Biology subjects

Lin, D.

Publications and source records attributed to Lin, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

High-Resolution Characterization of rAAV Genomes for Vector Quality Using Long-Read Sequencing

Recombinant adeno-associated virus (rAAV)-mediated gene therapy has been applied for human diseases. However, the rAAV capsids contain heterogeneous mixtures of full-length and truncated genomes and, depending on the manufacturing process, residual host cell and plasmid DNA. Therefore, a method is needed to characterize the encapsidated DNA of rAAV in order to support process development and batch release. The emerging long-read sequencing (LRS) has achieved AAV single-genome resolution. Here we propose a Python-based LRS profiling framework to classify and quantitate residual DNA species in rAAV products. We designed a reference that contains universal genetic components that are commonly used in rAAV production, including AmpR, KanR, Rep and Cap genes along with HPV18, Ad5 and hg38 genomes. We accessed the impurities of rAAV production from public and in-house LRS datasets. Analyzing the lambda fragments supplemented in these datasets showed that sequencing introduced size biases, which couldnt be fully corrected by regression but is improvable within library preparation. Functional potential of impurities were assessed through indicators derived from long-read alignments, which enabled us to quantitatively compare impurities between manufacturing batches. We demonstrated that LRS provides informative metrics for rAAV production and can facilitate process development to ensure therapeutic product safety and quality.

genomics↗

bioRxiv2025

Arabidopsis Group I Pumilio RNA-binding factors are vital for embryo development and balancing between growth and stress resistance

Pumilio (PUM) RNA binding proteins are crucial for regulating gene expression by binding to a conserved motif in the 3'-untranslated region (3'-UTR). Despite their importance, the role of PUM in plants is largely unexplored. Here, we investigated the functions of Arabidopsis group I PUMs (APUM1-APUM6), which are ubiquitously expressed and localized in the cytosol. While single apum mutants exhibit no visible phenotypes, CRISPR/Cas9-generated apum1 apum2 apum3 triple mutants (apum1/2/3) display reduced growth in both vegetative and reproductive organs, alongside hypersensitivity to various stresses. Remarkably, apum1/2/3/4 quadruple mutants are embryonically lethal, highlighting their essential role in embryo development. Transcriptomic profiling revealed that differentially expressed genes (DEGs) upregulated in apum1/2/3 are enriched in pathways related to photosynthesis, stress responses and anthocyanin biosynthesis, while downregulated DEGs are associated with biotic stress defense and hydrogen peroxide metabolism. This suggests that APUM1/2/3 act as molecular hubs balancing plant growth and stress adaptation. Biochemical assays showed that recombinant APUM homologous domains bind to the 5-UGUGUAUA-3 core motif in the 3-UTR of the transcription factor Production of Anthocyanin Pigment1 (PAP1), crucial for anthocyanin biosynthesis. Notably, single nucleotide substitutions, except for the third U, do not affect binding, while multiple mutations disrupt interaction. Consistently, apum1/2/3 mutants accumulate significantly more anthocyanin than wild-type plants. Furthermore, we predicted 7053 potential target genes for APUM1/2/3, with 1609 present among the upregulated DEGs in apum1/2/3. Taken together, our findings demonstrate that group I APUMs are vital posttranscriptional regulators, providing a new perspective on the trade-offs between growth and stress resilience in plants.

plant biology↗

bioRxiv2025

Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone

BackgroundHybrid zones play a central role in evolutionary biology because they serve as natural laboratories for studying how traits and taxa diverge. Changes in gene regulation make important contributions to this process. However, the degree to which admixture shapes gene regulatory variation in hybrid populations remains poorly understood. Here, we combine genome-wide resequencing and DNA methylation data from 295 hybrid baboons--members of a single, intensively studied natural population--to investigate how admixture affects the genetic architecture of this important epigenetic mark. ResultsWe find that local genetic ancestry frequently predicts DNA methylation levels and recapitulates differences between the parent species. By performing methylation quantitative trait locus (meQTL) mapping, we show that these differences predominantly arise due to evolved differences in allele frequencies. Thus, admixture in the hybrid population increases variance in DNA methylation, including by introducing meQTL that would otherwise be invariant. Finally, we integrate massively parallel reporter assay data to show that admixture-derived variation in DNA methylation alters enhancer activity and gene expression. ConclusionsTogether, these results demonstrate how admixture can meaningfully alter the genetic architecture of gene regulatory traits in natural hybrid zones. They also suggest that the genetic architecture of DNA methylation is conserved across closely related primates, suggesting that genetic effects on gene regulation may remain stable over timescales that range into the millions of years.

evolutionary biology↗

bioRxiv2025

Mechanistic Insights into Dual-Active Liver and Blood-Stage Antiplasmodials

The identification of novel antimalarials with activity against both the liver and blood stages of the parasite lifecycle would have the dual benefit of prophylactic and curative potential. However, one challenge of leveraging chemical hits from phenotypic screens is subsequent target identification. Here, we use in vitro evolution of resistance to investigate nine compounds from the Tres Cantos Antimalarial Set (TCAMS) with dual liver and asexual blood stage activity. We succeeded in eliciting resistance to four compounds, yielding mutations in acetyl CoA synthetase (AcAS), cytoplasmic isoleucine tRNA synthetase (cIRS), and protein kinase G (PKG) respectively. Using a combination of CRISPR editing and in vitro activity assays with recombinant proteins, we validate these as targets for TCMDC-125075 (AcAS), TCMDC-124602 (cIRS), and TCMDC-141334 and TCDMC-140674 (PKG). Notably, for the latter two compounds, we obtained a T618I mutation in the gatekeeper residue of PKG, consistent with direct interaction with the active site, which we modelled with molecular docking. Finally, we performed cross-resistance evaluation of the remaining five resistance-refractory compounds using the Antimalarial Resistome Barcode sequencing assay (AReBar), which examined a pool of 52 barcoded lines with mutations covering >30 common modes of action. None of the five compounds where in vitro evolution of resistance was not successful yielded validated hits using AReBar, indicating they likely act via novel mechanisms and may be candidates for further exploration.

microbiology↗

bioRxiv2025

Genetically encoded assembly recorder temporally resolves cellular histories in cellulo and in vivo

Mapping cellular activity with high spatiotemporal precision in complex tissues is essential for understanding organ physiology, pathology, and regenerative processes. Here, we introduce Granularly Expanding Memory for Intracellular Narrative Integration (GEMINI), an in cellulo recording platform that leverages a computationally designed protein assembly as an intracellular memory device to record individual cells activity histories. GEMINI grows predictably within live cells with minimal interference to cellular functions, capturing cellular activities as tree-ring-like fluorescent patterns in the expanding scaffolds for imaging-based retrospective readout. Absolute chronological information of activity histories was attainable with hour-level accuracy through the integration of fiducial timestamps. GEMINI effectively resolved differential NF{kappa}B-mediated transcriptional changes, distinguishing fast dynamics of 15 minutes, and providing quantifiable signal amplitudes. In a xenograft model, GEMINI recorded inflammation-induced signaling dynamics across tissue with cellular resolution, revealing spatial heterogeneity linked to vascular density. When expressed in the mouse brain, GEMINI exhibited negligible impact on neuronal survival, with animals maintaining normal motor and cognitive behaviors. In physiological contexts, GEMINI successfully resolved both transcriptional changes and activity patterns of neurons in the brain. Together, GEMINI provides a robust and generalizable means for spatiotemporal mapping of cell dynamics underlying physiological and pathological processes in both culture and intact tissues.

bioengineering↗

bioRxiv2025

A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population

Human reference genomes have been instrumental in advancing genomic and biomedical research, but South and Southeast Asian populations are underrepresented, despite accounting for a large proportion of world population. As a part of effort on generating reference genomes for these populations, we present the first gapless, telomere-to-telomere (T2T) diploid genome assembly created by using a trio sample set of Indian ancestry (I002C), with NG50 of 154.89 Mb and 146.27 Mb for the maternal and paternal haplotypes, including the fully assembled rDNA array for the maternal chromosome 21 and Y chromosome. With the Merqury QVs of 82.05, 83.08 and 82.64 for the maternal, paternal and haploid assemblies respectively, I002C represents the highest-quality human genome assembled in both diploid and haploid forms to date. Compared to CHM13, the I002C genome displays substantial sequence diversity, resulting in 14,943 structural variants, including 3,236 novel variants absent from public databases. Analysis of trio-phased haplotypes further revealed elevated inter-haplotype divergence within centromeric and subtelomeric regions, along with identification of differentially methylated regions (DMRs) as candidates for novel imprinting loci. As a result of substantial SVs between them, I002C is a more suitable reference than CHM13 for the genomic analysis of South Asian samples with less reference bias and better performance in mapping and variant calling, particularly for long read sequencing data. As the first high-quality T2T diploid reference genome for Indian, the largest worlds population, I002C contributes to the growing set of population-specific reference genomes and helps to overcome a significant gap in human genome diversity.

genomics↗

bioRxiv2025

The neural mechanisms supporting the rise and fall of maternal aggression

To protect the helpless young, lactating females dramatically increase aggression towards intruders, known as maternal aggression. However, attack is costly and risky. When pups no longer exist, maternal aggression rapidly declines. Our study reveals the critical role of the pathway from posterior amygdala cells expressing estrogen receptor alpha (PAEsr1) to the ventrolateral part of ventromedial hypothalamus cells expressing neuropeptide Y receptor Y2 (VMHvlNpy2r) in the rise and fall of maternal aggression. Functional manipulations and recordings demonstrate that VMHvl-projecting PAEsr1 (PAEsr1[->]VMHvl) cells are naturally active and required for maternal aggression. During lactation, PA-VMHvlNpy2r connection strengthens, and VMHvlNpy2r excitability increases to facilitate attack. Furthermore, PAEsr1 expresses abundant oxytocin receptors, enabling oxytocin to boost PAEsr1 cell output. After pup separation, the oxytocin level drops, causing decreased maternal aggression, which can be restored by optogenetically increasing the oxytocin level. Thus, diverse forms of plasticity occur at the PAEsr1-VMHvlNpy2r circuit to support need-based maternal aggression.

neuroscience↗

bioRxiv2025

Spleen-derived Small Extracellular Vesicles Protect against Myocardial Infarction via Mediating Spleen-heart Crosstalk

Background and AimsAcute myocardial infarction (AMI) triggers systemic responses that influence cardiac injury and repair, but protective mediators within the cardiosplenic axis remain incompletely understood. This study aimed to investigate whether spleen-derived small extracellular vesicles (sEVs) exert cardioprotection after AMI, identify critical cargo, and evaluate their clinical relevance. MethodsThe effects of splenectomy, spleen-derived sEVs and pharmacological inhibition of sEVs biogenesis on cardiac injury were evaluated in mice with AMI. Parabiosis, donor splenectomy, and fluorescent labelling traced the origin and myocardial recruitment of circulating sEVs. 4D-proteomics profiled sEVs cargo with a focus on pyruvate carrier-1 (MPC1). ResultsSplenectomy worsened survival, ventricular function, infarct size, and fibrosis in mice with AMI. AMI upregulated splenic extracellular-vesicle pathways, with sEVs release peaking at day 3 (M3D-sEVs). Labelled splenic sEVs preferentially accumulated in ischemic myocardium, confirmed by parabiosis experiments. M3D-sEVs improved survival and cardiac function and reduced infarct size, fibrosis, apoptosis, inflammation, and hypertrophy. In addition, anti-apoptotic effects were reproduced in vitro. Inhibition of sEVs biogenesis decreased circulating sEVs, aggravated injury, and was rescued by M3D-sEVs. M3D-sEVs were enriched in MPC1, and MPC1 neutralization or pharmacological blockade abrogated sEVs-mediated restoration of respiration, ATP generation, and reduction of reactive oxygen species. Plasma sEVs-associated MPC1 was highest in patients with AMI, intermediate in coronary heart disease, and lowest in controls. ConclusionsThe spleen responds adaptively to AMI by releasing MPC1lenriched sEVs that travel to injured myocardium, preserve mitochondrial energetics, and reduce damage, supporting cargolspecific sEVs augmentation and sEVslMPC1 as a potential therapeutic target and biomarker in ischemic heart disease. Structured graphical abstractAcute myocardial infarction activates a spleen-heart axis in which the spleen releases mitochondrial pyruvate carrier 1 (MPC1) enriched small extracellular vesicles that home to the infarcted myocardium, preserve mitochondrial oxidative phosphorylation, reduce ROS, and limit infarct size, apoptosis, fibrosis, and hypertrophy. Circulating sEVs-associated MPC1 might serve as a potential biomarker for estimating risk of ischemic heart disease. Translational perspectiveO_LIOur findings reveal a novel heart-spleen communication axis mediated by splenic small extracellular vesicles (sEVs) following AMI. These vesicular messengers predominantly deliver mitochondrial pyruvate carrier 1 (MPC1), enhancing cardiac mitochondrial energy metabolism in the injured myocardium, ultimately improving post-AMI functional recovery in experimental models. C_LIO_LIA higher plasma sEVs-associated MPC1 level was observed in AMI patients when compared with non-AMI patients. These findings support the clinical relevance of the spleen-heart axis, introduce sEVs-associated MPC1 as a potential circulating biomarker for early myocardial injury and therapeutic target. C_LI

molecular biology↗

bioRxiv2025

Perivascular matrix densification dysregulates angiogenesis and activates pro-inflammatory endothelial cells

Fibrosis is central to numerous fatal conditions including solid cancers, pulmonary fibrosis, cirrhosis and post-infarct cardiac fibrosis amongst many others, thereby collectively contributing to 45% of all deaths in developed nations. The potential for fibrosis across most organ systems may stem from its connections to wound healing and the ubiquitous presence of vascular endothelium. Endothelial cells (ECs) and angiogenesis, cells and associated biological program central to wound healing, have been heavily implicated in many organ-specific fibroses, but the relationship between angiogenesis and fibrogenesis remains debated and little has been established in terms of how the EC phenotype governs tissue healing vs. fibrosis. Here, we examine a murine lung injury model enabling EC lineage tracing and observe the invasion of aberrant ECs from the bronchial microvasculature following lung injury along with concurrent densification of matrix fibers surrounding these vessels. To investigate the underlying mechanisms governing their appearance, we established a microphysiological system (MPS) of arteriole/venule-scale microvessels embedded within a tunable stromal mimetic matrix and find that heightened extracellular matrix fiber density activates ECs, drives endothelial to mesenchymal transition, and promotes aberrant tip EC (ATEC) invasion into the matrix. ATECs remain adherent to fibrotic matrix and possess a pro-inflammatory phenotype that secretes TGF-{beta}2. Notably, our studies establish that the formation of ATECs is gated by destabilization of endothelial adherens junction upon EC adhesion to fibrous matrix, and associated regulation of TGF-{beta} signaling that is mediated by a novel VE-cadherin - TGF-{beta}R2 axis. The current lack of effective anti-fibrotic therapies suggests potential critical involvement of other cell types such as ECs, and our findings suggest new contributions of ECs to fibrotic progression that may better inform future targets for novel anti-fibrotic therapeutics.

bioengineering↗

bioRxiv2025

Longitudinal single-cell analysis reveals RUNX1T1 as an early driver in treatment-induced neuroendocrine transdifferentiation

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal form of advanced prostate cancer that can emerge from adenocarcinoma under androgen receptor pathway inhibition, but the tumor-cell states and regulators underlying this transition remain incompletely defined. Here, we analyzed longitudinal single-cell RNA sequencing data from the LTL331/331R patient-derived xenograft model across seven disease stages, comprising 32,269 tumor-cell transcriptomes from treatment-naive adenocarcinoma, post-castration regression, and relapsed NEPC. We identified an AR-low/NE-low intermediate state that emerged after castration and before overt relapse, as well as two transcriptionally distinct terminal NEPC states marked by ASCL1high/FOXA2low and ASCL1low/FOXA2high programs. RUNX1T1 was induced in the intermediate state and remained elevated across both terminal states. RUNX1T1 enhanced NE-associated features and cell viability during enzalutamide treatment in adenocarcinoma cells, whereas its knockdown in NCI-H660 cells reduced NE-associated transcriptional programs, proliferation, and survival and shifted the transcriptome toward an intermediate-like state. Chromatin interactome analysis and co-immunoprecipitation linked RUNX1T1 to G9A/LASP1-containing chromatin repressor complexes. These findings define a temporal framework for treatment-induced NEPC progression and identify RUNX1T1 as an early-induced and sustained regulator of NE lineage transition and maintenance of established NEPC.

cancer biology↗

bioRxiv2025

SynLS: A novel diffusion-transformer framework for generating high-quality wearable sensor time series data to enhance health monitoring

While global medical research is poised to benefit from the rapid advance of artificial intelligence (AI) technologies, veterinary medicine research often faces significant limitations due to data scarcity and availability issues. To address this issue, we proposed a generative modeling framework, SynLS, for generating highly realistic synthetic wearable sensor data. Leveraging diffusion architecture and transformer encoder mechanism, SynLS addressed the intricate challenges posed by these real-world wearable sensor data, including varied length, multiple dimensions, high diversity, high noise, periodicity, and trend. We have validated SynLS on four publicly-available livestock wearables databases with records for three health events (calving, estrus and diseases), and demonstrated its ablility in producing high-fidelity wearable sensor data, which could improve the downstream health events prediction tasks by 18.5% and 26.8% under two evaluation scenarios based on instance and timestamp, respectively. Additionally, introducting raw tri-axial accelerometer databases collected from animals and human further demonstrated extensibility of our framework, significantly enhancing downstream behavior classification tasks by 38.8% and 83.8%, respectively. The technical framework proposed in this work offers a potential generalized solution for data supplementation in wearables sensor databases, with potential applicability across veterinary medicine and other medical domains facing resource constraints.

bioinformatics↗

bioRxiv2025

Longitudinal single-cell RNA sequencing of a neuroendocrine transdifferentiation model reveals transcriptional reprogramming in treatment-induced neuroendocrine prostate cancer

Neuroendocrine transdifferentiation (NEtD) of prostate adenocarcinoma (PRAD) leads to aggressive neuroendocrine prostate cancer (NEPC). The LTL331 patient-derived xenograft (PDX) model consistently progresses to NEPC following castration, mimicking clinical responses to androgen-deprivation therapy. Here we tracked NEtD using longitudinal single-cell RNA sequencing (scRNA-seq) across eight time points in LTL331 from pre- to post-castration. Castration led to the loss of AR-high PRAD cells, expansion of AR-low populations, and emergence of an AR- and NE-negative (AR-/NE-) intermediate state that transitioned into NEPC. We delineate a model in which pre-EMT cells enriched in ciliogenesis and cell-adhesion pathways differentiate into EMT-like populations before branching into distinct ASCL1+ and ASCL1- NEPC states. The EMT-enriched intermediate, marked by progenitor and neural crest stem-cell genes, acts as a transition bridge, suggesting EMT-associated stemness underlies lineage plasticity. A terminal ASCL1-NEPC state also suggests that ASCL1 is not essential for NEPC maintenance. Gene regulatory analysis highlighted key regulators driving NEtD, including MSX1 and ASCL1 in early EMT-like and NEPC states, respectively. These transcriptional states were validated in both patient-derived bulk and scRNA-seq data. Our findings offer insights into intervention strategies to delay or prevent NEtD with the potential of identifying novel prognostic and therapeutic targets.

cancer biology↗

bioRxiv2025

The LINC complex component Kms1 and CENP-B protein Cbp1 cooperate to enforce faithful homology-directed DNA repair at the nuclear periphery in S. pombe

While homologous recombination (HR) is often considered to be an error-free DNA repair mechanism, the fidelity of this pathway depends on the cells ability to engage the ideal template, the replicated sister chromatid. This is particularly challenging during repair of repetitive genome regions for which non-allelic sequences can errantly be used as templates. Here, we develop a model to study spontaneous DNA damage and repair that occurs at repetitive protein coding genes of the S. pombe flocculin family. We observe that genes encoding most members of this protein family constitutively reside at the nuclear periphery by virtue of their close proximity to binding sites for the CENP-B like protein, Cbp1. Tethering via Cbp1 to the nuclear periphery enhances the stability of the flocculin genes against intragenic recombination and restrains intergenic recombination between homoeologous repeat-encoding sequences. The LINC complex component Kms1 also antagonizes both intragenic and intergenic recombination at the flocculin genes as well as microhomology-mediated end-joining (MMEJ). Our observations suggest that S. pombe leverages nuclear compartmentalization to maintain the stability of repetitive genic regions at the nuclear periphery while association of DSBs with Kms1-containing LINC complexes enforces stringency to avoid mutagenic end-joining and use of the incorrect template during HR.

genetics↗

bioRxiv2025

An unrecognized and crucial role of chloroplast division in leaf variegation in Arabidopsis thaliana

Leaf variegation provides a valuable model for elucidating the molecular mechanisms that underlie chloroplast biogenesis, including both chloroplast development and division. While there has been notable advancement in comprehending the role of the Arabidopsis Yellow Variegated2 (VAR2), which encodes the AtFtsH2 subunit of the thylakoid FtsH metalloprotease complex, the exact mechanism governing leaf variegation formation remains elusive. In this study, time-course microscopy analyses of chloroplast number per cell from the first leaf pair revealed that most var2 cells lack chloroplasts. Interestingly, chloroplast biogenesis in the green sector of var2 leaves is significantly delayed but prolonged compared to the wild type (WT), leading to increased heterogeneity in chloroplast number and size among cells. These results suggest that chloroplast biogenesis in the green sector can partially compensate for the defect in the white sector. Additionally, approximately 15% of cells in var2 white sectors are devoid of plastids, and chloroplast number in guard cells is significantly lower in var2 than in WT, indicating that VAR2 mutations impair chloroplast division. Consistently, the var2 phenotype is exacerbated by knocking out key plastid division genes, including Paralog of Accumulation and Replication of Chloroplasts6 (PARC6) and Plastid Division1 (PDV1), but is fully rescued by overexpressing PDV1 or PDV2. Furthermore, VAR2 mutations inhibit etioplast development, while accelerating chloroplast biogenesis by knocking out Constitutively Photomorphogenic1 (COP1) rescues the var2 phenotype. Together, our findings reveal a novel role for VAR2 in plastid division and its essential function in chloroplast biogenesis, providing new insights into the mechanism underlying variegated leaf formation.

plant biology↗

bioRxiv2025

Non-canonical HIPPO-MST1/2 promotes hyper-proliferation of pulmonary vascular cells through CDC20

HIPPO components mammalian Ste20-like protein kinases 1 and 2 (MST1/2) are well described growth suppressors. However, in pulmonary arterial hypertension (PAH), MST1/2 switch their roles and become pro-proliferative and pro-survival molecules, supporting hyper-proliferation of pulmonary artery (PA) smooth muscle cells (PASMCs) and adventitial fibroblasts (PAAFs), remodeling of small PAs, and pulmonary hypertension. Here, we report that MST1/2 promotes hyper-proliferation and apoptosis resistance of human PAH PASMCs and PAAFs by up-regulating cell division cycle protein 20 (CDC20), establishing novel link between HIPPO-MST1/2 and cell cycle regulation in PAH. Authors Contributionsconception and design of the work (EAG, SSP, TVK); acquisition, analysis, and interpretation of data (TD, IZ, LJ, SOO, AP, TA, DL, DG, JRG, PJW, HD, TK); drafting and editing the manuscript (EAG, SSP, TVK, JRG, PJW).

cell biology↗

bioRxiv2025

De novo biosynthesis of cannabinoid and its analogs in Yarrowia lipolytica

Cannabis sativa has long been a cornerstone of both medicinal and cultural practices, with its therapeutic use spanning over 2,700 years. Central to its therapeutic effects are cannabinoids, which interact with the endocannabinoid system to influence various physiological processes such as anxiety, pain, and inflammation. Despite its benefits, cannabinoid production faces challenges and scarcity from plant extraction. This work leverages Yarrowia lipolytica as a platform for cannabinoid biosynthesis. By optimizing precursor supply, engineering biomolecular condensate-like dual prenyltransferase expression and expanding endogenous metabolism with a noncanonical polyketide synthase, we achieved the de novo biosynthesis of various cannabinoid and its analogs. Our engineered Y. lipolytica produced [~]3.5 mg/L of cannabigerolic acid, 18.8 mg/L of orsellinic acid, and 0.5 mg/L of cannabigerorcinic acid. Additionally, CBGA titer reached 15.7 mg/L with olivetolic acid supplement. This work demonstrates Y. lipolyticas versatility as a promising host for cannabinoid and its analogs production, which opens avenues for further research and medicinal applications.

synthetic biology↗

bioRxiv2025

Identification of a novel false-positive mechanism in RapidFire mass spectrometry and application in drug discovery

False-positives plague High Throughput Screening in general and are costly as they consume resource and time to resolve. Methods that can rapidly identify such compounds at the initial screen are therefore of great value. Advances in mass spectrometry have led to the ability to screen inhibitors in drug discovery applications by direct detection of an enzyme reaction product. The technique is free from some of the artefacts that trouble classical assays such as fluorescence interference. Its direct nature negates the need for coupling enzymes and hence is simpler with fewer opportunities for artefacts. Despite its myriad advantages, we report here a mechanism for false-positive hits which has not been reported in the literature. Further we have developed a pipeline for detecting these false-positive hits and suggest a method to mitigate against them. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC="FIGDIR/small/634670v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@a99654org.highwire.dtl.DTLVardef@1cc7ec8org.highwire.dtl.DTLVardef@978abaorg.highwire.dtl.DTLVardef@114c0d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Gestation length drives brain size and litter size variation in eutherian mammals

The length of gestation in eutherian mammals, which is key to their reproductive success, is closely connected to other life history traits and with body mass and brain mass, but causal relationships between these variables are unclear. Here, we used an integrative analytical framework to evaluate the evolutionary relationships between gestation length and eight other traits on a dataset of 3,258 eutherian mammals and infer causality. We identify variation in generation length and litter size as the primary predictors of eutherian gestation length variation, whereas additional traits, such as brain mass, significantly predict gestation length only in specific mammalian orders. Using a structural equation modeling approach known as phylogenetic path analysis to infer causality, we find that gestation length variation positively influences brain mass variation and negatively influences litter size variation. Furthermore, body mass causally influences gestation length variation only in certain orders. Consistent with these causal inferences, examination of trait-trait coevolution reinforces that gestation length is strongly positively associated with brain mass, strongly negatively associated with litter size, and only moderately correlated with body mass. These findings reveal how gestation length directly and indirectly influences, and is influenced by, other key eutherian traits. Our study establishes a robust framework for identifying causal relationships within suites of correlated and co-evolving traits.

evolutionary biology↗