bluuebunny/crossref_metadata_2025 huggingface dataset:
Tirzepatide for Lipodystrophy
Authors: Meral Rasimcan , Celik Guler Merve , Kaba Diarratou , Prativadi Jeevitha , Frontera Eric D , Foss-Freitas Maria Cristina , Nachawi Noura , Broome David T , Lightbourne Marissa , Brown Rebecca J , Taylor Simeon I , Oral Elif A
Published: September 2024

Background

Lipodystrophy encompasses a group of rare disorders associated with severe metabolic disease. These disorders are defined by abnormal fat distribution, with near-total (generalized lipodystrophy, GL) or partial (partial lipodystrophy, PL; i.e. familial partial lipodystrophy, FPLD) absence of adipocyte mass leading to a decreased ability to store lipids safely. Excess lipids are more likely to be stored in non-adipose tissues, which leads to the metabolic manifestations. We have recently shown that glucagon-like peptide-1 agonists are associated with metabolic improvements in FPLD. We hypothesized that tirzepatide, a dual incretin, may also lead to metabolic improvement in patients with lipodystrophy.

Methods

Observational cohort of patients with PL or GL who received tirzepatide clinically were tracked in the context of ongoing natural history studies.

Results

Seventeen patients received tirzepatide, 14 with FPLD (ages within 30-74 years; 12 female 2 male). After a median 8.7 months of follow-up, BMI (medianΔ -1.7; range -5.9 to 0.9 kg/m2;p=0.008), HbA1c (medianΔ -1.1%; range -6.3 to -0.1%;p<0.001), triglycerides [medianΔ - 65 mg/dL (-0.73 mmol/L); range -3820 to 43 mg/dL (-43.2 to 0.49 mmol/L);p=0.003] and total daily insulin requirements (medianΔ -109; range -315 to 0 units/day;p=0.002) were significantly reduced. Three patients with acquired GL (Ages within 35-64 years; all female) also demonstrated a robust response to tirzepatide with reduced BMI (22.2->20.9; 26.2->25.4; 19.5->17.6 kg/m2), HbA1c (8.5%->7.0%; 10.2%->7.8%; 9.1%->6.5%), triglycerides (91->80; 641->293; 1238->100 mg/dL or 1.03->0.90; 7.24->3.31; 14.0->1.13 mmol/L), and total daily insulin requirement (85->0; 0->0; 1000->750 units/day). Three patients did not tolerate dose escalation due to gastroesophageal reflux.

Conclusions

Tirzepatide may be an effective treatment for patients with lipodystrophy.
Powerful mapping ofcis-genetic effects on gene expression across diverse populations reveals novel disease-critical genes
Authors: Akamatsu Kai , Golzari Stephen , Amariuta Tiffany
Published: September 2024

While disease-associated variants identified by genome-wide association studies (GWAS) most likely regulate gene expression levels, linking variants to target genes is critical to determining the functional mechanisms of these variants. Genetic effects on gene expression have been extensively characterized by expression quantitative trait loci (eQTL) studies, yet data from non-European populations is limited. This restricts our understanding of disease to genes whose regulatory variants are common in European populations. While previous work has leveraged data from multiple populations to improve GWAS power and polygenic risk score (PRS) accuracy, multi-ancestry data has not yet been used to better estimatecis-genetic effects on gene expression. Here, we present a new method, Multi-Ancestry Gene Expression Prediction Regularized Optimization (MAGEPRO), which constructs robust genetic models of gene expression in understudied populations or cell types by fitting a regularized linear combination of eQTL summary data across diverse cohorts. In simulations, our tool generates more accurate models of gene expression than widely-used LASSO and the state-of-the-art multi-ancestry PRS method, PRS-CSx, adapted to gene expression prediction. We attribute this improvement to MAGEPRO’s ability to more accurately estimate causal eQTL effect sizes (p< 3.98 × 10-4, two-sided paired t-test). With real data, we applied MAGEPRO to 8 eQTL cohorts representing 3 ancestries (averagen= 355) and consistently outperformed each of 6 competing methods in gene expression prediction tasks. Integration with GWAS summary statistics across 66 complex traits (representing 22 phenotypes and 3 ancestries) resulted in 2,331 new gene-trait associations, many of which replicate across multiple ancestries, includingPHTF1linked to white blood cell count, a gene which is overexpressed in leukemia patients. MAGEPRO also identified biologically plausible novel findings, such asPIGB, an essential component of GPI biosynthesis, associated with heart failure, which has been previously evidenced by clinical outcome data. Overall, MAGEPRO is a powerful tool to enhance inference of gene regulatory effects in underpowered datasets and has improved our understanding of population-specific and shared genetic effects on complex traits.
Challenges and advances for huntingtin detection in cerebrospinal fluid: in support of relative quantification
Authors: Harding Rachel J. , Xie Yuanyun , Caron Nicholas S. , Findlay-Black Hailey , Lyu Caroline , Potluri Nalini , Chandrasekaran Renu , Hayden Michael R. , Leavitt Blair R. , Langbehn Douglas R. , Southwell Amber L.
Published: September 2024

Huntington disease (HD) is a progressive and devastating neurodegenerative disease caused by expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene above a critical threshold of ∼35 repeats resulting in expression of mutant HTT (mHTT). A promising treatment approach being tested in clinical trials is HTT lowering, which aims to reduce levels of the mHTT protein. Target engagement of these therapies in the brain are inferred using antibody-based assays to measure mHTT levels in the cerebrospinal fluid (CSF), which is frequently reported as absolute mHTT concentration based on a monomeric protein standard used to generate a standard curve. However, patient biofluids are a complex milieu of different mHTT protein species, suggesting that absolute quantitation is challenging, and a single, recombinant protein standard may not be sufficient to interpret assay signal as molar mHTT concentration. In this study, we used immunoprecipitation and flow cytometry (IP-FCM) to investigate different factors that influence mHTT detection assay signal. Our results show that HTT protein fragmentation, protein-protein interactions, affinity tag positioning, oligomerization and polyglutamine tract length affect assay signal intensity, indicating that absolute HTT quantitation in heterogeneous biological samples is not possible with current technologies using a single standard protein. We also explore the binding specificity of the MW1 anti-polyglutamine antibody, commonly used in these assays as a mHTT-selective reagent and demonstrate that mHTT binding is preferred but not specific. Furthermore, we find that MW1 depletion is not only incomplete, leaving residual mHTT, but also non-specific, resulting in pull down of some wildtype HTT protein. Based on these observations, we recommend that mHTT detection assays report only relative mHTT quantitation using normalized arbitrary units of assay signal intensity, rather than molar concentrations, in the assessment of central nervous system HTT lowering in ongoing clinical and preclinical studies, and that MW1-depletion not be used a method for quantifying wildtype HTT protein.
Innovative platelet-derived extracellular vesicle drug delivery system for the treatment of corneal neovascularization
Authors: Liu Guei-Sheung , Chen Huai-An , Chang Che-Yi , Chen Yin-Ju , Wu Yu-Yi , Widhibrata Ariel , Yang Ya-Han , Hsieh Erh-Hsuan , Delila Liling , Lin I-Chan , Burnouf Thierry , Tseng Ching-Li
Published: September 2024

Platelet-derived extracellular vesicles (PEVs) have drawn attention due to their multifunctionality, ease of procurement, and abundant supply from clinical-grade platelet concentrates. PEVs can be easily endocytosed owing to their lipid bilayer membrane and nanosized structure, thereby increasing the bioavailability and functionality of their therapeutic effects. PEVs also possess multiple trophic factors that make them effective therapeutic agents. Since nanomedicine offers advantages over traditional therapies for eye diseases by overcoming physical ocular barriers, PEVs combined with an anti-angiogenic agent, kaempferol (KM), were evaluated for their ability to inhibit abnormal vessel formation in the cornea. Characterization of the nanoparticles indicated successful preparation of KM- loaded PEVs (PEV-KM) with a mean diameter of ∼160 nm and an encapsulation efficiency of ∼61%. PEV-KM was efficiently internalized into human vascular endothelial cells, resulting in inhibited function, evidenced by lower wound closure rates, reduced tube formation capacity, and downregulation of angiogenesis-related gene expression. Moreover, prolonged ocular retention was observed followed by topical application of PEV and PEV-KM in mouse eyes. In an alkali-burned corneal neovascularization (CoNV) mouse model, PEV (1%) was found to reduce vessel formation in the injured cornea. PEV with KM (1% PEV with KM 6 µg/mL) showed an even stronger effect in suppressing CoNV and reducing the expression of proangiogenic and inflammatory cytokines. Together, our data suggests that topical administration of PEVs or in combination with KM (PEV-KM) is a promising therapeutic for managing CoNV.
The mitochondrialorf125affects male fertility ofSolanum tuberosum(+)S. commersoniisomatic hybrids and participates in the onset of “Tuberosum”-Type CMS and evolution of common potato
Authors: Tamburino Rachele , D’Agostino Nunzio , Aufiero Gaetano , Nicolia Alessandro , Facchiano Angelo , Giordano Deborah , Sannino Lorenza , Paparo Rosa , Arimura Shin-Ichi , Scotti Nunzia , Cardi Teodoro
Published: September 2024

Cytoplasmic male sterility (CMS) is an agronomically significant trait and a powerful tool to study interactions between nuclear and cytoplasmic genomes. In this study, the chondriomes of two isonuclear male-fertile and sterile somatic hybrids (SH9A and SH9B, respectively) between the common potato (Solanum tuberosumGroupTuberosum,tbr) and the wild speciesS. commersonii(cmm), were sequenced and compared to those of parental species to identify mitochondrial genes involved in the expression of male sterility. A putative novel gene (orf125) was found only intbrand in male-sterile hybrids. Two approaches, a physical or functional deletion oforf125by mtDNA editing in SH9B and its allotopic expression in SH9A, clearly demonstrate thatorf125affects male fertility. To trace the origin oforf125and hypothesize its role in the evolution of common potato, we searched it intbrvarieties, tuber-bearing potato relatives and other Solanaceae. The organization of the mitochondrial genome region implicated in CMS remained consistent across all common potato accessions in GenBank. An identicaltbrcopy oforf125was also detected in all six accessions belonging to theS. berthaultiicomplex (ber) analyzed. Such findings corroborate the hypothesis thatberaccessions with T/β cytoplasm crossed as female with Andean potato (S. tuberosumGroupAndigenum,adg), giving rise to the differentiation of the Chilean potato (S. tuberosumGroupChilotanum), and highlights the origin of mitochondrial factors contributing to genic-cytoplasmic male sterility intbrxadg(or some wild species) hybrids.
Genetic and phenotypic characterization of globalLupinus albusgenetic resources for the development of a CORE collection
Authors: Tanwar Umesh Kumar , Tomaszewska Magdalena , Czepiel Katarzyna , Neji Mohamed , Jamil Humaira , Rocchetti Lorenzo , Pieri Alice , Bitocchi Elena , Bellucci Elisa , Pipan Barbara , Meglič Vladimir , Kroc Magdalena , Papa Roberto , Susek Karolina
Published: September 2024

Lupinus albusis a food grain legume recognized for its high levels of seed protein (30–40%) and oil (6–13%), and its adaptability to different climatic and soil conditions. To develop the next generation ofL. albuscultivars, we need access to well-characterized, genetically and phenotypically diverse germplasm. Here we evaluated more than 2000L. albusaccessions with passport data based on 35 agro-morphological traits to develop Intelligent CORE Collections. The reference CORE (R-CORE), representing global diversity, exemplified the genotypic variation of cultivars, breeding/research materials, landraces and wild relatives. A subset of 300 R-CORE accessions was selected as a training CORE (T-CORE), representing the diversity in the entire collection. We divided theL. albusR-CORE into four phenotypic groups (A1, A2, A3 and B) based on principal component analysis, with groups A3 and B distinguished by pod shattering and seed ornamentation, respectively. The coefficient of additive genetic variation differed across morphological traits, phenotypic groups, geographic regions, and according to biological status. These CORE collections will facilitate agricultural research by identifying the genes responsible for desirable traits in crop improvement programs, and by shedding light on the use of orphan genetic resources for origin and domestication studies inL. albus. Understanding the variation in these genetic resources will allow us to develop sustainable tools and technologies that address global challenges such as providing healthy and sustainable diets for all, and contrasting the current climate change crisis.
In SilicoEngineering of Stable siRNA Lipid Nanoparticles: Exploring the Impact of Ionizable Lipid Concentrations for Enhanced Formulation Stability
Authors: Biswal Malay Ranjan , Roy Sudip , Singh Jayant K
Published: September 2024

Lipid nanoparticles (LNPs) are crucial in advancing the delivery of RNA-based therapeutics within the domain of gene therapy. A comprehensive understanding of their formation and stability is critical for optimizing the clinical efficacy of LNPs. This study systematically investigates the influence of concentration variations of positive and neutral ionizable lipids - specifically, 2-[2,2-bis[(9Z,12Z)-octadeca-9,12-dienyl]-1,3-dioxolan-4-yl]-N,N-dimethylethanamine (DLinKC2-DMA) and 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) - along with cholesterol and polyethylene glycol, on the formation of LNPs and encapsulation of small interfering RNA (siRNA). Utilizing coarse-grained classical molecular dynamics (MD) simulations with a system size matching experimental range (approximately 0.6 million beads), we conduct a comparative analysis and offer mechanistic insights into siRNA formulation within LNPs containing positive and neutral DLinKC2-DMA. We found that the LNPs with positive ionizable lipids encapsulate more than twice the siRNA compared to the LNPs with neutral ionizable lipids. In addition to the formation of LNPs, our study extends to the forces governing siRNA escape from LNPs, employing steered molecular dynamics simulations. The force experienced by siRNA to cross the LNP lipid layer containing positive ionizable lipids was 400kJ/mol/nm more than that of neutral ionizable lipids, suggesting the encapsulation is more favorable with positive ionisable lipids.
Differential responses and recovery dynamics of HSPC populations followingPlasmodium chabaudiinfection
Authors: Bruno Federica , Georgiou Christiana , Cunningham Deirdre , Atkinson Samantha , Bett Lucy , Secchi Marine , Gonzalez Anton Sara , Birch Flora , Langhorne Jean , Celso Cristina Lo
Published: September 2024

Severe infections such as malaria are on the rise worldwide, driven by both climate change and increasing drug-resistance. It is therefore paramount that we better understand how the host’s organism responds to severe infection. Hematopoiesis is particularly of interest in this context because hematopoietic stem and progenitor cells (HSPCs) maintain the turnover of all blood cells, including all immune cells. Severe infections have been widely acknowledged to affecting HSPCs, however this disruption has been mainly studied during the acute phase, and the process and level of HSPC recovery remains understudied. Using a self-resolving model of natural rodent malaria, infection byPlasmodium chabaudi, here we systematically assess HSPCs’ acute response and recovery upon pathogen clearance. We demonstrate that during the acute phase of infection the most quiescent and functional stem cells are depleted, multipotent progenitor compartments are drastically enlarged, and oligopotent progenitors virtually disappear, underpinned by dramatic, population-specific and sometimes unexpected changes in proliferation rates. HSPC populations return to homeostatic size and proliferation rate again through specific patterns of recovery. Overall, our data demonstrate that HSPC populations adopt different responses to cope with severe infection and suggest that the ability to adjust proliferative capacity becomes more restricted as differentiation progresses.
Heterogeneous Appetite Patterns in Depression: Computational Modeling of Nutritional Interoception, Reward Processing, and Decision-Making
Authors: Uchida Yuuki , Hikida Takatoshi , Honda Manabu , Yamashita Yuichi
Published: September 2024

Accurate interoceptive processing in decision-making is essential to maintain homeostasis and overall health. Disruptions in this process have been associated with various psychiatric conditions, including depression. Recent studies have focused on nutrient homeostatic dysregulation in depression for effective subtype classification and treatment. Neurophysiological studies have associated changes in appetite in depression with altered activation of the mesolimbic dopamine system and interoceptive regions, such as the insular cortex, suggesting that disruptions in reward processing and interoception drive changes in nutrient homeostasis and appetite. This study aimed to explore the potential of computational psychiatry in addressing these issues. Using a homeostatic reinforcement learning model formalizing the link between internal states and behavioral control, we investigated the mechanisms by which altered interoception affects homeostatic behavior and reward system activity via simulation experiments. Simulations of altered interoception demonstrated behaviors similar to those of depression subtypes, such as appetite dysregulation. Specifically, reduced interoception led to decreased reward system activity and increased punishment, mirroring the neuroimaging study findings of decreased appetite in depression. Conversely, increased interoception was associated with heightened reward activity and impaired goal-directed behavior, reflecting an increased appetite. Furthermore, effects of interoception manipulation were compared with traditional reinforcement learning parameters (e.g., inverse temperatureβand delay discountγ), which represent cognitive-behavioral features of depression. The results suggest that disruptions in these parameters contribute to depressive symptoms by affecting the underlying homeostatic regulation. Overall, this study findings emphasize the importance of integrating interoception and homeostasis into decision-making frameworks to enhance subtype classification and facilitate the development of effective therapeutic strategies.
Disarming emotional memories using Targeted Memory Reactivation during Rapid Eye Movement sleep
Authors: Greco Viviana , Foldes Tamas A. , Harrison Neil A. , Murphy Kevin , Wawrzuta Marta , Abdellahi Mahmoud E. A. , Lewis Penelope A.
Published: September 2024

Emotional responses are dampened across sleep, and this is thought to be mediated by neural reactivation during Rapid Eye Movement (REM) Sleep. Such reactivation can be triggered by targeted memory reactivation (TMR), a technique in which a tone previously associated with a memory during wake is re-presented during subsequent sleep. Prior work has shown that TMR in REM reduces arousal responses to negative stimuli. The present study builds on this by measuring autonomic responses and brain activity as well as behaviour. Participants rated the arousal of 48 affective images, paired with semantically matching sounds. Half of these sounds were cued during REM in the subsequent overnight sleep cycle. Participants rated the images in a Magnetic Resonance Imaging (MRI) scanner with pulse oximetry 48 hours after encoding, and again after two weeks. Results showed that TMR during REM was also associated with reduced brain activity in the two primary nodes of the Salience Network (SN): the Anterior Insula and dorsal Anterior Cingulate Cortex (dACC), as well as the orbitofrontal cortex, subgenual cingulate, and left amygdala, all of which are known to be important for emotional processing. TMR markedly reduced the emotional heart rate deceleration (HRD) response, and also reduced subjective arousal ratings for highly arousing images, while increasing ratings for less arousing images. We conclude that REM TMR can facilitate a decrease in physiological and neurological responses to arousal. These findings have potential implications for the use of TMR in treatment of depression and anxiety disorders.

Highlights

TMR in REM sleep reduces Salience Network responses to emotional pictures.

TMR in REM sleep reduces heart rate deceleration to emotional pictures.

TMR in REM sleep reduces subjective arousal ratings of highly arousing images.

TMR in REM sleep provides a promising potential avenue for treatment of PTSD.
The immune landscape of tumor-associated macrophage reprogramming
Authors: Duval Florent , Lourenco Joao , Hicham Mehdi , Boivin Gaël , Guichard Alan , Wyser-Rmili Celine , Fournier Nadine , De Palma Michele , Mansouri Nahal
Published: September 2024

Tumor-associated macrophages (TAMs) generally acquire immunosuppressive and tumor-promoting phenotypes, which may contribute to tumor resistance to immunotherapy. We previously showed that suppression of microRNA activity through geneticDicer1inactivation rewires TAM’s transcriptomes and prompts their immunostimulatory activation. This phenotypic switch enhanced recruitment and activation of CD8+cytotoxic T cells (CTLs) and improved the efficacy of immunotherapy in mouse cancer models. Here, we performed single-cell RNA sequencing of whole tumors grown in either wild-type mice or mice with macrophage-specificDicer1deletion. The analysis of multiple cell populations, including several discrete monocyte and macrophage subsets, indicated broad and convergent immunostimulatory programming of the tumor microenvironment, which was dependent on CTL-derived interferon-gamma (IFNγ), in mice with DICER-deficient macrophages. Intriguingly, dynamic inferences on monocyte/macrophage ontogeny and differentiation by pseudotime analysis revealed trajectories associated with progression into cell cycle, monocyte-to-macrophage differentiation, and transition from an immunostimulatory to an immunosuppressive phenotype in tumors with DICER-proficient macrophages.Dicer1deficiency interfered with this trajectory and stalled TAMs at an intermediate state between immature monocytes and macrophages with T cell-stimulatory capacity, thereby impeding immunosuppressive TAM development. This translated into enhanced response to antiangiogenic immunotherapy in an immunotherapy-resistant model of non-small cell lung cancer. Cycling/M2-like macrophages were conserved in human melanoma and hepatocellular carcinoma and should represent a more promising therapeutic target than the bulk of TAMs.
Morning Engagement of Hepatic Insulin Receptors Improves Afternoon Hepatic Glucose Disposal and Storage
Authors: Waterman Hannah L. , Moore Mary Courtney , Smith Marta S. , Farmer Ben , Yankey Kalisha , Scott Melanie , Edgerton Dale S. , Cherrington Alan D.
Published: September 2024

Glucose tolerance improves significantly upon consuming a second, identical meal later in the day (second meal phenomenon). We previously established that morning hyperinsulinemia primes the liver for increased afternoon hepatic glucose uptake (HGU). Although the route of insulin delivery is an important determinant of the mechanisms by which insulin regulates liver glucose metabolism (direct hepatic vs indirect insulin action), it is not known if insulin’s delivery route affects the second meal response. To determine whether morning peripheral insulin delivery (as occurs clinically (subcutaneous)) can enhance afternoon HGU, conscious dogs were treated in the morning with insulin delivered via the portal vein, or peripherally (leg vein), while glucose was infused to maintain euglycemia. Consequently, arterial insulin levels increased similarly in both groups, but relative hepatic insulin deficiency occurred when insulin was delivered peripherally. In the afternoon, all animals were challenged with the same hyperinsulinemic-hyperglycemic clamp to simulate identical postprandial-like conditions. The substantial enhancement of HGU in the afternoon caused by morning portal vein insulin delivery was lost when insulin was delivered peripherally. This indicates that morning insulin does not cause the second meal phenomenon via its indirect actions on the liver, but rather through direct activation of hepatic insulin signaling.

Article Highlights

Morning insulin delivery primes the liver for increased hepatic glucose uptake (HGU) later in the day, but the mechanism (direct hepatic and/or indirect insulin action) remains unclear.

This study compared insulin infusion via physiologic (hepatic portal vein) and clinical (peripheral) routes to assess their impact on afternoon hepatic glucose disposal.

Morning peripheral insulin delivery failed to induce a significant enhancing effect on afternoon HGU and glycogen storage, unlike morning hepatic portal vein insulin delivery, which did.

These findings highlight the importance of achieving appropriate hepatic insulin exposure in the morning to effectively prime the liver for efficient glucose disposal.
The protein structurome ofOrthornaviraeand its dark matter
Authors: Mutz Pascal , Camargo Antonio Pedro , Sahakyan Harutyun , Neri Uri , Butkovic Anamarija , Wolf Yuri I. , Krupovic Mart , Dolja Valerian V. , Koonin Eugene V.
Published: September 2024

Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdomOrthornaviraein the realmRiboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile-based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships. We constructed anOrthornavirae‘structurome’ consisting of already annotated as well as unannotated (‘dark matter’) proteins and domains encoded in viral genomes. We used protein structure modeling and similarity searches to illuminate the remaining dark matter in hundreds of thousands of orthornavirus genomes. The vast majority of the dark matter domains showed either ‘generic’ folds, such as single α-helices, or no high confidence structure predictions. Nevertheless, a variety of lineage-specific globular domains that were new either to orthornaviruses in general or to particular virus families were identified within the proteomic dark matter of orthornaviruses, including several predicted nucleic acid-binding domains and nucleases. In addition, we identified a case of exaptation of a cellular nucleoside monophosphate kinase as an RNA-binding protein in several virus families. Notwithstanding the continuing discovery of numerous orthornaviruses, it appears that all the protein domains conserved in large groups of viruses have already been identified. The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions.

IMPORTANCE

Advanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. This is particularly pertinent for proteins encoded by viruses that are known evolve rapidly and as a result often cannot be adequately characterized by analysis of the protein sequences. We performed an exhaustive structure prediction and comparative analysis for uncharacterized proteins and domains (‘dark matter’) encoded by viruses with RNA genomes. The results show the dark matter of RNA virus proteome consists mostly of disordered and all α-helical domains that cannot be readily assigned a specific function and that likely mediate various interactions between viral proteins and between viral and host proteins. The great majority of globular proteins and domains of RNA viruses are already known although we identified several unexpected domains represented in individual viral families.
Museomics analyses inform aboutChannichthysicefish species diversity
Authors: Garmann-Aarhus Benedicte , Nikolaeva Ekaterina , Desvignes Thomas , Straube Nicolas , Matschiner Michael
Published: September 2024

The rapid diversification of notothenioid fishes in the waters surrounding the Antarctic continent is a prime example of the process of adaptive radiation. Within around 10 million years, Antarctic notothenioids have diversified into over 100 species with a broad range of lifestyles and ecological adaptations. However, the exact number of species within this radiation has long been unclear. Particularly challenging is the taxonomy of the genusChannichthys, for which between one and nine species have been recognized by different authors. The putative species from this genus are known from a limited number of representative specimens, of which most were sampled decades ago. Here, we investigated the mitochondrial genomes of museum specimens representing the four recently recognized species Unicorn Icefish (C. rhinoceratus), Red Icefish (C. rugosus), Sailfish Pike (C. velifer), and Charcoal Icefish (C. panticapaei), complemented by morphological analyses. All analyzed specimens were collected in the 1960s and 1970s and fixed in formaldehyde, and their DNA has thus been heavily degraded. Applying ancient-DNA protocols for DNA extraction and single-stranded library preparation, we were nevertheless able to obtain sufficient endogenous DNA to reconstruct the mitochondrial genomes of one specimen of each species. These mitochondrial genome sequences were nearly identical for the three specimens assigned to Unicorn Icefish, Red Icefish, and Sailfish Pike, while greater mitochondrial divergence was observed for the Charcoal Icefish specimens. We discuss possible explanations of the contrast between these molecular results and the recognizable morphological variation found among the four species, and recommend that at least the Charcoal Icefish be included the list of valid icefish and notothenioid species.
Ecological dynamics explain modular denitrification in the ocean
Authors: Sun Xin , Buchanan Pearse , Zhang Irene H. , Roman Magdalena San , Babbin Andrew R. , Zakem Emily
Published: September 2024

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is the multi-step denitrification, the dominant pathway for bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain only subsets (“modules”) of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the observed prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when growth is limited by organic matter (OM), explaining the viability of populations respiring nitrite and N2O in a nitrate-filled ocean. Results predict denitrifier community succession along environmental gradients: shorter versus longer modules are favored when OM versus N limits growth, respectively, suggesting a niche for the NO3−⟶NO2−module in free-living communities and for the complete pathway in organic particles, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3−⟶NO2−module. Results also capture observations that nitrate is the dominant source of N2O. These results advance the mechanistic understanding of the relationship between microbial ecology and N loss, which is essential for accurately predicting the ocean’s future.
Impact of Interval Censoring on Data Accuracy and Machine Learning Performance in Biological High-Throughput Screening
Authors: Doffini Vanni , Nash Michael A.
Published: September 2024

High-throughput screening (HTS) combined with deep mutational scanning (DMS) and next-generation DNA sequencing (NGS) have great potential to accelerate discovery and optimization of biological therapeutics. Typical workflows involve generation of a mutagenized variant library, screening/selection of variants based on phenotypic fitness, and comprehensive analysis of binned variant populations by NGS. However, in such cases, the HTS data are subject to interval censoring, where each fitness value is calculated based on the assignment of variants to bins. Such censoring leads to increased uncertainty, which can impact data accuracy and, consequently, the performance of machine learning (ML) algorithms tasked with predicting sequence-fitness pairings. Here, we investigated the impact of interval censoring on data quality and ML performance in biological HTS experiments. We theoretically analyzed the impact of data censoring and propose a dimensionless number, theRatio of Discretization(RD), to assist in optimizing HTS parameters such as the bin width and the sampling size. This approach can be used to minimize errors in fitness prediction by ML and to improve the reliability of these methods. These findings are not limited to biological HTS techniques and can be applied to other systems where interval censoring is an advantageous measurement strategy.
Natural Language Processing Algorithms Outperform ICD Codes in the Development of Fall Injuries Registry
Authors: Taseh Atta , Sasanfar Souri , Chan Jia-Zhen M. , Sirls Evan , Nazarian Ara , Batmanghelich Kayhan , Bean Jonathan F. , Ashkani-Esfahani Soheil
Published: September 2024

Background

Standardized registries are commonly built using administrative codes assigned to patient encounters, such as the International Classification of Diseases (ICD) codes. However, fall patients are often coded using subsequent injury codes, such as hip fractures. This necessitates manual screening to ensure the accuracy of data registries. Herein, we aimed to automate the extraction of fall incidents and mechanisms using Natural Language Processing (NLP) and compare this approach with the ICD method.

Methods

Clinical notes for patients with fall-induced hip fractures were retrospectively reviewed by medical experts. Fall incidences were detected, annotated, and classified among patients who had fall-induced hip fracture (case group). The control group included patients with hip fracture without any evidence of fall. NLP models were developed using the annotated notes of the study groups to fulfill two separate tasks: fall occurrence detection and fall mechanism classification. The performances of the models were compared using accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), F1-score, and area under the ROC curve (AUC-ROC).

Results

A total of 1,769 clinical notes were included in the final analysis for the fall occurrence task, and 783 clinical notes were analyzed for the fall mechanism classification task. The highest F1 score using NLP for fall occurrence was 0.97 (specificity=0.96; sensitivity=0.97) and for fall mechanism classification was 0.61 (specificity=0.56; sensitivity=0.62). NLP could detect up to 98% of the fall occurrences and 65% of the fall mechanisms accurately compared to 26% and 12%, respectively, by ICD codes.

Conclusion

Our findings showed promising performance with a higher accuracy of NLP algorithms compared to the conventional method for detecting fall occurrence and mechanism in developing disease registries using clinical notes. Our approach can be introduced to other registries that are based on large data and are in need for accurate annotation and classification.
Transcriptome and evolutionary analysis ofPseudotrichomonas keilini, a free-living anaerobic eukaryote
Authors: Abu-Elmakarem Hend , Taerum Stephen J. , Petitjean Celine , Kotyk Michael , Kay Christopher , Čepička Ivan , Bass David , Gile Gillian H. , Williams Tom A.
Published: September 2024

The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are key to answering these questions. The Parabasalia are an ancient lineage of anaerobes, and the most speciose lineage of Metamonada, a major lineage of eukaryotes. The most well-studied metamonads are parasitic parabasalids includingTrichomonas vaginalis, Tritrichomonas foetus, andGiardia intestinalis, but very little genome-scale data is available for free-living members of the group. Here, we sequenced the transcriptome ofPseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated thatP. keilinipossesses a metabolism and gene complement that are in many respects similar to its parasitic relativeTrichomonas vaginalis, and that in the time since their most recent common ancestor, it is theTrichomonas vaginalislineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared betweenP. keiliniandTrichomonas vaginalisinclude a hydrogenosome (anaerobic mitochondrial homologue) that we predict to function much as inTrichomonas vaginalis, and a complete glycolytic pathway that is likely to represent one of the primary means by whichP. keiliniobtains ATP. Phylogenomic analysis indicates thatP. keilinibranches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved towards parasitic or free-living lifestyles from an endobiotic, anaerobic or microaerophilic common ancestor.
Diverse defense systems synergistically drive the microbe-virus arms race in deep sea cold seeps
Authors: Han Yingchun , Liao Jing , Li Chengpeng , Xing Fengmin , Peng Jiaxue , Liu Xinyue , Xie Wentao , Wu Fabai , Jian Huahua , Cheng Rui , Dong Xiyang
Published: September 2024

Cold seeps are unique deep-sea ecosystems that host diverse uncharacterized microbes and viruses, many of which potentially possess novel defense and counter-defense systems. Despite their ecological significance, the diversity of microbial defense systems, their interactions, and the evolutionary arms race with viral anti-defense strategies in cold seeps remain largely unexplored. To address this, we analyzed 3,813 microbial and 13,336 viral genomes from 193 metagenomic samples collected across 17 cold seep sites. Cold seep microbes harbor an extensive repertoire of ‘defense systems (n = 26,389), with 63% representing novel systems. Laboratory experiments confirm that several of these novel systems effectively protect against viral infections. These defense systems frequently co-occur and interact synergistically to combat viral infections. They are widely distributed across different sediment depths and geographical locations, exhibiting active expression. In response, cold seep viruses have evolved a diverse array of anti-defense genes (n = 1,197), employing complex strategies to counteract host defenses. The concurrent presence of multiple viral anti-defense genes and various microbial defense genes in their hosts highlights the intricate and dynamic interactions between viruses and their microbial counterparts. Functionally critical lineages, such as anaerobic methanotrophic archaea (ANME), sulfate-reducing bacteria (SRB), and diazotrophs, adapt their defensive strategies according to ecological niches and environmental pressures. Notably, SRB strains were found to harbor multiple Gabija defense systems, enhancing their resistance to viral attacks, while corresponding viruses carry anti-Gabija genes, illustrating a specific evolutionary adaptation. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in extreme deep-sea subseafloor environments.
The neural time course of size constancy in natural scenes
Authors: Yeh Lu-Chun , Gayet Surya , Kaiser Daniel , Peelen Marius V.
Published: September 2024

Accurate real-world size perception relies on size constancy, a mechanism that integrates an object’s retinal size with distance information. The neural time course of extracting pictorial distance cues from scenes and integrating them with retinal size information - a process referred to as scene-based size constancy - remains unknown. In two experiments, participants viewed objects with either large or small retinal sizes, presented at near or far distances in outdoor scene photographs, while performing an unrelated one-back task. We applied multivariate pattern analysis (MVPA) to time-resolved EEG data to decode the retinal size of large versus small objects, depending on their distance (near versus far) in the scenes. The objects were either perceptually similar in size (large-near versus small-far) or perceptually dissimilar in size (large-far versus small-near), reflecting size constancy. We found that the retinal size of objects could be decoded from 80 ms after scene onset onwards. Distance information modulated size decoding at least 120 ms later: from 200 ms after scene onset when objects were fixated, and from 280 ms when objects were viewed in the periphery. These findings reveal the neural time course of size constancy based on pictorial distance cues in natural scenes.
Differential Kinetics of SARS-CoV-2 Proteases Revealed by a Dual-Color, BRET-based Protease Biosensor, DuProSense
Authors: Fatima Asma , Geethakumari Anupriya M , Uddin S M Nasir , Biswas Kabir H
Published: September 2024

While SARS-CoV-2 Mproand PLproproteases are known to cleave polyproteins pp1a and pp1ab at multiple sites, these have not been comprehensively characterized in living cells. Here we engineered a two-color Bioluminescence Resonance Energy Transfer (BRET)-based, dual protease (DuProSense) biosensor platform relying on a proximity-dependent energy transfer from a luciferase donor to two spectrally separated fluorescent protein acceptors enabling simultaneous monitoring of processing of two cleavage sites in a single assay with high specificity. DuProSense revealed a similar Mproand PLprocleavage kinetics for their N-terminal autocleavage sites. Importantly, systematic characterization of various Mproand PLprocleavage sites using DuProSense revealed significant differences in cleavage rates and nirmatrelvir potency of Mprocleavage sites but no correlation between the cleavage rates and nirmatrelvir IC50values. Overall, our results provide deeper insights into the proteolytic processing of SARS-CoV-2 polyproteins and the dual color BRET platform will find wider applications in the future.

Highlights

Engineered a two-color BRET-based, dual protease biosensor (DuProSense)

DuProSense biosensor enabled simultaneous and specific monitoring of Mproand PLproactivities

DuProSense platform revealed differential cleavage kinetics of Mprocleavage sites in live cells

DuProSense platform revealed Mprocleavage site-dependent nirmatrelvir potency in live cells
Evolutionary trends in the emergence of skeletal cell types
Authors: Damatac Amor , Koska Sara , Ullrich Kristian K , Domazet-Lošo Tomislav , Klimovich Alexander , Kaucká Markéta
Published: September 2024

The emergence of novel cell types fuels evolutionary innovations and contributes to the diversity of life forms and their morphological and functional traits. Cell types are fundamental functional units of multicellular organisms defined by their specific gene expression programs. The evolution of these transcriptional programs is driven by genetic changes, such as gene co-option and cis- regulatory evolution, known to facilitate the assembly or rewiring of molecular networks and give rise to new cell types with specialized functions. However, the role of novel genes in this complex evolutionary process is underexplored. Here, we examine the trends in skeletal cell type evolution with a focus on lineage-specific genes. We find that immature chondrocytes express the oldest transcriptome and resemble ancestral skeletogenic cell type, supporting the existence of a conserved genetic program for cartilage development in bilaterians. The subsequent acquisition of lineage-restricted genes led to the individuation of the ancient gene expression program and powered the emergence of osteoblasts and hypertrophic chondrocytes. We found a significant enrichment of Vertebrate-specific genes in osteoblasts and Gnathostome-specific genes in hypertrophic chondrocytes. By identifying the functional properties of the recruited genes, coupled with the recently discovered fossil evidence, our findings challenge the long-standing view on the evolution of vertebrate skeletal structures and suggest that endochondral ossification and chondrocyte hypertrophy evolved already in the last common ancestors of gnathostomes. Finally, our findings highlight the critical role of novel genes in shaping cellular diversity.
Topological Excitations govern Ordering Kinetics in Endothelial Cell Layers
Authors: Ruider Iris , Thijssen Kristian , Vannier Daphné Raphaëlle , Paloschi Valentina , Sciortino Alfredo , Doostmohammadi Amin , Bausch Andreas R.
Published: September 2024

Many physiological processes, such as the shear flow alignment of endothelial cells in the vasculature, depend on the transition of cell layers between disordered and ordered phases. Here, we demonstrate that such a transition is driven by the non-monotonic evolution of nematic topological defects and the emergence of topological strings that bind the defects together, unveiling an intermediate phase of ordering kinetics in biological matter. We used time-resolved large-scale imaging and physical modeling to resolve the nature of the non-monotonic decrease in the number of defect pairs. The interaction of the intrinsic cell layer activity and the alignment field determines the occurrence of defect domains, which defines the nature of the transition. Defect pair annihilation is mediated by topological strings spanning multicellular scales within the cell layer. We propose that these long-range interactions in the intermediate ordering phase have significant implications for a wide range of biological phenomena in morphogenesis, tissue remodeling, and disease progression.
Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages, Semi-Tryptic and Non-Tryptic Peptides
Authors: Vande Moortele Tibo , Devlaminck Bram , Van de Vyver Simon , Van Den Bossche Tim , Martens Lennart , Dawyndt Peter , Mesuere Bart , Verschaffelt Pieter
Published: September 2024

Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples. From the onset, Unipept’s capabilities focused on tryptic peptides, utilizing the predictability and consistency of trypsin digestion to efficiently construct a protein reference database. However, the evolving landscape of proteomics and emerging fields like immunopeptidomics necessitate a more versatile approach that extends beyond the analysis of tryptic peptides. In this article, we present a significant update to the underlying index structure of Unipept, which is now powered by a Sparse Suffix Array index. This advancement enables the analysis of semi-tryptic peptides, peptides with missed cleavages, and non-tryptic peptides such as those encountered in other research fields such as immunopeptidomics (e.g. MHC- and HLA-peptides). This new index benefits all tools in the Unipept ecosystem such as the web application, desktop tool, API and command line interface. A benchmark study highlights significantly improved performance in handling missed cleavages, preserving the same level of accuracy.

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