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Biomedical subjects

Liang Li

Publications and source records attributed to Liang Li.

At least 19 recordsLinked to original sources
PubMed2026

Discovery and validation of novel plasma protein biomarkers for severe tuberculosis patients.

OBJECTIVE: Severe tuberculosis (STB) imposes a substantial disease burden, yet reliable biomarkers for distinguishing STB from mild/moderate tuberculosis (MTB) remain scarce. This study aimed to identify and independently validate plasma protein biomarkers associated with tuberculosis severity. METHODS: In this multicenter prospective study, 298 adults with confirmed pulmonary tuberculosis were enrolled into screening (n = 128) and independent validation (n = 170) cohorts. Plasma samples were analysed using data-independent acquisition proteomics. Differentially expressed proteins were screened via Limma and four machine-learning algorithms, with candidate proteins measured by enzyme-linked immunosorbent assays. Receiver operating characteristic analysis assessed individual and combined diagnostic performance. RESULTS: STB patients were older and presented with lymphopenia, hypoalbuminemia, neutrophilia, and elevated lactate dehydrogenase. Among 166 differentially expressed proteins, HSPA5, HSP90B1, EEF1D, and SULT1A1 were selected for validation. In STB patients, HSPA5, HSP90B1, and EEF1D were upregulated, whereas SULT1A1 was downregulated. The four-protein panel achieved an AUC of 0.908 (95% CI 0.864-0.952), with 87.5% sensitivity and 83.8% specificity, modestly outperforming HSPA5 alone (AUC = 0.894). Functional enrichment implicated cholesterol metabolism, immune-inflammatory pathways, and endoplasmic reticulum stress. CONCLUSIONS: The four-protein panel effectively discriminated STB from MTB; however, its marginal improvement over HSPA5 alone suggests that an HSPA5-based assay may offer a simpler, more practical, and potentially cost-effective strategy for severity stratification.

Humans↗
PubMed2026

Single-cell transcriptomics reveals heterogeneous stress responses and Mg2+-mediated survival mechanisms in Lactobacillus delbrueckii subsp. bulgaricus during freeze-drying and storage.

Maintaining the viability of lactic acid bacteria during dehydration and subsequent storage remains a significant challenge. Here, we employed single-cell RNA sequencing to reveal the heterogeneous stress responses of Lactobacillus delbrueckii subsp. bulgaricus, identifying seven distinct transcriptional clusters across the liquid culture, freeze-drying, and storage phases. The dominant clusters in the freeze-drying and storage were not completely consistent, showing significant functional differentiation. Genomic stability may be important for survival during freeze-drying and storage, while intracellular energy homeostasis appears important for viability during storage. The magnesium transporter mgtB was highly expressed in clusters tolerant to freeze-drying and storage, suggesting a critical role for Mg2+ homeostasis. Further experimental validation confirmed that Mg2+ treatment significantly bolstered stress resistance, increasing immediate post-freeze-drying survival by over 2-fold (up to 92.90%) and post-storage survival by over 5-fold (up to 5.98%). Proteomic data indicated that Mg2+ supplementation correlated with the maintenance of several biological functions potentially relevant to bacterial survival during freeze-drying and storage, including DNA repair, translation, and central carbon metabolism. These findings provide a map of microbial stress resistance through population heterogeneity and offer a potential strategy that may be adapted for enhancing the stability of other industrial lactic acid bacteria products.

Freeze Drying↗
PubMed2025

PreDigs: A Database of Context-specific Cell Type Markers and Precise Cell Subtypes for Digestive Cell Annotation.

Research on cell type markers helps investigators explore the diverse cellular composition of gastrointestinal tumors, thereby enhancing our understanding of tumor heterogeneity and its impact on disease progression and treatment response. However, the integration of large-scale datasets and the standardization of cell type identification remain challenging. Here, we developed PreDigs, a user-friendly database of predicted signatures for the digestive system, which offers 124 curated single-cell RNA sequencing datasets, covering over 3.4 million cells, all available for download. After unsupervised clustering, we unified the identification and nomenclature of cell subtype labels, constructing a cell ontology tree with 142 cell types across 8 hierarchical levels. Meanwhile, we calculated three different context-specific cell type markers, including "Cell Markers", "Subtype Markers", and "TPN Markers", based on various application requirements within or across tissues. Through the integrated analysis of PreDigs data, we identified distinct cell subpopulations exclusive to tumors, one of which corresponds to tumor-specific endothelial cells. Additionally, PreDigs offers online cell annotation tools, allowing users to classify single cells with greater flexibility. PreDigs is accessible at https://www.biosino.org/predigs/.

Humans↗
PubMed2025

PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions.

Recent advancements in spatial transcriptomics (ST) have significantly enhanced biological research in various domains. However, the high cost for current ST data generation techniques restricts the large-scale application of ST. Consequently, maximization of the use of available resources to achieve robust statistical power for ST data is a pressing need. One fundamental question in ST analysis is detection of differentially expressed genes (DEGs) under different conditions using ST data. Such DEG analyses are performed frequently, but their power calculations are rarely discussed in the literature. To address this gap, we developed PoweREST, a power estimation tool designed to support the power calculation for DEG detection with 10X Genomics Visium data. PoweREST enables power estimation both before any ST experiments and after preliminary data are collected, making it suitable for a wide variety of power analyses in ST studies. We also provide a user-friendly, program-free web application that allows users to interactively calculate and visualize study power along with relevant parameters.

Gene Expression Profiling↗
PubMed2024

PoweREST: Statistical Power Estimation for Spatial Transcriptomics Experiments to Detect Differentially Expressed Genes Between Two Conditions.

Recent advancements in Spatial Transcriptomics (ST) have significantly enhanced biological research in various domains. However, the high cost of current ST data generation techniques restricts its application in large-scale population studies. Consequently, there is a pressing need to maximize the use of available resources to achieve robust statistical power. One fundamental question in ST analysis is to detect differentially expressed genes (DEGs) among different conditions using ST data. Such DEG analysis is often performed but the associated power calculation is rarely discussed in the literature. To address this gap, we introduce, PoweREST (https://github.com/lanshui98/PoweREST), a power estimation tool designed to support power calculation of DEG detection with 10X Genomics Visium data. PoweREST enables power estimation both before any ST experiments or after preliminary data are collected, making it suitable for a wide variety of power analyses in ST studies. We also provide a user-friendly, program-free web application (https://lanshui.shinyapps.io/PoweREST/), allowing users to interactively calculate and visualize the study power along with relevant the parameters.

Differentially expressed genes↗
PubMed2007

Mitogen-activated protein kinase-dependent activation of the Na+/H+ exchanger is mediated through phosphorylation of amino acids Ser770 and Ser771.

We investigated regulation of the type 1 isoform of the Na(+)/H(+) exchanger by phosphorylation. Four specific groups of serine and threonine residues in the regulatory carboxyl-terminal tail were mutated to alanine residues: group 1, S693A; group 2, T718A and S723A/S726A/S729A; group 3, S766A/S770A/S771A; and group 4, T779A and S785A. The proteins were expressed in Na(+)/H(+) exchanger-deficient cells, and the activity was characterized. All of the mutants had proper expression, localization, and normal basal activity relative to wild type NHE1. Sustained intracellular acidosis was used to activate NHE1 via an ERK-dependent pathway that could be blocked with the MEK inhibitor U0126. Immunoprecipitation of (32)P-labeled Na(+)/H(+) exchanger from intact cells showed that sustained intracellular acidosis increased Na(+)/H(+) exchanger phosphorylation in vivo. This was blocked by U0126. The Na(+)/H(+) exchanger activity of mutants 1 and 2 was stimulated similar to wild type Na(+)/H(+) exchanger. Mutant 4 showed a partially reduced level of activation. However, mutant 3 was not stimulated by sustained intracellular acidosis, and loss of stimulation of activity correlated to a loss of sustained acidosis-mediated phosphorylation in vivo. Mutation of the individual amino acids within mutant 3, Ser(766), Ser(770), and Ser(771), showed that Ser(770) and Ser(771) are responsible for mediating increases in NHE1 activity through sustained acidosis. Both intact Ser(770) and Ser(771) were required for sustained acidosis-mediated activation of NHE1. Our results suggest that amino acids Ser(770) and Ser(771) mediate ERK-dependent activation of the Na(+)/H(+) exchanger in vivo.

Acidosis↗
PubMed2007

Formation of fibril structures in polymerizable, rod-coil-oligomer-modified epoxy networks.

This paper describes the in situ preparation of fibrils in epoxy networks in which the fibril-like structures are cured polymerizable rod-coil oligomers. The epoxy-terminated alpha,omega-modified PEO oligomers, which are ABA rod-coil-rod oligomers with a poly(ethylene oxide) coil unit and two aromatic azomethine liquid-crystalline rod units, were synthesized and then further blended with an epoxy precursor. Uniform nanoscale columnar structures were observed in the neat rod-coil oligomers as well as in the crosslinked liquid-crystalline state. During the curing of the blends, the supramolecular nanoscale columnar structures of the rod-coil oligomers are transformed into polymeric fibrils where the epoxy functional end groups have co-reacted with epoxy precursors to form a crosslinked network.

Journal Article↗
PubMed2007

Proteome profile of cytosolic component of zebrafish liver generated by LC-ESI MS/MS combined with trypsin digestion and microwave-assisted acid hydrolysis.

The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the cytosolic component of a zebrafish liver tissue sample. Our methods involve cell-compartment fractionation of liver tissue samples, four levels of protein digestion, and off-line two-dimensional liquid chromatography (2-D LC) separations of resultant peptides. Proteins are identified using an electrospray ionization quadrupole time-of-flight tandem mass spectrometer (ESI-QTOF MS/MS), which provides high-resolution and high-accuracy mass measurement of peptide ions and their fragment ions. We demonstrate that greater proteome coverage can be achieved by combining the results obtained from four methods of protein digestion: three tryptic digests (one in buffer, one in methanol, and another in SDS), and a microwave-assisted acid hydrolysate of the protein extracts. Identified proteins--which included several groups of established protein biomarkers--were functionally classified. We discuss the functions and implications of these biomarkers within the context of zebrafish toxicology.

Animals↗
PubMed2007

HMDB: the Human Metabolome Database.

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca.

Databases, Factual↗
PubMed2006

Thermal properties of bi nanowire arrays with different orientations and diameters.

The thermal properties of single-crystalline Bi nanowire arrays with different orientations and diameters were studied by differential scanning calorimeter and in situ high-temperature X-ray diffraction. Bi nanowires were fabricated by a pulsed electrodeposition technique within the porous anodic alumina membrane. The relationships between the orientation and diameter of Bi nanowires and the corresponding thermal properties are deduced solely from experimental results. It is shown that the melting point decreases with decreasing nanowire diameter, and there is an anisotropic thermal expansion property of Bi nanowires with different orientations and diameters. The transition of the thermal expansion coefficient from positive at low temperature to negative at high temperature for Bi nanowire arrays was analyzed and discussed.

Journal Article↗
PubMed2006

Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins.

High-throughput screening and optimization experiments are critical to a number of fields, including chemistry and structural and molecular biology. The separation of these two steps may introduce false negatives and a time delay between initial screening and subsequent optimization. Although a hybrid method combining both steps may address these problems, miniaturization is required to minimize sample consumption. This article reports a "hybrid" droplet-based microfluidic approach that combines the steps of screening and optimization into one simple experiment and uses nanoliter-sized plugs to minimize sample consumption. Many distinct reagents were sequentially introduced as approximately 140-nl plugs into a microfluidic device and combined with a substrate and a diluting buffer. Tests were conducted in approximately 10-nl plugs containing different concentrations of a reagent. Methods were developed to form plugs of controlled concentrations, index concentrations, and incubate thousands of plugs inexpensively and without evaporation. To validate the hybrid method and demonstrate its applicability to challenging problems, crystallization of model membrane proteins and handling of solutions of detergents and viscous precipitants were demonstrated. By using 10 microl of protein solution, approximately 1,300 crystallization trials were set up within 20 min by one researcher. This method was compatible with growth, manipulation, and extraction of high-quality crystals of membrane proteins, demonstrated by obtaining high-resolution diffraction images and solving a crystal structure. This robust method requires inexpensive equipment and supplies, should be especially suitable for use in individual laboratories, and could find applications in a number of areas that require chemical, biochemical, and biological screening and optimization.

Crystallization↗
PubMed2006

Auditory evoked responses in the rat: transverse mastoid needle electrodes register before cochlear nucleus and do not reflect later inferior colliculus activity.

A previously described technique putatively differentiates short-latency auditory evoked potentials in peripheral and central neural pathways of the mouse and rat [Galbraith G, Waschek J, Armstrong B, Edmond J, Lopez I, Liu W, et al. Murine auditory brainstem evoked response: putative two-channel differentiation of peripheral and central neural pathways. J Neurosci Methods 2006;153:214-20]. This technique involves recording from orthogonally oriented subdermal needle electrode pairs, using fast sample rates (100k/s) to accurately measure differences in neural timing and waveform morphology. Electrodes oriented in a transverse plane (mastoid-to-mastoid) register an initial positive-going peak earlier than peaks recorded from electrodes oriented along the scalp midline (anterior and posterior to the interaural line). The absolute latency of the early mastoid component is consistent with an origin in the primary auditory nerve, while delayed midline latencies implicate activity in central neural pathways. We report here the results of recording simultaneously from transverse mastoid (M) needle electrodes and electrodes acutely implanted in cochlear nucleus (CN) and inferior colliculus (IC). The results show a highly consistent pattern in which the initial mastoid component leads CN by an average of 0.16 ms, suggesting an obligatory neural site of origin of the mastoid response that is distal to IC, namely the auditory nerve. Moreover, later IC components (beyond approximately 3.5 ms) are completely absent in mastoid recordings, indicating that the transverse mastoid recordings provide a relatively isolated measure of early auditory neural activity.

Acoustic Stimulation↗
PubMed2006

The influence of the perceptual or fear learning on rats' prepulse inhibition induced by changes in the correlation between two spatially separated noise sounds.

Perceptually grouping a sound source with its reflections and separating them from irrelevant background noise sounds need computation of sound correlations and are critical for identifying and localizing the sound source in a complex acoustic environment. Using the prepulse inhibition of the acoustic startle reflex (ASR) as a measure, the present study investigated whether rats are able to detect correlation changes between sounds from different spatial locations. The results show that the rat's ASR amplitude was suppressed when the startle-eliciting stimulus was preceded by either an uncorrelated noise fragment or an anti-phase noise fragment that was embedded in two identical (correlated) but spatially separated noises. Suppression of the ASR amplitude increased as the duration of the noise fragment increased from 5ms to 40ms. The suppressive effect was also progressively enhanced after rats underwent successive testing sessions. Moreover, an enhanced suppression of the ASR amplitude was observed after rats were exposed to footshock that was precisely paired with a 100-ms correlation-change fragment. The results indicate that rats are able to detect the correlation change between sounds from two separated spatial locations, and the detection can be facilitated by both perceptual learning and emotional learning.

Acoustic Stimulation↗
PubMed2006

Effective deposition potential induced size-dependent orientation growth of Bi-Sb alloy nanowire arrays.

The influence of effective deposition potential on the orientation and diameter of Bi(1-x)Sbx alloy nanowire arrays by pulsed electrodeposition technique was reported. X-ray diffraction, field-emission scanning electron microscopy, and transmission electron microscopy analysis show that the orientation of the Bi(1-x)Sbx nanowires can be turned from the [110] to the [202] direction by increasing the effective deposition potential, and the nanowires fully fill in the pores of the AAM in the lower potential region, while in the higher potential region the nanowires partly fill the pores of the AAM. The origin of those phenomena and the growth mechanism of the nanowire are discussed together with composition analysis.

Journal Article↗
PubMed2006

A general exact method for synthesizing parallel-beam projections from cone-beam projections via filtered backprojection.

In recent years, image reconstruction methods for cone-beam computed tomography (CT) have been extensively studied. However, few of these studies discussed computing parallel-beam projections from cone-beam projections. In this paper, we focus on the exact synthesis of complete or incomplete parallel-beam projections from cone-beam projections. First, an extended central slice theorem is described to establish a relationship between the Radon space and the Fourier space. Then, data sufficiency conditions are proposed for computing parallel-beam projection data from cone-beam data. Using these results, a general filtered backprojection algorithm is formulated that can exactly synthesize parallel-beam projection data from cone-beam projection data. As an example, we prove that parallel-beam projections can be exactly synthesized in an angular range in the case of circular cone-beam scanning. Interestingly, this angular range is larger than that derived in the Feldkamp reconstruction framework. Numerical experiments are performed in the circular scanning case to verify our method.

Algorithms↗
PubMed2006

Neuroprotective effects of (-)-epigallocatechin-3-gallate in a transgenic mouse model of amyotrophic lateral sclerosis.

The purpose of this study is to evaluate neuroprotective effects of (-)-Epigallocatechin-3-gallate (EGCG) in a transgenic mouse model of Amyotrophic lateral sclerosis (ALS). SOD1-G93A transgenic mice and wild-type mice were randomly divided into EGCG-treated groups (10 mg/kg, p.o) and vehicle-treated control groups. Rotarod measurement was performed to assess the motor function of mice starting at the age of 70 days. Nissl staining to examine the number of motor neurons and CD11b immunohistochemical staining to evaluate activation of microglia in the lumbar spinal cords were conducted at the age of 120 days. In addition, for further observation of regulation of cell signaling pathways by EGCG, we used immunohistochemical analysis for nuclear factor kappa B (NF-kappaB) and cleaved caspase-3 as well as western blot analysis to determine the expression of nitric oxide synthase (iNOS) and NF-kappaB in the spinal cord. This study demonstrated that oral administration of EGCG beginning from a pre-symptomatic stage significantly delayed the onset of disease, and extended life span. Furthermore, EGCG-treated transgenic mice showed increased number of motor neurons, diminished microglial activation, reduced immunohistochemical reaction of NF-kappaB and cleaved caspase-3 as well as reduced protein level of iNOS and NF-kappaB in the spinal cords. In conclusion, this study provides further evidences that EGCG has multifunctional therapeutic effects in the mouse model of ALS.

Amyotrophic Lateral Sclerosis↗
PubMed2006

Metabotropic glutamate subtype 5 receptors modulate fear-conditioning induced enhancement of prepulse inhibition in rats.

Non-startling acoustic events presented shortly before an intense startling sound can inhibit the acoustic startle reflex. This phenomenon is called prepulse inhibition (PPI), and is widely used as a model of sensorimotor gating. The present study investigated whether PPI can be modulated by fear conditioning, whose acquisition can be blocked by the specific antagonist of metabotropic glutamate receptors subtype 5 (mGluR5), 2-methyl-6-(phenylethynyl)-pyridine (MPEP). The results show that a gap embedded in otherwise continuous noise sounds, which were delivered by two spatially separated loudspeakers, could inhibit the startle reflex induced by an intense sound that was presented 50 ms after the gap. The inhibitory effect depended on the duration of the gap, and was enhanced by fear conditioning that was introduced by temporally pairing the gap with footshock. Intraperitoneal injection of MPEP (0.5 or 5mg/kg) 30 min before fear conditioning blocked the enhancing effect of fear conditioning on PPI, but did not affect either the baseline startle magnitude or PPI if no fear conditioning was introduced. These results indicate that PPI is enhanced when the prepulse signifies an aversive event after fear conditioning. Also, mGlu5Rs play a role in preserving the fear-conditioning-induced enhancement of PPI.

Analysis of Variance↗