Biology subjects

Le, T. N.

Publications and source records attributed to Le, T. N..

7 recordsLinked to original sources

bioRxiv2024

New components of the community based DNA-repair mechanism in Sulfolobales

After exposure to UV light, Sulfolobus acidocaldarius cells aggregate in a species-specific manner to exchange DNA and repair double-strand breaks via homologous recombination. The formation of cell-cell interactions is mediated by Ups pili. DNA exchange subsequently occurs through the Ced system, which imports DNA. To identify novel players in these processes, we investigated several genes upregulated after UV exposure by creating in-frame deletion mutants and performing cell aggregation and DNA exchange assays. This led to the identification of two novel components involved in the Ups and Ced systems: UpsC, a minor pilin of the Ups pili, and CedD, a VirD4-like ATPase essential for DNA import. Altogether, these findings provide new insights into the fascinating DNA damage response of Sulfolobales.

microbiology↗

bioRxiv2024

Molecular Phylogeny and Cryptic Morphology: A Combined Approach to Taxonomic Novelties in Polycarpaea (Caryophyllaceae) from Vietnam

Three new species of Polycarpaea from Vietnam, P. vanana, P. chungana, P. duongana are described and illustrated based on evidence of molecular sequence data from two markers (ITS1-5.8S-ITS2 and rps16) and combined morphological characteristics. Polycarpaea vanana is closely related to Polycarpaea gaudichaudi, P. arenaria, P. duongana but differs by its stem glabrous, leaf ovate to elliptic, glabrous, ovary oblong ovoid, base obtuse, apex attenuate, capsule oblong void, 3.8 mm long. P. duongana differs from the three species mentioned above by its stem being densely villous, leaf spathulate, ciliate, ovary ovoid, base acute, apex obtuse, capsule ovoid, 1.2 mm long. Polycarpaea chungana is most similar to P. lignosa but differs in having leaf oblong or linear, sparse ciliate, sepal and petal apex deeply concaved or slightly bifid, ovary ovoid, ovoid, 0.8-1.0 mm long. Furthermore, the achievements of analysis using molecular data on the systematic positions of 7 other species are results that have not been in previous molecular analyses.

plant biology↗

bioRxiv2023

Consecutive treatments of methamphetamine promote the 4 development of cardiac pathological symptoms in zebrafish

Chronic methamphetamine use, a widespread drug epidemic, has been associated with cardiac morphological and electrical remodeling, leading to the development of numerous cardiovascular diseases. While methamphetamine has been documented to induce arrhythmia, most results originate from clinical trials from users who experienced different durations of methamphetamine abuse, providing no documentation on the use of methamphetamine in standardized settings. Additionally, the underlying molecular mechanism on how methamphetamine affects the cardiovascular system remains elusive. A relationship was sought between cardiotoxicity and arrhythmia with associated methamphetamine abuse in zebrafish to identify and to understand the adverse cardiac symptoms associated with methamphetamine. Zebrafish were first treated with methamphetamine 3 times a week over a 2-week duration. Immediately after treatment, zebrafish underwent electrocardiogram (ECG) measurement using an in-house developed acquisition system for electrophysiological analysis. Subsequent analyses of cAMP expression and Ca2+ regulation in zebrafish cardiomyocytes were conducted. cAMP is vital to development of myocardial fibrosis and arrhythmia, prominent symptoms in the development of cardiovascular diseases. Ca2+ dysregulation is also a factor in inducing arrhythmias. During the first week of treatment, zebrafish that were administered with methamphetamine displayed a decrease in heart rate, which persisted throughout the second week and remained significantly lower than the heart rate of untreated fish. Results also indicate an increased heart rate variability during the early stage of treatment followed by a decrease in the late stage for methamphetamine-treated fish over the duration of the experiment, suggesting a biphasic response to methamphetamine exposure. Methamphetamine-treated fish also exhibited reduced QTc intervals throughout the experiment. Results from the cAMP and Ca2+ assays demonstrate that cAMP was upregulated and Ca2+ was dysregulated in response to methamphetamine treatment. Collagenic assays indicated significant fibrotic response to methamphetamine treatment. These results provide potential insight into the role of methamphetamine in the development of fibrosis and arrhythmia due to downstream effectors of cAMP.

physiology↗

bioRxiv2022

Neural responses to movie naturalistic stimuli are related to listening demand in cochlear implant users

There is a weak relationship between clinical and self-reported speech perception outcomes in cochlear implant (CI) listeners. Such poor correspondence may be due to differences in clinical and "real-world" listening environments and stimuli. Speech sounds in the real world are often accompanied by visual cues, background environmental noise and is generally in the context of a connected conversation. The aims of this study were to determine if brain responses to naturalistic speech could index speech perception and listening demand in CI users. Accordingly, we recorded high density EEG while CI users listened/watched a naturalistic stimulus (i.e., the television show, "The Office"). We used continuous EEG to quantify "speech neural tracking" (i.e., TRFs, temporal response functions) to the television show audio track and additionally 8-12 Hz (alpha) brain rhythms commonly related to listening effort. Background noise at three different signal-to-noise ratios (SNRs), +5, +10, and +15 dB were presented to vary the difficulty of following the television show mimicking a natural noisy environment. The task included an additional condition of audio-only (no video). After each condition, participants subjectively rated listening demand and the degree of words and conversations they felt they could understand. Fifteen CI users reported progressively higher degrees of listening demand and less words and conversation with increasing background noise. Listening demand and conversation understanding in the audio-only condition was comparable to that of the highest noise condition (+5 dB). The addition of the background noise reduced the degree of speech neural tracking. Mixed effect modeling showed that listening demand and conversation understanding were correlated to cortical speech tracking such that high demand and low conversation understanding lower associated with lower amplitude TRFs. In the high noise condition, greater listening demand was negatively correlated to parietal alpha power such that higher demand was related to lower alpha power. No significant correlations were observed between TRF/alpha and clinical speech perception scores. These results are similar to previous findings showing little relationship between speech perception and quality of life in CI users. However, the physiological responses to complex natural speech may anticipate aspects of quality-of-life measures such as self-perceived listening demand.

neuroscience↗

bioRxiv2021

Cardiotoxic effects of methamphetamine associated with electrophysiological and epigenetic aberrations in Zebrafish

Long-term methamphetamine (Meth) abuse damages functional and molecular changes in the brain that causes chronic and relapsing disease. In this study, we sought to investigate a relationship between cardiotoxicity and arrhythmia with associated Meth abuse in zebrafish to identify and to understand the adverse cardiac symptoms associated with Meth as well as to assess the applicability of zebrafish as an appropriate model for cardiac-related drug screening studies. Over a two-week duration, zebrafish were first treated with various concentrations of Meth, ranging from 0 to 50 M. Immediately after treatment, zebrafish underwent electrocardiogram (ECG) measurement for electrophysiological analysis. Results show that a higher incidence of increased heart rate over the duration of the experiment, corroborating with results from previous human case studies involving Meth users. However, abnormalities commonly cited in those same case studies, such as prolongation of QTc, were not significantly presented in obtained ECG recordings. We have also conducted genetic, epigenetic, and histochemical analysis in an attempt to understand the cardiotoxic effects of Meth on zebrafish cardiac function. These results suggested myocardial damage and decrease in gene expression associated with normal physiological function. Finally, this paper provides insights into potential reasons for the apparent discrepancies in our data with prior research as well as an outlook of zebrafish cardiotoxic drug screening studies.

physiology↗

bioRxiv2021

Fetal Electrocardiogram Extraction from the Mother's Abdominal Signal Using the Ensemble Kalman Filter

Fetal electrocardiogram (fECG) assessment is essential throughout pregnancy to monitor the wellbeing and development of the fetus, and to possibly diagnose potential congenital heart defects. Due to the high noise incorporated in the abdominal ECG (aECG) signals, the extraction of fECG has been challenging. And it is even a lot more difficult for fECG extraction if only one channel of aECG is provided, i.e. in a compact patch device. In this paper, we propose a novel algorithm based on the Ensemble Kalman Filter (EnKF) for non-invasive fECG extraction from a single-channel aECG signal. To assess the performance of the proposed algorithm, we used our own clinical data, obtained from a pilot study with 10 subjects each of 20 min recording, and data from the PhysioNet 2013 Challenge bank with labeled QRS complex annotations. The proposed methodology shows the average positive predictive value (PPV) of 97.59%, sensitivity (SE) of 96.91%, and F1-score of 97.25% from the PhysioNet 2013 Challenge bank. Our results also indicate that the proposed algorithm is reliable and effective, and it outperforms the recently proposed Extended Kalman Filter (EKF) based algorithm.

bioengineering↗

bioRxiv2020

CREB-binding protein gene, HAC701, negatively regulates WRKY45-dependent immunity in rice

CREB-binding protein (CBP) is a known transcriptional coactivator and an acetyltransferase that functions in several cellular processes by regulating gene expression. However, how it functions in plant immunity remains unexplored. By characterizing hac701, we demonstrate that HAC701 negatively regulates the immune responses in rice. hac701 shows enhanced disease resistance against a bacterial pathogen, Pseudomonas syringae pv. oryzae (Pso), which causes bacterial halo blight of rice. Our transcriptomic analysis revealed that rice WRKY45, one of the main regulators of rice immunity, is upregulated in hac701 and possibly conferring the resistance phenotype against Pso. The morphological phenotypes of hac701 single mutants were highly similar to WRKY45 overexpression transgenic lines reported in previous studies. In addition, we also compared the list of genes in these studies when WRKY45 is overexpressed and chemically induced transiently with the differentially expressed genes (DEGs) in hac701, and found that they largely overlap. When we investigated for cis-elements found 1kb upstream of WRKY45 gene and WRKY45-dependent DEGs, we found that WRKY45 promoter contains the CRE motif, a possible target of HAC701-mediated regulation. Genome-wide H3K9 acetylation profiling showed depletion of acetylation at large set of genes in hac701. However, consistent with the upregulation of WRKY45 gene expression, our ChIP-sequencing analysis demonstrated that regions of WRKY45 promoter are enriched in H3K9 acetylation in hac701 compared to the segregated wild type control in the mock condition. WRKY45 promoter might be on the receiving end for possible genome-wide compensatory effects when a global regulator like HAC701 is mutated. Finally, we show that HAC701 may have roles in systemic immune signaling. We therefore propose that wild type HAC701 negatively regulates WRKY45 gene expression, thereby suppressing immune responses. SIGNIFICANCEHAC701 is a member of CREB-binding protein (CBP) family that acts as transcriptional coactivator and acetyltransferase. However, little is known how it regulates innate immunity in plants. Herein we reported that rice HAC701 suppresses WRKY45-dependent defense pathway. Our study showed that HAC701 seemingly interacts genetically with WRKY45 in rice to modulate immune responses against pathogens.

plant biology↗