bluuebunny/crossref_metadata_2025 huggingface dataset:
Daily time constraints limit behavioural capacity to cope with thermally increased metabolic demands
Authors: Byrnes Evan E. , Adam Timo , Feldmann Carlina C. , Kaplinskaya Larisa , Sticker Kevin , Fredebeul Raphael Joshua , Lear Karissa O. , Morgan David L. , Beatty Stephen J. , Langrock Roland , Gleiss Adrian C.
Published: November 2023

Increased environmental temperatures result in greater energy demands for ectotherms, however, it is currently not clear if these energy demands can effectively be met by increased foraging effort. Here, we tested the temperature dependence of foraging effort and metabolic rate in an aquatic ectotherm across its entire natural thermal range. We developed a novel hidden Markov model to detect behavioural states in long-term body acceleration data collected from free-ranging bull sharks between 19 and 33 °C, and found that increasing temperature altered both the timing and extent of foraging effort. Our data revealed asymmetrical increases of metabolic demands and foraging effort; standard metabolic rates increased exponentially with temperature, but foraging effort increased logarithmically. The observed decoupling of foraging effort and energy demand suggests individuals face increased energy deficits at higher temperatures, confirmed by concomitant reductions in body condition measured in this population with increasing temperatures. We suggest that alterations in the well-established trade-offs between foraging and predation risk coupled with time constraints imposed by high temperatures limit the capacity of animals to cope with environmental temperatures well below critical temperatures.
Determination of Metabolic Fluxes by Deep Learning of Isotope Labeling Patterns
Authors: Law Richard C. , O’Keeffe Samantha , Nurwono Glenn , Ki Rachel , Lakhani Aliya , Lai Pin-Kuang , Park Junyoung O.
Published: November 2023

Fluxomics offers a direct readout of metabolic state but relies on indirect measurement. Stable isotope tracers imprint flux-dependent isotope labeling patterns on metabolites we measure; however, the relationship between labeling patterns and fluxes remains elusive. Here we innovate a two-stage machine learning framework termed ML-Flux that streamlines metabolic flux quantitation from isotope tracing. We train machine learning models by simulating atom transitions across five universal metabolic models starting from 2613C-glucose,2H-glucose, and13C-glutamine tracers within feasible flux space. ML-Flux employs deep-learning-based imputation to take variable measurements of labeling patterns as input and successive neural networks to convert the ensuing comprehensive labeling information into metabolic fluxes. Using ML-Flux with multi-isotope tracing, we obtain fluxes through central carbon metabolism that are comparable to those from a least-squares method but orders-of-magnitude faster. ML-Flux is deployed as a webtool to expand the accessibility of metabolic flux quantitation and afford actionable information on metabolism.
Sex chromosome turnover in hybridizing stickleback lineages
Authors: Yi Xueling , Wang Dandan , Reid Kerry , Feng Xueyun , Löytynoja Ari , Merilä Juha
Published: November 2023

Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. We first identified an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses. We then verified this region as the SDR in most other WL populations and demonstrated an ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosomes replace the older and heteromorphic LG12 sex chromosomes. The results provide a rare glimpse of ongoing sex chromosome turnover and indicate possible existence of additional but yet undiscovered sex chromosome diversity inPungitiussticklebacks.

Teaser

Evolutionarily young sex chromosomes replace the older ones in the hybrid zone of EuropeanPungitiusstickleback lineages.
Network medicine-based epistasis detection in complex diseases: ready for quantum computing
Authors: Hoffmann Markus , Poschenrieder Julian M. , Incudini Massimiliano , Baier Sylvie , Fitz Amelie , Maier Andreas , Hartung Michael , Hoffmann Christian , Trummer Nico , Adamowicz Klaudia , Picciani Mario , Scheibling Evelyn , Harl Maximilian V. , Lesch Ingmar , Frey Hunor , Kayser Simon , Wissenberg Paul , Schwartz Leon , Hafner Leon , Acharya Aakriti , Hackl Lena , Grabert Gordon , Lee Sung-Gwon , Cho Gyuhyeok , Cloward Matthew , Jankowski Jakub , Lee Hye Kyung , Tsoy Olga , Wenke Nina , Pedersen Anders Gorm , Bønnelykke Klaus , Mandarino Antonio , Melograna Federico , Schulz Laura , Climente-Gonzalez Héctor , Wilhelm Mathias , Iapichino Luigi , Wienbrandt Lars , Ellinghaus David , Van Steen Kristel , Grossi Michele , Furth Priscilla A. , Hennighausen Lothar , Di Pierro Alessandra , Baumbach Jan , Kacprowski Tim , List Markus , Blumenthal David B.
Published: November 2023

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1–3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-basedepistasisdetection vialocal search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.
MS/MS fragmentation pattern analysis confirms the production of the new esterified bile acids by the human gut microbiota
Authors: Garcia Carlos J. , García-Villalba Rocio , Beltrán David , Frutos-Lisón Maria D. , Tomás-Barberán Francisco A.
Published: November 2023

The pathophysiology of bile acids (BAs) has been widely studied. The BAs are signaling molecules that affect lipids and glucose homeostasis via activation of BAs FRX and TGR5 receptors in the liver and peripheral tissues. The ratio of conjugated/unconjugated BAs seems relevant to quantify these interactions and, therefore, the impact on the metabolism. The gut microbiota plays a key role because they convert the primary BAs into the secondary BAs, hydrolyzes the hepatically conjugated BAs and re-conjugates BAs with amino acids. New re-conjugated BAs with amino acids (MCBAs) in the form of amides or esters have been recently suggested, but it was not possible to confirm them. This study evaluates the production of MCBAs by human gut microbiota in in vitro colonic fermentations and designs a bioanalytical method to discriminate between amides and esters. Amides and seven new esters of re-conjugated BAs composed of lithocholic acid conjugated with leucine, valine and aminobutyric acid were identified and confirmed by MS/MS after incubation with chenodeoxycholic acid and lithocholic acid. There were no specific fragments in negative polarity to discriminate between amides and esters. However, in positive polarity the amides showed a characteristic MS/MS fragment consisting of the loss of water from the released amino acid, while the esters showed the loss of water plus carbon monoxide. This study confirmed for the first time the presence of esterified MCBAs, in addition to amides, and characterized the specific MS/MS fragmentation patterns to identify and discriminate them. These results show for the first time the existence of re-conjugated BAs by ester bond and the capability to produce them by the gut microbes. This bioanalytical method will allow including these new MCBAs in the BAs analysis.
Novel role ofPeriploca laevigataextracts as anti-diabetic and anti-inflammatory function in pancreatic β cells exposed to hyperglycaemia
Authors: Trabelsi Ghada , Mellado Susana , Kalboussi Zahar , Chekir-Ghedira Leila , Pascual María
Published: November 2023

Type 2 Diabetes (T2D) is a major health problem worldwide. This metabolic disease is associated with high blood glucose levels due to insufficient insulin production by the pancreas, leading to an inflammatory immune response. Considering the beneficial roles of medicinal plants to control the diabetic complications of T2D, as well as the therapeutic roles of the extracts fromPeriploca laevigata(PL), this study evaluates the anti-diabetic and anti-inflammatory properties of PL extracts in the pancreatic β cell line INS-1E under hyperglycaemic. Our findings demonstrated, for the first time, that whereas PL extracts tends to upregulate the insulin gene expression, PL extract from leaves increase significantly the gene expression of GLUT-2 and the transcription factor PDX-1 in glucose-treated INS-1E cells. Notably, some PL extracts are also capable to decrease significantly the gene expression of iNOS and to increase the IL-10 gene expression in glucose-treated INS-1E cells. However, the PL extracts show a tendency to decrease the gene expression of NF-kB and MCP-1 in glucose-treated INS-1E cells. In conclusion, our findings suggest that the treatment with PL extracts could benefit the pancreatic β cell function and alleviate the pancreatic inflammation, thereby representing potential advantages of the glucose metabolism in the T2D.
Signals of microbial growth learned from single amplicon samples
Authors: Chlenski Philippe , Ricaurte Deirdre , Pe’er Itsik
Published: November 2023

Irregularities in metagenomic whole-genome shotgun (WGS) read coverage can arise in quickly replicating microbial populations. These irregularities, summarized as peak-to-trough ratios (PTRs), are correlated with growth rates. This study seeks to explore the presence of similar coverage irregularities in 16S amplicon datasets, where multicopy diverged 16S genes provide an opportunity to explore coverage at different positions on the bacterial chromosome. To this end, we propose a model of Operational Taxonomic Unit (OTU) observations under replication and sequence similarity, from which we derive a method for simultaneous copy number correction and dynamics estimation by gradient descent. We conduct a series of benchmarks on synthetic data, determining a set of heuristics for when such methods may be applied, and compare our method with WGS-based methods on a real dataset. We find no correlation between coPTR estimates and our method, suggesting further modifications to our method may be required.
MYC amplifies mitotic perturbations elicited by LXY18 to enable synthetic lethality
Authors: Kalashova Julia , Yang Chenglu , Long Yan , Li Hongmei , Zhang Shenqiu , Zhang Ting , Yu Duo , Liu Xumei , Lv Gang , Choudhry Namrta , Liu Hong , Shi Qiong , Yang Dun
Published: November 2023

The MYC oncoprotein represents an intriguing target for cancer treatment, but its therapeutic potential has been hindered by the absence of specific pharmacological inhibitors. In this study, we demonstrate that the phenoxy quinoline compound LXY18 selectively targets and eliminates cells overexpressing MYC, leaving non-transformed cells unharmed. This synthetic lethality arises from an acute induction of multipolarity, resulting in a persistent arrest in early mitosis followed by cell death in mitosis or after mitotic slippage. Distinctively, LXY18’s action contrasts with other antimitotic compounds, as they either fail to induce mitotic arrest or elicit mitotic arrest irrespective of MYC abundance. Furthermore, the MYC abundance in a panel of 98 tumor cell lines correlates with their sensitivity to LXY18. Collectively, our findings uncover LXY18 as an MYC- enabled mitotic blocker and open a new avenue to selectively target MYC-overexpressing tumor cells without affecting normal cells.
Feeding-structure morphogenesis in “rhabditid” and diplogastrid nematodes is not controlled by a conserved genetic module
Authors: Theska Tobias , Sommer Ralf J.
Published: November 2023

Disentangling the evolution of the molecular processes and genetic networks that facilitate the emergence of morphological novelties is one of the main objectives in evolutionary developmental biology. Here, we investigated the evolutionary history of a gene regulatory network controlling the development of novel tooth-like feeding-structures in diplogastrid nematodes. Focusing on NHR-1 and NHR-40, the two transcription factors that regulate the morphogenesis of these feeding structures inPristionchus pacificus, we sought to determine whether they have a similar function in out-group nematodeCaenorhabditis elegans, which has typical “rhabditid” flaps instead of teeth. Contrary to our initial expectations, we found that they do not have a similar function. While both receptors are co-expressed in the tissues that produce the feeding structures in the two nematodes, genetic inactivation of either receptor had no impact on feeding-structure morphogenesis inC. elegans. Transcriptomic experiments revealed that NHR-1 and NHR-40 have highly species-specific regulatory targets. These results suggest two possible evolutionary scenarios: either the genetic module responsible for feeding-structure morphogenesis in Diplogastridae already existed in the last common ancestor ofC. elegansandP. pacificus, and subsequently disintegrated in the former as NHR-1 and NHR-40 acquired new targets, or it evolved in conjunction with teeth in Diplogastridae. These findings indicate that feeding-structure morphogenesis is regulated by different genetic programs inP. pacificusandC. elegans, hinting at developmental systems drift during the flap-to-tooth transformation. Further research in other “rhabditid” species is needed to fully reconstruct the developmental genetic changes which facilitated the evolution of novel feeding structures in Diplogastridae.

Research Highlights

Combining CRISPR-based mutagenesis, geometric morphometrics, and transcriptomics, we found that the genetic module governing the morphogenesis of novel feeding structures in diplogastrid nematodes is not conserved in the “rhabditid”C. elegans.
Modelling the demographic history of human North African genomes points to soft split divergence between populations
Authors: Serradell Jose M , Lorenzo-Salazar Jose M , Flores Carlos , Lao Oscar , Comas David
Published: November 2023

Background

North African human populations present a complex demographic scenario. The presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa, have shaped the genetic composition of its people through time.

Results

We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through the utilization of the Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole-genomes at >30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both methods point to a back-to-Africa origin of North African individuals and a close relationship of North African with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, as early as 22.3 Kya. GP4PG model supports Arabization as the main source of Middle Eastern ancestry in North Africa. The GP4PG model better explaining the observed data includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous gene flow after the split between populations (migration decay). In contrast to what we observed in the ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa.

Conclusions

We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations, emphasizing the complex demographic history at a population level.
Statistical framework for calling allelic imbalance in high-throughput sequencing data
Authors: Buyan Andrey , Meshcheryakov Georgy , Safronov Viacheslav , Abramov Sergey , Boytsov Alexandr , Nozdrin Vladimir , Baulin Eugene F. , Kolmykov Semyon , Vierstra Jeff , Kolpakov Fedor , Makeev Vsevolod J. , Kulakovskiy Ivan V.
Published: November 2023

High-throughput sequencing facilitates large-scale studies of gene regulation and allows tracing the associations of individual genomic variants with changes in gene expression. Compared to classic association studies, allelic imbalance at heterozygous variants captures the functional effects of the regulatory genome variation with smaller sample sizes and higher sensitivity. Yet, the identification of allele-specific events from allelic read counts remains non-trivial due to multiple sources of technical and biological variability, which induce data-dependent biases and overdispersion. Here we present MIXALIME, a novel computational framework for calling allele-specific events in diverse omics data with a repertoire of statistical models accounting for read mapping bias and copy-number variation. We benchmark MIXALIME against existing tools and demonstrate its practical usage by constructing an atlas of allele-specific chromatin accessibility, UDACHA, from thousands of available datasets obtained from diverse cell types.

Availability

https://github.com/autosome-ru/MixALime,https://udacha.autosome.org
Dissecting the properties of circulating IgG against Group A Streptococcus through a combined systems antigenomics-serology workflow
Authors: Chowdhury Sounak , Gomez Toledo Alejandro , Hjortswang Elisabeth , Sorrentino James T , Lewis Nathan E , Bläckberg Anna , Ekström Simon , Izadi Arman , Nordenfelt Pontus , Malmström Lars , Rasmussen Magnus , Malmström Johan
Published: November 2023

Most individuals maintain circulating antibodies against various pathogenic bacteria as a consequence of previous exposures. However, it remains unclear to what extent these antibodies contribute to host protection. This knowledge gap is linked to the need for better methods to characterize antimicrobial polyclonal antibodies, including their antigen and epitope repertoires, subclass distribution, glycosylation status, and effector functions. Here, we showcase a generic mass spectrometry-based strategy that couples systems antigenomics and systems serology to characterize human antibodies directly in clinical samples. The method is based on automated affinity purification workflows coupled to an integrated suite of high-resolution MS-based quantitative, structural- and glyco-proteomics readouts.

We focused onStreptococcus pyogenes(Group AStreptococcus; GAS), a major human pathogen still awaiting an approved vaccine. Our methodology reveals that both healthy and GAS infected individuals have circulating Immunoglobulin G (IgG) against a subset of genomically conserved streptococcal proteins, including numerous toxins and virulence factors. The antigen repertoire targeted by these antibodies was relatively constant across healthy individuals, but considerably changed in GAS bacteremia. Detailed analysis of the antigen-specific IgG indicates inter-individual variation regarding titers, subclass distributions, and Fc-signaling capacity, but not in epitope and Fc-glycosylation patterns. Importantly, we show that the IgG subclass has a major impact on the ability of GAS-antibodies to trigger immune signaling, in an antigen- and Fc receptor-specific fashion. Overall, these results uncover exceeding complexity in the properties of GAS-specific IgG, and showcase our methodology as high-throughput and flexible workflow to understand adaptive immune responses to bacterial pathogens.

Significance statement

Most people develop polyclonal antibodies against bacterial pathogens during infections but their structural and functional properties are poorly understood. Here, we showcase a combined systems antigenomics and systems serology strategy to quantify key antibody properties directly in clinical samples. We applied this method to characterize polyclonal antibody responses against Streptococcus pyogenes, a major human pathogen. We mapped the antigen and epitope landscape of anti-streptococcal antibodies circulating in healthy adult plasma, and their changes during blood infections. We further demonstrate the analytical power of our approach to resolve individual variations in the structure and effector functions of antigen-specific antibodies, including a dependency between immunoglobulin subclass and Fc-signaling capacity.
Early antigen receptor signaling in natural killer cells alters STAT4-dependent fate decisions via epigenetic remodeling
Authors: Grassmann Simon , Santosa Endi K. , Mujal Adriana M. , Kim Hyunu , Fan Sherry X. , Owyong Mark , Lau Colleen M. , Sun Joseph C.
Published: November 2023

Natural Killer (NK) cells are innate cytotoxic lymphocytes that possess features of adaptive immunity, including antigen specificity and clonal expansion. NK cells rapidly respond to cytokines released during the innate phase of viral infection and are thought to migrate from circulation into infected organs to execute their early effector functions. However, recent evidence suggests that tissue-resident NK cells are among the first responders to viral infection. In this study, we observe that antigen receptor signaling precedes substantial proinflammatory cytokine signaling in a population of NK cells during mouse cytomegalovirus infection. Early antigen receptor signals epigenetically prime NK cells for optimal expansion during the later adaptive phase of the antiviral response. Mechanistically, receptor signaling increases chromatin accessibility at STAT4-binding genomic sites within differentiating NK cells. To promote adaptive programming of NK cells during infection, activating receptor-dependent epigenetic remodeling antagonizes IL-12 driven terminal maturation, poises NK cells for proliferation via sustained CDK6 expression, and antagonizes early apoptosis of short-lived effector cells via suppression of Bim. Thus, antigen receptor signaling alters an IL-12 dependent fate decision during the innate-to-adaptive transition of antiviral NK cells.
The entropic heart: Tracking the psychedelic state via heart rate dynamics
Authors: Rosas Fernando E. , Mediano Pedro A.M. , Timmermann Christopher , Luppi Andrea I , Candia-Rivera Diego , Abbasi-Asl Reza , Gazzaley Adam , Kringelbach Morten L. , Muthukumaraswamy Suresh , Bor Daniel , Garfinkel Sarah , Carhart-Harris Robin L.
Published: November 2023

A growing body of work shows that autonomic signals provide a privileged evidence-stream to capture various aspects of subjective and neural states. This work investigates the potential for autonomic markers to track the effects of psychedelics — potent psychoactive drugs with important scientific and clinical value. For this purpose, we introduce a novel Bayesian framework to estimate the entropy of heart rate dynamics under psychedelics. We also calculate Bayesian estimates of mean heart rate and heart rate variability, and investigate how these measures relate to subjective reports and neural effects. Results on datasets covering four drugs — lysergic acid diethylamide (LSD), dimethyltryptamine (DMT), psilocybin, and sub-anaesthetic doses of the dissociative agent ketamine — show consistent increases in mean heart rate, high-frequency heart rate variability, and heart rate entropy during the psychedelic experience. Moreover, these effects have predictive power over various dimensions of the psychedelic experience. Changes in heart rate entropy were found to be correlated with increases in brain entropy, while other autonomic markers were not. Overall, our results show that a cost-efficient autonomic measure has the potential to reveal surprising detail about subjective and brain states, opening up a range of new research avenues to explore in both basic and clinical neuroscience.
Precise age estimation in clonal species using a somatic genetic clock
Authors: Yu Lei , Renton Jessie , Burian Agata , Khachaturyan Marina , Kotta Jonne , Stachowicz John J. , DuBois Katherine , Baums Iliana B. , Werner Benjamin , Reusch Thorsten B. H.
Published: November 2023

Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, algae and fungi, the sexually produced offspring (the genet) grows indeterminately by producing iterative modules, or ramets. The age of large genets often remains elusive, while estimates based on their spatial extent as proxy for age are unreliable. Here, we present a method for age estimation using a molecular clock based on the accumulation of fixed somatic genetic variation (SoGV) that segregates among ramets of the same genet. Using a stochastic model of a generic clonal organism, we demonstrate that the accumulation of fixed SoGV via somatic genetic drift will approach linearity after a short lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size (N), number of founder cells for the formation of new modules (N0), and the ratio of symmetric vs. asymmetric stem cell divisions. We apply the somatic genetic clock to the clonal plant modelZostera marina(eelgrass) and show that linearity is approached within a few years. Taking advantage of two long-term cultivation experiments forZ. marina(4 and 17 years respectively) as calibration points, we find genet ages up to 1,403 years in a global data set of 20 eelgrass populations. The somatic genetic clock is applicable to any multicellular clonal species where a small number of founder cells are recruited to form new ramets, opening novel research avenues to study longevity and hence, demography and population dynamics of clonal species.
Ubiquitinated protein levels remain high during ageing inC. elegans
Authors: Daigle Sandrine E. , Doucet Savannah , Lapierre Louis R.
Published: November 2023

A wealth of literature in different model organisms have shown that proteostasis declines with age, which results in the accumulation of aggregated proteins that generally carry polyubiquitin chains. In Koyuncu et al. (Nature, 2021), the authors use a relatively mild homogenization approach to analyze total polyubiquitinated protein levels longitudinally inC. elegansand found that the overall level of polyubiquitinated proteins decreases in wild-type nematodes. Specifically, the substantial presence of polyubiquitinated proteins in early adulthood markedly decreases at day 10 and 15 of adulthood. This finding represents the central basis of their study where they subsequently suggest that age-dependent decrease in protein polyubiquitination in wild-type animals is due to enhanced deubiquitination. Here, we find that the mild homogenization ofC. elegansused in Koyuncuet al. fails to properly extract allC. elegansproteins, because it largely omits relatively insoluble proteins in the pellet. When we perform complete homogenization of wild-type nematode proteins using SDS, sonication and heat, we unequivocally observe that polyubiquitinated protein levels do not decrease with age inC. elegans. Overall, the levels of polyubiquitinated proteins remains relatively constant post-reproduction. Therefore, our findings invalidate the main conclusion of Koyuncu et al. that the ubiquitinated proteome is rewired during ageing and demonstrate thatC. elegansharbor polyubiquitinated proteins throughout their lifespan.
Evidence for peripheral and central actions of codeine to dysregulate deglutition in the anesthetized cat
Authors: Bolser Donald C. , Shen Tabitha Y. , Musselwhite M. Nicholas , Rose Melanie J. , Hayes John A. , Pitts Teresa G.
Published: November 2023

Systemic administration of opioids has been associated with aspiration and swallow dysfunction in humans. We speculated that systemic administration of codeine would induce dysfunctional swallowing and that this effect would have a peripheral component. Experiments were conducted in spontaneously breathing, anesthetized cats. The animals were tracheotomized and electromyogram electrodes were placed in upper airway and chest wall respiratory muscles for recording swallow related motor activity. The animals were allocated into three groups: vagal intact (VI), cervical vagotomy (CVx), and supra-nodose ganglion vagotomy (SNGx). A dose response to intravenous codeine was performed in each animal. Swallowing was elicited by injection of 3 ml of water into the oropharynx. The number of swallows after vehicle was significantly higher in the VI group than in SNGx. Codeine had no significant effect on the number of swallows induced by water in any of the groups. However, the magnitudes of water swallow-related EMGs of the thyropharyngeus muscle were significantly increased in the VI and CVx groups by 2-4 fold in a dose-related manner. In the CVx group, the geniohyoid muscle EMG during water swallows was significantly increased. There was a significant codeine dose-related increase in spontaneous swallowing in each group. The spontaneous swallow number at the 10 mg/kg dose of codeine was significantly larger in the CVx than that in the SNGx groups. During water-evoked swallows, intravenous codeine increased upper airway motor drive in a dose-related manner, consistent with dysregulation. The appearance of spontaneous swallowing in response to codeine in all groups supports a central action of this drug on the swallow pattern generator and also is consistent with dysregulation. At the highest dose of codeine, the reduced spontaneous swallow number in the SNGx group relative to CVx is consistent with a peripheral excitatory action of codeine either on pharyngeal/laryngeal receptors or in the nodose ganglion itself.
Acetyl-CoA carboxylase Inhibition increases RPE cell fatty acid oxidation and limits apolipoprotein efflux
Authors: Hass Daniel T. , Pandey Kriti , Engel Abbi , Horton Noah , Robbings Brian M. , Lim Rayne , Sadilek Martin , Zhang Qitao , Autterson Gillian A. , Miller Jason M.L. , Chao Jennifer R. , Hurley James B.
Published: November 2023

Purpose

In age-related macular degeneration (AMD) and Sorsby’s fundus dystrophy (SFD), lipid-rich deposits known as drusen accumulate under the retinal pigment epithelium (RPE). Drusen may contribute to photoreceptor and RPE degeneration in AMD and SFD. We hypothesize that stimulating β-oxidation in RPE will reduce drusen accumulation. Inhibitors of acetyl-CoA carboxylase (ACC) stimulate β-oxidation and diminish lipid accumulation in fatty liver disease. In this report we test the hypothesis that an ACC inhibitor, Firsocostat, limits the accumulation of lipid deposits in cultured RPE cells.

Methods

We probed metabolism and cellular function in mouse RPE-choroid, human fetal- derived RPE cells, and induced pluripotent stem cell-derived RPE cells. We used13C6-glucose and13C16-palmitate to determine the effects of Firsocostat on glycolytic, Krebs cycle, and fatty acid metabolism.13C labeling of metabolites in these pathways were analyzed using gas chromatography-linked mass spectrometry. We quantified ApoE and VEGF release using enzyme-linked immunosorbent assays. Immunostaining of sectioned RPE was used to visualize ApoE deposits. RPE function was assessed by measuring the trans-epithelial electrical resistance (TEER).

Results

ACC inhibition with Firsocostat increases fatty acid oxidation and remodels lipid composition, glycolytic metabolism, lipoprotein release, and enhances TEER. When human serum is used to induce sub-RPE lipoprotein accumulation, fewer lipoproteins accumulate with Firsocostat. In a culture model of Sorsby’s fundus dystrophy, Firsocostat also stimulates fatty acid oxidation, improves morphology, and increases TEER.

Conclusions

Firsocostat remodels intracellular metabolism and improves RPE resilience to serum-induced lipid deposition. This effect of ACC inhibition suggests that it could be an effective strategy for diminishing drusen accumulation in the eyes of patients with AMD.
Behavior Clusters in Ischemic Stroke using NIHSS
Authors: Tshimanga Louis Fabrice , Zanola Andrea , Facchini Silvia , Bisogno Antonio Luigi , Pini Lorenzo , Atzori Manfredo , Corbetta Maurizio
Published: November 2023

BACKGROUND

Stroke is one of the leading causes of death and disability. The resulting behavioral deficits can be measured with clinical scales of motor, sensory, and cognitive impairment. The most common of such scales is the National Institutes of Health Stroke Scale, or NIHSS. Computerized tomography (CT) and magnetic resonance imaging (MRI) scans show predominantly subcortical or subcortical-cortical lesions, with pure cortical lesions occurring less frequently. While many experimental studies have correlated specific deficits (e.g. motor or language impairment) with stroke lesion locations, the mapping between symptoms and lesions is not straightforward in clinical practice. The advancement of machine learning and data science in recent years has shown unprecedented opportunities even in the biomedical domain. Nevertheless, their application to medicine is not simple, and the development of data driven methods to learn general mathematical models of diseases from healthcare data is still an unsolved challenge.

METHODS

In this paper we measure statistical similarities of stroke patients based on their NIHSS scores, and we aggregate symptoms profiles through two different unsupervised machine learning techniques: spectral clustering and affinity propagation.

RESULTS

We identify clusters of patients with largely overlapping, coherent lesions, based on the similarity of behavioral profiles.

CONCLUSIONS

Overall, we show that an unsupervised learning workflow, open source and transferable to other conditions, can identify coherent mathematical representations of stroke lesions based only on NIHSS data.
High prevalence of asymptomatic and sub-patentPlasmodium falciparuminfections in Urban Bouaké, Côte d’Ivoire, but nohrp2deletions: Implications for Malaria Control
Authors: Sagna André Barembaye , Gebre Yilekal , Vera-Arias Claudia Abigail , Traoré Dipomin François , Tchekoi Bertin N’cho , Assi Serge Brice , Koffi Amnan Alphonsine , Rogier Christophe , Remoue Franck , Koepfli Cristian
Published: November 2023

AsymptomaticPlasmodium falciparuminfections are common in endemic settings, yet diagnosing these infections remains challenging because they are often below the limit of detection of conventional light microscopy (LM) or rapid diagnostic tests (RDTs). Deletions of thehrp2/3gene, encoding the protein detected by the most sensitive class of RDTs, present a further threat. In this study, the prevalence of asymptomatic and sub-patentP. falciparuminfections was characterized in the rainy season in the city of Bouaké, Central Côte d’Ivoire. A cross-sectional survey was conducted in nine neighborhoods of Bouaké, Côte d’Ivoire, in 2016. Matched LM, RDTs, andvarATS qPCR, were used to determine the prevalence ofP. falciparuminfections and to compare the performance of the different diagnostic methods.P. falciparum hrp2/3deletions were typed by digital PCR. Among 2313 individuals, malaria prevalence was 10.8% by microscopy, 13.0% by RDT, 35.1% by qPCR, and 37.3% (863/2313) when all three methods were combined. 96.4% (832/863) of individuals withP. falciparuminfections did not report a recent fever. 57.1% (493/863) of infections were sub-patent. The prevalence was highly heterogeneous across the neighborhoods, ranging from 15% to 55.2%, and differed among age groups (<5 years: 17.7%, 5-14 years: 42.7%, ≥15 years: 35.9%). Compared tovarATS qPCR, LM and RDT had a low sensitivity of 24.3% and 34.2%, respectively, although both methods were highly specific (>96%). Sub-microscopic malaria infections were more prevalent in ≥15-year-olds (69.9%, 349/499) and in the neighborhood of Dar es Salam (75.9%, 44/58). No hrp2 deletions were observed, and two samples carriedhrp3deletion/wild-type mixed infections. The high prevalence of asymptomatic and sub-patent infections prompts the implementation of strategies targeting these parasite reservoirs to achieve reductions in malaria burden in this high-transmission city of Côte d’Ivoire.
The association of skeletal muscle energetics with recurrent falls in older adults within the Study of Muscle, Mobility and Aging (SOMMA)
Authors: Kramer Philip A. , Zamora Ezequiel , Barnes Haley N. , Strotmeyer Elsa S. , Glynn Nancy W , Lane Nancy E. , Coen Paul M. , Cawthon Peggy M. , Goodpaster Bret H. , Newman Anne B. , Kritchevsky Stephen B. , Cummings Steven R.
Published: November 2023

Background

Falls in the older population are a major public health concern. While many physiological and environmental factors have been associated with fall risk, muscle mitochondrial energetics has not yet been investigated.

Methods

In this analysis, 835 Study of Muscle, Mobility and Aging (SOMMA) participants aged 70-94 were surveyed for recurrent falls (2+) after one year. Skeletal muscle energetics were assessed at baseline in vivo using31P Magnetic Resonance Spectroscopy (MRS) (ATPmax) and ex vivo by High Resolution Respirometry (HRR) of permeabilized muscle fibers from the vastus lateralis (MaxOXPHOS).

Results

SOMMA participants who reported recurrent falls (12%) had a slower 400m walk gait speed compared to those with 0-1 falls (1.0 +/-0.2 vs. 1.1 +/-0.2, p<.001) and took a greater number of medication in the 30 days before their baseline visit (5.6 +/-4.4 vs. 4.2 +/-3.4, p<0.05). MaxOXPHOS was significantly lower in those who reported recurrent falls (p=0.008) compared to those with one or fewer falls, but there was no significant difference in ATPmax (p=0.369). Neither muscle energetics measure was significantly associated with total number of falls or injurious falls, but recurrent falls were significantly higher with lower MaxOXPHOS (RR=1.33, 95% CI= 1.02-1.73, p=0.033). However, covariates accounted for the increased risk.

Conclusions

Ex vivo maximal muscle mitochondrial energetics were lower in older adults who experienced recurrent falls, but covariates accounted for its association with recurrent fall risk, suggesting this “hallmark of aging” may not be directly implicated in the complex etiology of falls.
Associations of behavioral problems with white matter circuits connecting to the frontal lobes in school-aged children born at term and preterm
Authors: Hosoki Machiko , Eidsness Margarita Alethea , Bruckert Lisa , Travis Katherine E. , Feldmana Heidi M
Published: November 2023

Introduction

This study investigated whether behavioral problems in children were associated with fractional anisotropy (FA) of white matter tracts connecting from other brain regions to right and left frontal lobes. We considered internalizing and externalizing behavioral problems separately and contrasted patterns of associations in children born at term and very preterm.

Methods

Parents completed the Child Behavior Checklist/6-18 questionnaire to quantify behavioral problems when their children were age 8 years (N=36 FT and 37 PT). Diffusion magnetic resonance scans were collected at the same age and analyzed using probabilistic tractography. We used multiple linear regression to investigate the strength of association between age-adjusted T-scores of internalizing and externalizing problems and mean fractional anisotropy (mean-FA) of right and left uncinate, arcuate, and anterior thalamic radiations, controlling for birth group and sex.

Results

Regression models predicting internalizing T-scores from mean-FA found significant group-by-tract interactions for the left and right arcuate and right uncinate. Internalizing scores were negatively associated with mean-FA of left and right arcuate only in children born at term (pleftAF=0.01,prightAF=0.01). Regression models predicting externalizing T-scores from mean-FA found significant group-by-tract interactions for the left arcuate and right uncinate. Externalizing scores were negatively associated with mean-FA of right uncinate in children born at term (prightUF=0.01) and positively associated in children born preterm (prightUFpreterm=0.01). Other models were not significant.

Conclusions

In this sample of children with scores for behavioral problems across the full range, internalizing and externalizing behavioral problems were negatively associated with mean-FA of white matter tracts connecting to frontal lobes in children born at term; externalizing behavioral problems were positively associated with mean-FA of the right uncinate in children born preterm. The different associations by birth group suggest that the neurobiology of behavioral problems differs in the two birth groups.

’Highlights’

⍰ Internalizing problems were negatively associated with arcuate FA in term children.

Externalizing problems negatively associated with right uncinate FA in term children.

Externalizing problems were positively associated with right uncinate FA in preterm.
Cellular and transcriptomic response to pathogenic and non-pathogenicVibrio parahaemolyticusstrains causing acute hepatopancreatic necrosis disease (AHPND) inLitopenaeus vannamei
Authors: López-Landavery Edgar A. , Urquizo-Rosado Ángela , Saavedra-Flores Anaid , Tapia-Morales Sandra , Fernandino Juan I. , Zelada-Mázmela Eliana
Published: November 2023

The shrimp industry has historically been affected by viral and bacterial diseases. One of the most recent emerging diseases is the Acute Hepatopancreatic Necrosis Disease (AHPND), which causes severe mortality. Despite its significance to both sanitation and economics, little is known about the molecular response of shrimp to this disease. Here, we present the cellular and transcriptomic responses ofLitopenaeus vannameiexposed to twoVibrio parahaemolyticusstrains for 98h, wherein one is non-pathogenic (VpN) and the other causes AHPND (VpP). Exposure to VpN strain resulted in minor alterations in hepatopancreas morphology, including reductions in the size of R and B cells as well as detachments of small epithelial cells from 72 h onwards. On the other hand, exposure to VpP strain is characterized by acute detachment of epithelial cell from the hepatopancreatic tubules and infiltration of hemocytes in the inter-tubular spaces. At the end of exposure, RNA-Seq analysis revealed functional enrichment in biological processes, such as thetoll3receptor signaling pathway, apoptotic processes, and production of molecular mediators involved in the inflammatory response of shrimp exposed to VpN treatment. The biological processes identified in the VpP treatment include superoxide anion metabolism, innate immune response, antimicrobial humoral response, andtoll3receptor signaling pathway. Furthermore, KEGG enrichment analysis revealed metabolic pathways associated with survival, cell adhesion, and reactive oxygen species, among others, for shrimp that were exposed to VpP. Our study proves the differential immune responses to two strains ofV. parahaemolyticus,one pathogenic and the other nonpathogenic, enlarges our knowledge on the evolution of AHPND inL. vannamei, and uncovers unique perspectives on establishing genomic resources that may function as a groundwork for detecting probable molecular markers linked to the immune system in shrimp.
Elimination of contamination in the published 16S rRNA gene sequence ofRothia amaraetype strain J18Tduring phylogenetic studies of a bacterial isolate from a suspension cell culture ofArabidopsis thaliana(Heynh.)
Authors: Shchyogolev Sergei Yu. , Dykman Lev A. , Sokolov Alexander O. , Sokolov Oleg I. , Matora Larisa Yu.
Published: November 2023

In our phylogenetic studies of a bacterial strain isolated from anArabidopsissuspension culture, we obtained convincing evidence for contamination of the published 16S rRNA gene sequence ofRothia amaraetype strain J18T(GenBankAY043359.1). Correction of this sequence by deleting the contamination region eliminated contradictions in bioinformatic results that included comparisons of the small-subunit (SSU) rRNA secondary structures. Further, correction of the contaminated sequence yielded sequence identity values for the 16S rRNA genes of the isolate andR. amaraetype strain J18T(and more than a dozen otherR. amaraemembers) above the threshold for species demarcation. The phylogram of the 16S rRNA gene sequences of the type strains closely related to the isolate under study (interspecies sequence identity values, 96–98.7%) united members of the familyMicrococcaceae(the generaRothia, KocuriaandArthrobacter). A great diversity of habitat conditions was noted for these bacteria, isolated from animals, soil, aqueous media, plant tissues and other sources. This applies, in particular, toR. amaraemembers that are most closely related to the isolate under study by the 16S rRNA gene sequence criterion (sequence identity, near 100%) and belong to four ecotypes: Antarctic, aquatic, soil and endophytic.
Prominin 1 and Tweety Homology 1 both induce extracellular vesicle formation
Authors: Bell Tristan A. , Luce Bridget E. , Hakim Pusparanee , Ananda Virly Y. , Dardari Hiba , Nguyen Tran H. , Monshizadeh Arezu , Chao Luke H.
Published: November 2023

Prominin-1 (Prom1) is a five-transmembrane-pass integral membrane protein that associates with curved regions of the plasma membrane. Prom1 interacts with membrane cholesterol and actively remodels the plasma membrane. Membrane bending activity is particularly evident in photoreceptors, where Prom1 loss-of-function mutations cause failure of outer segment homeostasis, leading to cone-rod retinal dystrophy (CRRD). The Tweety Homology (Ttyh) protein family has been proposed to be homologous to Prominin, but it is not known whether Ttyh proteins have an analogous membrane-bending function. Here, we characterize the membrane-bending activity of human Prom1 and Ttyh1 in native bilayer membranes. We find that Prom1 and Ttyh1 both induce formation of extracellular vesicles (EVs) in cultured mammalian cells and that the EVs produced are physically similar. Ttyh1 is more abundant in EV membranes than Prom1 and produces EVs with membranes that are more tubulated than Prom1 EVs. We further show that Prom1 interacts more stably with membrane cholesterol than Ttyh1 and that this may contribute to membrane bending inhibition in Prom1 EVs. Intriguingly, a loss-of-function mutation in Prom1 associated with CRRD induces particularly stable cholesterol binding. These experiments provide mechanistic insight into Prominin function in CRRD and suggest that Prom and Ttyh belong to a single family of functionally related membrane-bending, EV-generating proteins.