Biology subjects

Jung, A.

Publications and source records attributed to Jung, A..

14 recordsLinked to original sources

bioRxiv2026

Finely tuned DDA-PASEF-based immunopeptidomics workflow enhances HLA class I coverage

Mass spectrometry-based immunopeptidomics is essential for the direct identification of HLA-presented peptides, but its application to low-input and clinical samples remains challenging. In this study, we present an optimized DDA-PASEF-based workflow to improve HLA class I peptide coverage. First, we optimized a magnetic bead-based sample preparation protocol to support analysis from reduced starting material and increase compatibility with automation. We then evaluated LC gradient length and column dimensions to define complementary configurations for high-throughput and high-coverage analysis. For MS acquisition, we fine-tuned key parameters, including ion accumulation time, number of PASEF scans, ion mobility range, and polygon filtering, to improve sensitivity while maintaining a suitable cycle time and limiting pre-CID truncations. The customized polygon filter improved the detection of singly charged HLA class I peptides, thereby broadening the identified immunopeptide repertoire. Finally, TIMS2Rescore was integrated to improve confidence in peptide identification. Overall, this optimized workflow improves HLA class I immunopeptide coverage across different sample types, even from low injected sample amounts, supporting its future applicability to clinically relevant samples.

biochemistry↗

bioRxiv2026

Revisiting Analog Electrical Stimulation with Current Focusing in a Guinea Pig Model of Cochlear Implants.

Modern cochlear implants (CIs) use pulsatile stimulation to restore hearing for individuals with severe hearing loss. CIs provide robust speech recognition in quiet but poorly represent temporal fine structure (TFS), needed for challenging listening situations. Analog stimulation preserves the acoustic waveform and may better encode TFS, yet it has not been evaluated combined with modern current-focusing strategies. We compared neural responses in the inferior colliculus (IC) evoked by CI stimuli consisting of 100 pulses/s biphasic pulse trains and 100 cycles/s sinusoidal analog stimulation with monopolar, bipolar, and tripolar electrode configurations in urethane-anesthetized guinea pigs. Following cochlear implantation, multiunit activity was recorded from the tonotopic axis of the central nucleus of the IC using 16-channel silicon probes. Detection thresholds, spread of excitation, vector strength, sustained response percentage, and temporal response properties were quantified. Analog stimulation consistently evoked significantly lower activation thresholds than pulsatile stimulation while maintaining comparable or sometimes narrower spatial selectivity across stimulation modes. In contrast, analog stimulation generated lower vector strength, larger tonic response components, and a pronounced level-dependent polarity effect. At low stimulus levels, responses were dominated by the cathodic phase of the sinusoidal waveform, whereas increasing stimulus level responses were elicited by both phases, producing synchronization at twice the stimulus frequency. These findings demonstrate that stimulation waveform strongly influences temporal coding while having relatively little effect on the spatial distribution of neural activation. These results provide a physiological basis for reexamining analog stimulation as an alternative strategy for cochlear implant sound coding.

neuroscience↗

bioRxiv2026

An enzymatic metabolic sensing axis in taste cells detects glucose-yielding carbohydrates

Glucose is a potent reinforcer of intake, yet most foods contain complex saccharides that do not yield free glucose until after digestion. How the oral sensory system rapidly evaluates the potential metabolic value of food remains unclear. Here, we identify an oral enzymatic-metabolic sensing mechanism that enables detection of glucose-yielding carbohydrates independent of canonical sweet taste receptors. Using genetic, virogenetic, molecular, and behavioral approaches in mice, we show that glucokinase (GCK) in taste cells is necessary for the attraction to glucose-containing sugars. We further demonstrate that maltase glucoamylase (MGAM), a glycosidic enzyme expressed on and near taste cells, facilitates rapid oral sugar sensing. Disruption of either GCK or MGAM in the major taste fields selectively attenuates the attraction to maltose and a carbohydrate-rich mixed diet, establishing both as intermediaries in the initial transduction pathway for complex saccharides that ultimately give rise to nutrient reward. Molecular profiling of taste papillae further revealed that deficient sweet sensing was accompanied by a compensatory increase in lingual MGAM, highlighting an adaptive mechanism for maintaining oral carbohydrate sensitivity. Together, these findings reveal that the oral epithelium actively preprocesses and metabolically evaluates dietary carbohydrates, providing a mechanism for rapid estimation of energetic value prior to ingestion. Significance StatementCarbohydrates strongly motivate eating, yet most are consumed in complex forms that do not immediately release glucose. We show that the oral epithelium contains an adaptive enzymatic-metabolic sensing system that enables rapid evaluation of glucose-yielding carbohydrates before digestion. Two enzymes, maltase glucoamylase and glucokinase, act locally in taste fields to preprocess and metabolically assess complex sugars, biasing ingestive behavior toward energetically favorable foods. This mechanism operates independently of canonical sweet taste receptors and is dynamically regulated by dietary experience and receptor sensitivity. These findings reveal that the mouth actively estimates the energetic value of food prior to ingestion, reshaping our understanding of how nutrient sensing guides dietary choice.

neuroscience↗

bioRxiv2025

mRNABench: A curated benchmark for mature mRNA property and function prediction

Messenger RNA (mRNA) is central in gene expression, and its half-life, localization, and translation efficiency drive phenotypic diversity in eukaryotic cells. While supervised learning has widely been used to study the mRNA regulatory code, self-supervised foundation models support a wider range of transfer learning tasks. However, the dearth and homogeneity of standardized benchmarks limit efforts to pinpoint the strengths of various models. Here, we present O_SCPLOWMC_SCPLOWRNABO_SCPLOWENCHC_SCPLOW, a comprehensive benchmarking suite for mature mRNA biology that evaluates the representational quality of mature mRNA embeddings from self-supervised nucleotide foundation models. We curate ten datasets and 59 prediction tasks that broadly capture salient properties of mature mRNA, and assess the performance of 18 families of nucleotide foundation models for a total of 135K experiments. Using these experiments, we study parameter scaling, compositional generalization from learned biological features, and correlations between sequence compressibility and performance. We identify synergies between two self-supervised learning objectives, and pre-train a new Mamba-based model that achieves state-of-the-art performance using 700x fewer parameters. O_SCPLOWMC_SCPLOWRNABO_SCPLOWENCHC_SCPLOW can be found at: https://github.com/morrislab/mRNABench.

genomics↗

bioRxiv2025

Sequence based prediction of cell type specific microRNA binding and mRNA degradation for therapeutic discovery

MicroRNAs and RNA binding proteins are crucial elements of post-transcriptional gene regulation, which governs the fate of mRNA molecules in the cell. However, the landscape of these regulatory interactions, particularly across different mammalian cell types, remains underexplored. We describe REPRESS, a deep learning model that predicts cell-type-specific microRNA binding and mRNA degradation directly from RNA sequence. REPRESS was trained on AGO2-CLIP, miR-eCLIP and Degradome-Seq data profiling millions of microRNA binding and mRNA degradation sites across multiple cell types in human and mouse. It reveals biology that other state-of-the-art methods did not, such as identifying repressive non-canonical miRNA target sites and decoding the regulatory effects of sequence context and miRNA binding site multiplicity. REPRESS outperforms other advanced methods and neural architectures on a comprehensive suite of seven orthogonal tasks, including identifying genetic variants that affect microRNA binding, predicting out-of-distribution data from massively parallel reporter assays, and predicting canonical and non-canonical miRNA mediated repression. To demonstrate the general utility of REPRESS, we show that it provides insights into novel biology and the design of RNA therapeutics. Code is available at : https://github.com/deepgenomics/repress

genomics↗

bioRxiv2023

Neural network emulation of the human ventricular cardiomyocyte action potential: a tool for more efficient computation in pharmacological studies

AbstractComputer models of the human ventricular cardiomyocyte action potential (AP) have reached a level of detail and maturity that has led to an increasing number of applications in the pharmaceutical sector. However, interfacing the models with experimental data can become a significant computational burden. To mitigate the computational burden, the present study introduces a neural network (NN) that emulates the AP for given maximum conductances of selected ion channels, pumps, and exchangers. Its applicability in pharmacological studies was tested on synthetic and experimental data. The NN emulator potentially enables massive speed-ups compared to regular simulations and the forward problem (find drugged AP for pharmacological parameters defined as scaling factors of control maximum conductances) on synthetic data could be solved with average root-mean-square errors (RMSE) of 0.47 mV in normal APs and of 14.5 mV in abnormal APs exhibiting early afterdepolarizations (72.5% of the emulated APs were alining with the abnormality, and the substantial majority of the remaining APs demonstrated pronounced proximity). This demonstrates not only very fast and mostly very accurate AP emulations but also the capability of accounting for discontinuities, a major advantage over existing emulation strategies. Furthermore, the inverse problem (find pharmacological parameters for control and drugged APs through optimization) on synthetic data could be solved with high accuracy shown by a maximum RMSE of 0.21 in the estimated pharmacological parameters. However, notable mismatches were observed between pharmacological parameters estimated from experimental data and distributions obtained from the Comprehensive in vitro Proarrhythmia Assay initiative. This reveals larger inaccuracies which can be attributed particularly to the fact that small tissue preparations were studied while the emulator was trained on single cardiomyocyte data. Overall, our study highlights the potential of NN emulators as powerful tool for an increased efficiency in future quantitative systems pharmacology studies.

cell biology↗

bioRxiv2023

Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and Barretts esophagus (BE) is a strong risk factor along with smoking. Smoking is well-known to induce microbial dysbiosis and we asked if BE and esophageal microbiomes had shared microbial alterations that could provide novel biomarkers. We extracted DNA from BE tissues (n=5) and tumors of 158 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNAseq (n = 173) and WGS (n = 139) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alternations that allow disease progression in esophageal cancer.

cancer biology↗

bioRxiv2023

The highly conserved stem-loop II motif is dispensable for SARS-CoV-2

The stem-loop II motif (s2m) is a RNA structural element that is found in the 3 untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also compared the secondary structure of the 3 UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2. IMPORTANCERNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contain functional structures to support virus replication, translation and evasion of the host antiviral immune response. The 3 untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is a RNA structural element that is found in many RNA viruses. This motif was discovered over twenty-five years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that the s2m is dispensable for SARS-CoV-2.

microbiology↗

bioRxiv2022

Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform

We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow optical end-point detection without reversible terminators. This platform enables sequencing billions of reads with longer read length ([~]300bp) and fast runs times (<20hrs) with high base accuracy (Q30 > 85%), at a low cost of $1/Gb. We establish system performance by whole-genome sequencing of the Genome-In-A-Bottle reference samples HG001-7, demonstrating high accuracy for SNPs (99.6%) and Indels in homopolymers up to length 10 (96.4%) across the vast majority (>98%) of the defined high-confidence regions of these samples. We demonstrate scalability of the whole-genome sequencing workflow by sequencing an additional 224 selected samples from the 1000 Genomes project achieving high concordance with reference data.

genomics↗

bioRxiv2022

The highly conserved stem-loop II motif is important for the lifecycle of astroviruses but dispensable for SARS-CoV-2

The stem-loop II motif (s2m) is an RNA element present in viruses from divergent viral families, including astroviruses and coronaviruses, but its functional significance is unknown. We created deletions or substitutions of the s2m in astrovirus VA1 (VA1), classic human astrovirus 1 (HAstV1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For VA1, recombinant virus could not be rescued upon partial deletion of the s2m or substitutions of G-C base pairs. Compensatory substitutions that restored the G-C base-pair enabled recovery of VA1. For HAstV1, a partial deletion of the s2m resulted in decreased viral titers compared to wild-type virus, and reduced activity in a replicon system. In contrast, deletion or mutation of the SARS-CoV-2 s2m had no effect on the ability to rescue the virus, growth in vitro, or growth in Syrian hamsters. Our study demonstrates the importance of the s2m is virus-dependent.

microbiology↗

bioRxiv2022

Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains

Omicron variant strains encode large numbers of changes in the spike protein compared to historical SARS-CoV-2 isolates. Although in vitro studies have suggested that several monoclonal antibody therapies lose neutralizing activity against Omicron variants1-4, the effects in vivo remain largely unknown. Here, we report on the protective efficacy against three SARS-CoV-2 Omicron lineage strains (BA.1, BA.1.1, and BA.2) of two monoclonal antibody therapeutics (S309 [Vir Biotechnology] monotherapy and AZD7442 [AstraZeneca] combination), which correspond to ones used to treat or prevent SARS-CoV-2 infections in humans. Despite losses in neutralization potency in cell culture, S309 or AZD7442 treatments reduced BA.1, BA.1.1, and BA.2 lung infection in susceptible mice that express human ACE2 (K18-hACE2). Correlation analyses between in vitro neutralizing activity and reductions in viral burden in K18-hACE2 or human Fc{gamma} R transgenic mice suggest that S309 and AZD7442 have different mechanisms of protection against Omicron variants, with S309 utilizing Fc effector function interactions and AZD7442 acting principally by direct neutralization. Our data in mice demonstrate the resilience of S309 and AZD7442 mAbs against emerging SARS-CoV-2 variant strains and provide insight into the relationship between loss of antibody neutralization potency and retained protection in vivo.

microbiology↗

bioRxiv2021

NFE2L1-mediated proteasome function protects from ferroptosis

ObjectiveFerroptosis continues to emerge as a novel modality of cell death with important therapeutic implications for a variety of diseases, most notably cancer and degenerative diseases. While susceptibility, initiation, and execution of ferroptosis have been linked to reprogramming of cellular lipid metabolism, imbalances in iron-redox homeostasis, and aberrant mitochondrial respiration, the detailed mechanisms of ferroptosis are still insufficiently well understood. Methods and ResultsHere we show that diminished proteasome function is a new mechanistic feature of ferroptosis. The transcription factor nuclear factor erythroid-2, like-1 (NFE2L1) protects from ferroptosis by sustaining proteasomal activity. In cellular systems, loss of NFE2L1 reduced cellular viability after the induction of both chemically and genetically induced ferroptosis, which was linked to the regulation of proteasomal activity under these conditions. Importantly, this was reproduced in a Sedaghatian-type Spondylometaphyseal Dysplasia (SSMD) patient-derived cell line carrying mutated glutathione peroxidase-4 (GPX4), a critical regulator of ferroptosis. Also, reduced proteasomal activity was associated with ferroptosis in Gpx4-deficient mice. In a mouse model for genetic Nfe2l1 deficiency, we observed brown adipose tissue (BAT) involution, hyperubiquitination of ferroptosis regulators, including the GPX4 pathway, and other hallmarks of ferroptosis. ConclusionOur data highlight the relevance of the NFE2L1-proteasome pathway in ferroptosis. Manipulation of NFE2L1 activity might enhance ferroptosis-inducing cancer therapies as well as protect from aberrant ferroptosis in neurodegeneration, general metabolism, and beyond. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY HighlightsO_LIProteasome function is diminished during ferroptosis C_LIO_LINFE2L1-mediated proteasomal activity protects from ferroptosis C_LIO_LIThe ubiquitination of the GPX4-glutathione pathway is implicated in Nfe2l1 deficiency C_LIO_LINFE2L1 deficiency in brown fat is associated with hallmarks of ferroptosis C_LI

biochemistry↗

bioRxiv2021

BugSeq 16S: NanoCLUST with Improved Consensus Sequence Classification

NanoCLUST has enabled species-level taxonomic classification from noisy nanopore 16S sequencing data for BugSeqs users and the broader nanopore sequencing community. We noticed a high misclassification rate of NanoCLUST-derived consensus 16S sequences due to its use of BLAST top hit taxonomy assignment. We replaced the consensus sequence classifier of NanoCLUST with QIIME2s VSEARCH-based classifier to enable greater accuracy. We use mock microbial community and clinical 16S sequencing data to show that this replacement results in significantly improved nanopore 16S accuracy (over 5% recall and 19% precision), and make this new tool (BugSeq 16S) freely available for academic use at BugSeq.com/free.

bioinformatics↗

bioRxiv2019

Phytoene Synthase 2 Can Compensate for the Absence of Psy1 in Pepper Fruit (Capsicum annuum)

Phytoene synthase 1 (PSY1) and Capsanthin-capsorubin synthase (CCS) are two major genes responsible for fruit color variation in pepper (Capsicum spp.), although fruit colors cannot be explained by variations in these two genes alone. Furthermore, the role of PSY2 in fruit color development in pepper is unknown. Here, we used a systemic approach to discover the genetic factors responsible for the yellow fruit color of C. annuum MicroPep Yellow (MY) and to reveal the role of PSY2 in fruit color. We detected a complete deletion of PSY1 and a retrotransposon insertion in CCS in MY. Despite the loss of PSY1 and CCS function, the MY and mutant F2 plants from a cross between MY and the MicroPep Red (MR) accumulated basal levels of carotenoids, indicating that other PSY genes may complement the loss of PSY1. A qRT-PCR analysis demonstrated that PSY2 is constitutively expressed in both MR and MY fruits, and a color complementation assay using Escherichia coli revealed that PSY2 is capable of biosynthesizing a carotenoid. Virus-induced gene silencing of PSY2 in MY resulted in white fruits. These findings suggest that PSY2 can compensate for the absence of PSY1 in fruit, resulting in the yellow color of MY fruits.\n\nHighlightWe reveal the novel function of PSY2 in the development of yellow pepper fruit coloration using a psy1 knockout mutant. This gene function was not previously identified in solanaceous crops.

plant biology↗