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Biology subjects

Nguyen, D.

Publications and source records attributed to Nguyen, D..

At least 19 recordsLinked to original sources

Opioid addiction vs. sugar addiction: Mesocorticolimbic stimulation controls motivation for remifentanil or alternative reward

Addiction is characterized by intense incentive motivation that becomes narrowly focused on particular targets. Laboratory studies have modeled intensification, directional targeting, and narrowing of the focus of incentive motivation using paired optogenetic stimulation of central amygdala CeA circuitry, which can create addictive-like motivation focused on either cocaine or on sucrose, as directed by experimenters. However, opioid drugs have been suggested to be different from cocaine in both reward and addictive effects, to be less dependent on mesolimbic incentive salience circuitry, and so may be potentially exempt from such control. To test if opoioid motivation is subject to similar control, CeA ChR2 rats were allowed to freely choose between intravenous remifentanil (2 ug/kg) or sucrose. One group had CeA stimulation selectively paired with earning sucrose, while the other group had stimulation paired with remifentanil. The sucrose-paired CeA ChR2 rats came to nearly exclusively pursue sucrose, ignoring remifentanil. By contrast, remifentanil-paired CeA ChR2 rats specifically pursued remifentanil, ignoring sucrose (control eYFP rats had no overall preference). To confirm whether CeA ChR2 pairing also intensified incentive motivation for remifentanil, as well as controlling its target, a separate CeA ChR2 group chose between two remifentanil options: one paired with CeA Stimulation, and the other unpaired. CeA ChR2 stimulation both focused pursuit specifically on laser-paired remifentanil, and escalated breakpoint for laser-paired remifentanil in a progressive ratio test of motivation intensity. Despite this ability to control motivation for opioid or sucrose, CeA ChR2 laser on its own had only low to moderate incentive value. For example, some CeA ChR2 rats above completely failed to self-stimulate CeA laser by itself. It appears that amygdala-related recruitment of mesocorticolimbic circuitry can transform the incentive salience of opioid drugs, similar to that for cocaine or sucrose, and gate the induction of intense but narrowly focused wanting in an addictive-like fashion.

neuroscience↗

Exploring the antibiotic-producing capabilities of Canadian High Arctic bacteria

Microbial communities in harsh environments such as the Canadian high Arctic, remain a relatively unexplored source of antimicrobial natural products. In this study, we developed a pipeline for screening and evaluating bacterial isolates cultured from 23 Canadian high Arctic soil, sediment, and active-layer permafrost samples to discover antibacterial compounds. The pipeline incorporated an undergraduate studentsourcing program and produced created a collection of over 350 bacterial isolates with preliminary antibacterial activity. Following dereplication, whole genome sequencing and secondary screening by co-culture assays, five isolates were prioritized to test crude extracts for antibacterial activity. Among bioactive crude extracts from these isolates, the Pseudomonas isolate with the most potent activity against S. aureus was analyzed. Using liquid chromatography bioactivity guided fractionation, we identified a potential bioactive compound known as koreenceine A, a compound previously only isolated from a Pseudomonas from temperate soil and involved in gene expression of other their microbial community. Here we expanded the known antibiotic activity of koreenceine A and confirmed that a {triangleup}kecBCD genetic knockout of the putative biosynthetic gene cluster significantly abrogated the antibacterial activity.

microbiology↗

Inferotemporal cortex stimulation is perceived before its onset

Neural response latency measures when stimulus-evoked activity becomes detectable, but it does not reveal when the brain assigns the causal contribution of that activity to events in the external world. We define this temporal adjustment as projected delay and measure it in the macaque inferotemporal cortex using optogenetic stimulation and behavior. Two rhesus macaques performed a cortical perturbation detection task in which a visual masker appeared at different times relative to stimulation. Detection was selectively impaired when the masker began 200 ms before stimulation. We then tested this timing using Perceptography, a method that optimizes image perturbations to mimic stimulation-evoked visual events. Image perturbations presented 200 ms before stimulation elicited higher false-alarm rates than perturbations presented at stimulation onset. Here, we show that stimulation-evoked visual events in inferotemporal cortex depend preferentially on visual information originating approximately 200 ms before the cortical perturbation. This projected delay exceeds typical inferotemporal response latencies and suggests temporally extended readout mechanisms relevant to causal models of visual perception and the timing of cortical visual prostheses.

neuroscience↗

RiboFlow v2: a configurable ribosome profiling pipeline reveals measurements sensitive to read-mapping methodology

Ribosome profiling experiments capture a snapshot of translation by sequencing ribosome-protected fragments (RPFs). Alignment to a well-curated transcriptome captures most RPF signal, but can miss ribosome activity when expressed exons are absent from the reference. Genome alignment of RPFs expands the detectable sequence space, but can expose ambiguity between homologous loci. Existing workflows often couple reference choice with the handling of ambiguously mapped reads, making it difficult to isolate the effects of either decision on downstream analyses. Here, we developed RiboFlow v2 by adding genome alignment and configurable handling of multimapping reads to the existing transcriptome workflow. Using 24 human ribosome profiling libraries and their matched RNA-seq data, we found that nucleotide-level coverage at matched coding-sequence positions and translation efficiency (TE) were broadly concordant between alignment strategies under stringent alignment filters. Even under these conditions, individual genes showed substantial differences in coverage and TE estimates. These differences included coverage in alternative exons absent from selected transcripts and ambiguous alignments between protein-coding genes and processed pseudogenes. Clustering genes by read-assignment patterns identified groups associated with pseudogene prevalence and highlighted shared exonic sequence among reference transcripts as a source of alignment discrepancies. RiboFlow v2 extends the analysis beyond selected reference transcripts and enables identification of genes whose ribosome coverage and abundance estimates depend on reference composition and how ambiguously mapped reads are handled.

bioinformatics↗

iPSC-Derived Myotubes from ME/CFS Patients Reveal Signature Genes, Isoforms and Pathways with Drug Repurposing Potential

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex multisystem disorder. Its hallmark feature, post-exertional malaise (PEM), is a delayed and prolonged worsening of symptoms following even minor exertion. As PEM commonly includes muscle pain, weakness, exercise intolerance and impaired recovery, skeletal muscle dysfunction may contribute to its pathophysiology, but the underlying molecular processes remain poorly understood. We generated induced pluripotent stem cell-derived skeletal muscle myotubes from individuals with ME/CFS (n = 6) and healthy controls (n = 7) to investigate disease-associated transcriptomic alterations and identify potential therapeutic candidates. Myogenic progenitor cells from both groups differentiated into elongated, multinucleated myotubes expressing titin and myosin heavy chain, while qPCR profiling of myogenic differentiation markers further supported successful differentiation. Gene-level analysis identified three differentially expressed genes at an FDR-adjusted p < 0.05: ERVH48-1, CDX4 and SLC2A14. Isoform-switching analysis identified 16 genes with significant differential isoform usage, including CACNA1H, MIEF2, SMAD2 and CHD4. Gene set enrichment analysis identified broader pathway-level alterations involving RNA processing, protein synthesis, proteostasis, mitochondrial quality control, metabolism and muscle-related processes. Library of Integrated Network-based Cellular Signatures Phase 2 (LINCS2) analysis further prioritised 14 compounds associated with mitochondrial metabolism, glucose and lipid regulation, PPAR signalling, calcium and excitatory signalling, neuroimmune activity and cellular stress responses. Overall, ME/CFS iPSC-derived myotubes showed modest gene-level differences alongside broader isoform- and pathway-level alterations, supporting their use for investigating skeletal muscle biology and prioritising candidates for functional validation.

cell biology↗

Adenosine refines the balance of spermatogonial proliferation and differentiation

The balance between spermatogonial proliferation and differentiation is essential for sustaining male fertility, yet the contribution of cellular metabolism remains poorly understood. Here, we showed that adenosine levels increased significantly during spermatogonial differentiation and promoted the formation of differentiating spermatogonia. Using a conditional knockout mouse model in which Ahcy, a gene encoding an enzyme in adenosine synthesis, is deleted from spermatogonia, we found that disruption of adenosine generation blocked spermatogonial differentiation, resulting in a transient delay in spermatogenesis. We further demonstrated that adenosine exerted its effects partially through ADORA2A- and ADORA2B-mediated signaling. Downregulating these receptor activities by specific inhibitors in spermatogonial culture or by genetic ablation in mice led to increased spermatogonial proliferation. Taken together, our study identified adenosine as a metabolic signal in refining the balance between spermatogonial proliferation and differentiation, linking cellular metabolism to critical developmental timing and stem cell fate decisions.

developmental biology↗

Striatal habit system drives behavioral rigidity in PTSD

Core symptoms of posttraumatic stress disorder (PTSD) like safety seeking and avoidance have long been described as habitual. Although widespread theoretical accounts posit a relationship between these behaviors and striatal-mediated habits, or rigid stimulus-response (S-R) associations, this idea has yet to be tested. Here, we implement a new task design to investigate how S-R associations are acquired, how flexibly they can be remapped, and how sensitive they are to changes in outcome value for individuals with PTSD as compared to individuals who experienced trauma without developing PTSD (trauma-exposed controls; TC). We find that individuals with PTSD, compared to TC, exhibit several hallmarks of habitual behavior, including more rigid habit-like perseveration following response remapping, and, with more severe symptoms, continued perseveration following outcome devaluation. We also observe that the PTSD group acquired these S-R associations more slowly. Using functional magnetic resonance imaging, we find significant putamen engagement when learning S-R associations that was especially pronounced in PTSD and predicted later perseveration. Finally, computational models indicate that the PTSD group leveraged gradual trial-by-trial updating to learn and later update associations, whereas the TC group leaned more on a stable, consistent choice strategy, both of which explained later behavioral rigidity. In addition to distinguishing individuals with PTSD, these habit-related processes were also more pronounced for individuals with more severe symptoms. Together, these results provide the first empirical evidence for the role of habits in PTSD.

neuroscience↗

scLANTERN: High-Throughput Retrospective Lineage Tracing via Full-Length Single-Cell Transcriptomics and Expressed Repeat Variation

Understanding the lineage relationships among individual cells is a key pursuit of modern biology, essential for unraveling the complexities of developmental processes and the adaptive mechanisms of disease progression, particularly in oncology. Retrospective single-cell clonal tracing has emerged as a transformative approach, offering a unique window into the evolutionary trajectories of cancer within clinical samples. While short-read single-cell transcriptomics (scRNA-seq) has revolutionized our ability to map cell states across human tumor atlases, it remains fundamentally limited in its capacity to link these states with high-resolution genomic alterations and the evolutionary trajectories inferred from these natural variants. Integrating somatic mutation discovery with transcriptomic profiles at single-cell resolution often requires separate, costly, and low-throughput genomic assays. Furthermore, existing methods frequently rely on exogenous genetic labeling or are restricted to short-read sequencing, which typically fails to resolve complex genomic rearrangements, large indels, or variations within highly repetitive regions,such as short tandem repeats (STRs), that could serve as potent endogenous clonal markers.

evolutionary biology↗

Paralemmin 2 is a shared, alternatively-spliced regulator of axon initial segments and paranodal junctions in oligodendrocytes

Nervous system function depends on highly specialized axonal membrane domains. For example, axon initial segments (AIS), nodes of Ranvier, and paranodal junctions are essential for action potential initia-tion and saltatory conduction. These domains use shared molecular machinery converging on the master scaffolding protein AnkyrinG (AnkG). Using endogenous AnkG-TurboID proximity proteomics, we identify Paralemmin 2 (Palm2), a previously uncharacterized CNS protein, as a shared component of the AIS and nodes of Ranvier in neurons, and paranodes in oligodendrocytes. Palm2 localizes transiently to the AIS and nodes during development, but is found at paranodes throughout life, reflecting cell type-specific splicing of a lipid-modified domain both necessary and sufficient for AnkG interaction. Mice lacking oli-godendroglial Palm2 assemble normal paranodes during development, but aged mice lose paranode in-tegrity due to loss of paranodal AnkG and Neurofascin-155. Our findings identify Palm2 as a lipid raft-associated regulator of axonal and oligodendroglial membrane domains and reveal cell type-specific pro-tein variants as a recurring principle for specializing axonal and glial membrane architectures.

neuroscience↗

Protein design to broadly reprogram engineered T cell function

The efficacy of engineered T cell therapies in solid tumors remains limited by T cell dysfunction, driven by complex processes that cannot be easily manipulated via genetic knockouts or overexpression of individual genes. Protein design can create new biological functions that can rewire these consequential cell fate decisions. Here, we introduce OUTLAST Regulators, designed proteins that reprogram critical T cell signaling pathways to enhance functional persistence. These proteins are capable of regulating diverse groups of proteins such as the NR4A family of pro-exhaustion transcription factors, E3 ligases Cbl-b and c-Cbl, and SOCS family proteins. Our designs markedly improve CAR-T and TCR-T performance in vitro and in vivo in stringent solid tumor preclinical models. OUTLAST Regulators are implemented as compact genetic modules compatible with standard viral vectors and cell therapy manufacturing processes, creating a powerful platform for programming new functions into enhanced cell and gene therapies.

synthetic biology↗

A lipid nanoparticle platform for high yield CRISPR-targeted homology directed repair enables fully non-viral CAR T cell generation

CRISPR-mediated homology directed repair (HDR) enables targeted CAR integration with improved fitness and therapeutic potential of CAR T cells. However, current methods for generating HDR-engineered CAR T cells rely on viral transduction or electroporation, approaches that limit global implementation and constrain patient access due to their cost, toxicity, and requirement for centralized manufacturing. Through a screen of ionizable lipids, we identified LNP systems that enable CRISPR-mediated gene knock-in (KI) in primary human T cells and are amenable to hand mixing by ethanol injection as a research tool or machine formulation for larger scale manufacturing. Modifying the linear dsDNA HDR template with truncated Cas9 target sequences (tCTS) enhanced HDR rates across multiple LNP systems. We optimized two LNP formulations capable of HDR-mediated KI of a large 4kB CD19 CAR-EGFR HDR template into the TRAC locus with rates of [&ge;]8% and >10x improved edited cell yields compared to electroporation. We demonstrate that LNP-generated CAR T cells exhibited similar growth kinetics, activation states, differentiation states, and killing capacity compared to electroporation-generated CAR T cells. Our LNP platform components are fully disclosed, commercially sourced, and enable efficient fully non-viral CRISPR-HDR cell engineering across diverse applications.

bioengineering↗

The Impact of Smoking Status on the Genomic Landscape of Lung Squamous Cell Carcinoma

PurposeComprehensive genomic profiling (CGP) has changed the treatment paradigm for non-small cell lung cancer (NSCLC) with the advent of molecularly targeted therapies for actionable genomic alterations (AGA). Despite this, the use of CGP is suboptimal, particularly in squamous cell lung cancer (sqNSCLC), which is more closely associated with smoking exposure and a lack of AGAs. We hypothesized that the prevalence of AGAs is inversely correlated with the chronicity and extent of smoking exposure in patients with sqNSCLC. Experimental DesignWe retrospectively evaluated all patients with liquid biopsy testing via Guardant 360CDX or Guardant360 in the context of any sqNSCLC diagnosis at the City of Hope Comprehensive Cancer Center between 10/2020 and 7/2023. The data was obtained on 2/23/24. Social and clinical histories were evaluated to assess the frequency of AGAs in patients with no or remote smoking history. ResultsOf the 56 patients in the initial evaluation, 24% (n=13) were non-smokers or remote smokers (greater than 20 years from cessation). Of these 13 patients, eight (61.5%) harbored AGA. Of these 8 patients, alterations observed included EGFR exon 19 deletion (50%, n=4), MET exon 14 skipping mutation (25%, n=2), EGFR G719S (13%, n=1), EGFR E114K (13%, n=1). Of those patients harboring AGAs that received NCCN-concordant matched targeted therapy, the objective response rate (ORR) with targeted agents was 50% and the clinical benefit rate (CBR) was 83.3%. ConclusionsThese data support the use of CGP in sqNSCLC particularly in patients with remote or no smoking exposure. Statement of translational relevanceThese data demonstrate high frequency of actionable genomic alterations (AGAs) in patients diagnosed with squamous cell lung cancer (sqNSCLC) with remote or no smoking history. Specifically, enrichment of EGFR and MET gene alterations were observed. These findings support the use of comprehensive molecular profiling in sqNSCLC. Furthermore, treatment outcomes demonstrate frequent objective responses and high clinical benefit rate supporting the use of targeted therapies in sqNSCLC harboring AGAs. This analysis provided rationale for further research of larger datasets investigating therapeutic approaches in sqNSCLC, which may have significant implications for consensus guideline recommendations and routine clinical practice.

cancer biology↗

Working memory demands modulate memory brain state engagement

The extent to which attention and memory processes rely on shared as opposed to distinct mechanisms is critical for understanding the role of both processes in cognition. As working memory sits at the intersection of external, perceptual input and long-term internal storage, it provides the ideal testbed for investigating overlaps between attention and memory. We hypothesize that memory brain states, whole-brain activity patterns that support long-term memory encoding and retrieval, map onto the external/internal axis of attention. Specifically, we hypothesize that external attention, focusing on sensory information, recruits the encoding state and internal attention, focusing on stored information, recruits the retrieval state. To test this hypothesis, we conducted a scalp electroencephalography study in which participants engaged in a working memory paradigm with and without maintenance demands. We used an independently validated cross-study multivariate pattern classifier to measure memory brain state engagement during change and target detection tasks. We find that the encoding state is recruited for stimulus presentation during both tasks, whereas the retrieval state is selectively recruited during the delay of the change detection task. Together, these results suggest that memory states map onto the external/internal axis of attention to support working memory, long-term memory, and cognition more broadly.

neuroscience↗

Beyond Exons: Linking Noncoding Heritability and Polygenicity across Complex Human Traits and Disorders

The genetic architecture of complex traits spans a continuum of polygenicity, yet it remains unclear how differences in polygenicity relate to the functional localization of SNP heritability across the genome. We use a MiXeR-based framework to partition heritability across exonic, intronic, and intergenic regions for 34 traits and introduce a likelihood-based annotation contribution score that quantifies annotation-specific impact on heritability. Exons explain a minority of heritability, and their contribution decreases with increasing polygenicity, from an average of 22% in less polygenic somatic diseases and biomarkers to 13% in highly polygenic psychiatric and cognitive phenotypes. Intergenic fractions show the opposite trend, whereas intronic fractions remain relatively stable. Analysis of a broader set of functional annotations reveals systematic differences along the polygenicity axis: highly polygenic traits show stronger contributions from comparative genomics and variant-effect scores, whereas less polygenic traits show stronger contributions in promoter, transcription, and chromatin annotations. Together, these results indicate that the functional partitioning of heritability systematically varies with polygenicity, pointing to a shift from gene-proximal regulatory architectures to architectures shaped by numerous dispersed regulatory effects as a key determinant of differences in polygenicity across traits.

genetics↗

Residual ellipticity in waveplate-compensated polarization-resolved SHG microscopy may arise from femtosecond laser spectral bandwidth

Polarization-resolved second harmonic generation microscopy provides structural information about non-centrosymmetric biological samples such as collagen. It involves illuminating the sample with a focused laser beam having a variable linear polarization angle and recording the second harmonic signal as a function of this angle. However, accurate linear polarization control is challenging due to ellipticity introduced by reflections from mirrors and dichroic mirrors in the optical path. Waveplate-based compensation has emerged as the standard approach to address these distortions, but its effectiveness for quantitative measurements remains incompletely characterized. Here, we attempt to fill this gap by implementing an established automated waveplate compensation method based on a rotating half-waveplate in combination with a compensating quarter-waveplate. This was done on a commercial Leica TCS SP8 MP multiphoton microscope, making various hardware improvements and carefully documenting important experimental details. Despite significant effort, we consistently observed substantial unwanted residual polarization ellipticity, with amplitudes up to 0.25, persisting under optimal waveplate configurations. Our simulation analysis provides evidence that this limitation may arise from wavelength-dependent dichroic mirror birefringence combined with the broad spectral bandwidth (10nm to 20nm full width at half maximum) of femtosecond laser pulses. While the approach investigated here can compensate a single wavelength, different spectral components within the pulse experience different phase retardations from wavelength-dependent optical elements, potentially resulting in residual ellipticity that cannot be eliminated. Our simulations qualitatively reproduced key features of the experimental observations. These findings have important implications for quantitative polarization-resolved second harmonic generation microscopy and suggest that alternative approaches, including specimen rotation or picosecond laser sources with narrower bandwidth, should be investigated for applications requiring precise polarization control. To facilitate community investigation of these effects, we provide open-source analysis code and simulation files.

bioengineering↗

Defective BRCA1-mediated DNA end resection drives tandem duplication formation and FANCM synthetic lethality

AbstractBRCA1-linked cancer genomes contain abundant genome-wide [~]10 kb Group 1 tandem duplications (TDs) that are drivers of tumorigenesis. Group 1 TD formation is recapitulated at a chromosomal Tus/Ter site-specific replication fork barrier in DNA end resection-defective mouse embryonic stem (mES) cells lacking Brca1 exon 11. To explore relationships between DNA end resection and Group 1 TD formation, we analyzed Brca1 coiled coil (CC) domain mutants--separation-of-function alleles that are impaired for homologous recombination but competent for DNA end resection. Notably, Brca1 CC mutants retain the ability to suppress Group 1 TDs in the Tus/Ter system and in a mouse model of Brca1-linked tumorigenesis. These data show that Brca1 CC domain mutant cancers follow a path of tumorigenesis distinct from that of other pathogenic Brca1 alleles. FANCM is a TD co-suppressor, the loss of which is synthetic lethal/sick in combination with Brca1 exon 11 mutation. In contrast, Fancm deletion is well-tolerated by Brca1 CC mutant mES cells. Thus, Group 1 TD formation and Fancm synthetic lethality are linked phenotypes related to defective BRCA1-mediated DNA end resection.

molecular biology↗

Discovery of Membrane Channel Modulators via DNA-Encoded Library Screening Using Native-Like Membrane Protein Nanoparticles

Developing novel drugs against membrane proteins is a major challenge in drug discovery due to the difficulty of stabilizing these targets for high-throughput screenings. Pannexin 1 (PANX1) is a membrane channel protein involved in various physiological and pathological processes, making it a promising target for drug discovery. However, efforts to develop PANX1-targeting therapeutics have been hindered by the inherent challenges of stabilizing the protein channel and conducting effective pharmacological screening. Here, we report a proof-of-concept workflow that integrates the Salipro lipid nanoparticle platform with DNA-Encoded Library screenings in a detergent-free format. In this case study, the Salipro DirectMX method was used to generate functional PANX1 nanoparticles for drug discovery and characterisation. Using a high-stringency selection strategy and computational approaches, we identified a specific set of candidate compounds with selective PANX1 enrichment. Surface Plasmon Resonance analysis confirmed the identification of hit compounds. Cryo-Electron Microscopy of the Salipro-PANX1-Compound complex provided structural insights into a potential compound binding site. Electrophysiological recordings in PANX1-expressing Xenopus laevis oocytes demonstrated dose-dependent inhibition of PANX1-mediated ion conductance by the compounds. These findings establish a robust workflow for ligand discovery against challenging membrane protein targets and provide novel chemical starting points for the development of PANX1 modulators.

biochemistry↗

A simple and efficient CTAB plate-based protocol for genomic DNA extraction from crop plants

Modern plant breeding and molecular genetics rely on genotyping large populations for applications such as genome editing and genomic selection. However, current DNA extraction methods often require expensive equipment or signif-icant manual labor, which limits their scalability. The objective of this study was to develop a scalable, cost-effective DNA extraction method. A bead-beating protocol was used to homogenize small amounts of leaf tissue from Arabidopsis, camelina, maize, sorghum, soybean, tobacco, and wheat, as well as developing soybean seeds. Samples were processed in 96-well plates using a standard CTAB (cetyltrimethylammonium bromide)-based extraction solution. DNA concentration was measured, and DNA quality was estimated using the A260/A280 and A260/A230 ratios and gel electrophoresis. The extracted DNA was then used for PCR assays to amplify targeted endogenous sequences, detect Cas9-edited sequences, and estimate gene copy numbers. This workflow enabled a single worker to process up to 960 samples per day. The total DNA yield was 2-3 {micro}g for leaf and 0.5-1 {micro}g for soybean seeds with good quality, which was sufficient for multiple PCR reactions. The DNA was successfully used for the intended PCR assays. The extracted DNA was suitable for reliable, downstream PCR-based genotyping. This method supports diverse analyses, including routine amplification, identification of genome edits, and copy number analysis.

plant biology↗