysin and post synaptic density protein 95 (PSD-95), markers of pre-synaptic and post-synaptic damage, respectively. Third, regression analyses were conducted to evaluate whether microglia proliferation mechanistically underlies neuronal damage in EcoHIV and control animals. Indeed, microglia proliferation accounts for 42-68.6% of the variance in synaptic dysfunction. Collectively, microglia proliferation induced by chronic HIV-1 viral protein exposure may underlie the profound synaptodendritic alterations in HIV-1. Understanding how microglia are involved in the pathogenesis of HAND and HIV-1-associated affective disorders affords a key target for the development of novel therapeutics.
Neuroimmune cortical organoids overexpressing C4A exhibit multiple schizophrenia endophenotypes
Authors: Stanton Morgan M. , Modan Sara , Taylor Patrick M. , Hariani Harsh N. , Sorokin Jordan , Rash Brian G. , Rao Sneha B. , López-Tobón Alejandro , Enriquez Luigi , Dang Brenda , Owango Dorah , O’Neill Shannon , Castrillo Carlos , Nicola Justin , Ye Kathy , Blattner Robert M. , Gonzalez Federico , Antonio Dexter , Ramkumar Pavan , Lash Andy , Flanzer Douglas , Bardehle Sophia , Gyoneva Stefka , Shah Kevan , Kato Saul , Skibinski Gaia
Published: January 2023

Elevated expression of the complement component 4A (C4A) protein has been linked to an increased risk of schizophrenia (SCZ). However, there are few human models available to study the mechanisms by which C4A contributes to the development of SCZ. In this study, we established a C4A overexpressing neuroimmune cortical organoid (NICO) model, which includes mature neuronal cells, astrocytes, and functional microglia. The C4A NICO model recapitulated several neuroimmune endophenotypes observed in SCZ patients, including modulation of inflammatory genes and increased cytokine secretion. C4A expression also increased microglia-mediated synaptic uptake in the NICO model, supporting the hypothesis that synapse and brain volume loss in SCZ patients may be due to excessive microglial pruning. Our results highlight the role of C4A in the immunogenetic risk factors for SCZ and provide a human model for phenotypic discovery and validation of immunomodulating therapies.
Woronin bodies move dynamically and bidirectionally by hitchhiking on early endosomes inAspergillus nidulans
Authors: Songster Livia D. , Bhuyan Devahuti , Christensen Jenna R. , Reck-Peterson Samara L.
Published: January 2023

The proper functioning of organelles depends on their intracellular localization, mediated by motor protein-dependent transport on cytoskeletal tracks. Rather than directly associating with a motor protein, peroxisomes move by hitchhiking on motile early endosomes in the filamentous fungusAspergillus nidulans. However, the cellular function of peroxisome hitchhiking is unclear. Peroxisome hitchhiking requires the protein PxdA, which is conserved within the fungal subphylum Pezizomycotina, but absent from other fungal clades. Woronin bodies are specialized peroxisomes that are also unique to the Pezizomycotina. In these fungi, multinucleate hyphal segments are separated by incomplete cell walls called septa that possess a central pore enabling cytoplasmic exchange. Upon damage to a hyphal segment, Woronin bodies plug septal pores to prevent wide-spread leakage. Here, we tested if peroxisome hitchhiking is important for Woronin body motility, distribution, and function inA. nidulans. We show that Woronin body proteins are present within all motile peroxisomes and hitchhike on PxdA-labeled early endosomes during bidirectional, long-distance movements. Loss of peroxisome hitchhiking by knocking outpxdAsignificantly affected Woronin body distribution and motility in the cytoplasm, but Woronin body hitchhiking is ultimately dispensable for septal localization and plugging.