Biomedical subjects

Lei Yu

Publications and source records attributed to Lei Yu.

At least 19 recordsLinked to original sources

PubMed2026

The complete chloroplast genome sequence and phylogenetic analysis of Amorphophallus gigas.

We sequenced the complete chloroplast genome of Amorphophallus gigas, a perennial monocotyledonous herb in Araceae, using HiFi technology. The genome is 173,034 bp in length with a GC content of 34.96%. It exhibits a typical quadripartite structure: a large single-copy (LSC) region of 95,283 bp, a small single-copy (SSC) region of 15,675 bp, and a pair of inverted repeat (IR) regions of 31,038 bp each. It encodes 130 genes (85 protein-coding, 37 tRNA, 8 rRNA). Phylogenetic analysis revealed that A. gigas is closely related to A. titanum, forming a distinct clade. This study provides valuable genomic resources for understanding the evolution of Amorphophallus and Araceae.

Complete chloroplast genome↗

PubMed2026

Detection of endocytobionts inhabiting the macronucleus of Frontonia paramagna (Ciliophora, Peniculida).

Bacterial endosymbionts of Frontonia, a widely distributed ciliate genus, remain poorly characterized. Here, we investigated the endosymbiotic microbiota of a Shanghai population of Frontonia paramagna using an integrated morphological and molecular approach. Fluorescence in situ hybridization (FISH) targeting the 16S rRNA gene, coupled with V3-V4 high-throughput sequencing, consistently identified Caedimonas as the bacterial symbiont, specifically localized within the host macronucleus. FISH and transmission electron microscopy confirmed this intramacronuclear colonization with high prevalence and revealed that the symbionts lack flagella and R-bodies. Phylogenetic analysis of full-length 16S rRNA gene sequences placed the F. paramagna symbionts within a well-supported clade containing Caedimonas from divergent hosts. Comparative analysis of the 16S rRNA internal excised element (IEE) showed substantial sequence and secondary structural divergence between the Frontonia-associated lineage and other Caedimonas strains from different ciliates. We conservatively designate this lineage as Caedimonas varicaedens Fpa. These distinct molecular features suggest that the diversity and host distribution of Caedimonas are far from fully described, and genomic approaches will be necessary to evaluate species delimitation within the genus and the possible presence, distribution, and horizontal transfer of R-body genetic determinants.

16S rRNA gene↗

PubMed2026

Proteogenomic features define subtypes of mantle cell lymphoma.

Mantle cell lymphoma (MCL) is a biologically heterogeneous B-cell malignancy. Although genomics and transcriptomics have delineated parts of the MCL disease spectrum, proteomics remains largely unexplored. Here, we conducted a comprehensive proteogenomic analysis integrating genomics, transcriptomics, and proteomics on peripheral blood samples from 27 patients with MCL and 4 healthy donors to investigate the translational and posttranslational dimensions of MCL. Our study identified 1296 downregulated and 468 upregulated proteins in MCL cells. The splicing pathways were significantly upregulated at both the mRNA and protein levels, suggesting a critical role for aberrant RNA splicing in MCL pathogenesis. Integration of proteomic data with genetic aberrations revealed immunoglobulin heavy chain variable mutational status and CCND1 mutation are associated with distinctive transcriptomic and proteomic profiles, which correspond to significant differences in clinical outcomes. A multiomics molecular stratification model incorporating proteomic data showed superior predictive power for patient survival compared with single-omics models (concordance index, 0.83 vs 0.74). This study provides, to our knowledge, the first comprehensive proteogenomic profile of MCL, offering novel insights into its molecular mechanisms and clinical behavior. The identification of molecular subtypes and prognostic protein signatures underscores the potential of proteomics to guide precision medicine strategies for MCL.

Humans↗

PubMed2025

KSHVbook: An Information-Sharing Database for Kaposi's Sarcoma-Associated Herpesvirus.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a double-stranded DNA virus belonging to the γ-herpesvirus subfamily. KSHV is the causative agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), multicentric Castleman's disease (MCD), and KSHV inflammatory cytokine syndrome (KICS). Since its discovery, research on KSHV has rapidly progressed, but existing information platforms relatively lack comprehensiveness and do not provide efficient analysis tools tailored for KSHV. To further promote the research on KSHV more effectively, we have developed KSHVbook (http://www.kshvbook.com), a specialized information-sharing database dedicated to KSHV. This platform offers extensive information on genes, coding sequences, proteins, and the gene regulatory region. Besides, the KSHVbook includes about 35 010 transcription factor binding sites (TFBSs), 342 010 pairs of KSHV miRNA-host target gene relationships, protein structures predicted by AlphaFold3, qPCR primers, and so on. We also develop analytical tools for viral genome regions, TFBSs, and KSHV miRNA target genes to discover previously unknown biological functions of KSHV. These analytical tools can effectively identify the potential regulatory relationships between host transcription factors and viral genes. Overall, this platform provides a centralized data resource for KSHV research by integrating multiple databases, offering accessible analysis tools, and simplifying data acquisition. The KSHVbook will continue to be updated, and more features can be found on the website.

Herpesvirus 8, Human↗

PubMed2007

Shared random effects analysis of multi-state Markov models: application to a longitudinal study of transitions to dementia.

Multi-state models are appealing tools for analysing data about the progression of a disease over time. In this paper, we consider a multi-state Markov chain with two competing absorbing states: dementia and death and three transient non-demented states: cognitively normal, amnestic mild cognitive impairment (amnestic MCI), and non-amnestic mild cognitive impairment (non-amnestic MCI). The likelihood function for the data is derived and estimates for the effects of the covariates on transitions are determined when the process can be viewed as a polytomous logistic regression model with shared random effects. The presence of a shared random effect not only complicates the formulation of the likelihood but also its evaluation and maximization. Three approaches for maximizing the likelihood are compared using a simulation study; the first method is based on the Gauss-quadrature technique, the second method is based on importance sampling ideas, and the third method is based on an expansion by Taylor series. The best approach is illustrated using a longitudinal study on a cohort of cognitively normal subjects, followed annually for conversion to mild cognitive impairment (MCI) and/or dementia, conducted at the Sanders Brown Center on Aging at the University of Kentucky.

Aged↗

PubMed2007

Epidemiological study on Clonorchis sinensis infection in Shenzhen area of Zhujiang delta in China.

To study the transmission route and epidemiological features of Clonorchis sinensis infection in Shenzhen area, which is the biggest immigration city in the south of China, we examined 1,473 individuals (710 males and 763 females) to assess the current status of C. sinensis infection among the people in a village of Shenzhen in Zhujiang delta of Guangdong province, China. Freshwater snails, 630, of different species known as the first intermediate host of C. sinensis were collected and examined for cercaria infection, and 430 freshwater fishes of different species as the second intermediate host were examined for metacercaria infection. Among 1,473 people examined, 70 (4.75%) were found infected with C. sinensis. By counting eggs per gram feces (EPG), it was found that the intensity of infection in males was stronger than that of females, and the average EPG was 41.87 in all population. Snails, 1.15%, were infected with cercariae of C. sinensis. The average infection rate of freshwater fishes of 15 species with metacercariae of C. sinensis was 16.97%, and the carps reached the highest infection rate (40.74%). A questionnaire was designed with 12 questions covering socioeconomic conditions and human behavior, contamination of the environment, and fishponds. Of 1,473 interviewees, 54% did not know about fluke disease or its transmission route, 12% of those who knew about the fluke believed that the infection causes no harm or only slight harm to their health. Of the interviewees, 27%, ate raw fish at least one to two times per month. Of families, 5% used the same utensils for both raw fish and cooked food. Of the fishpond owners, 40% fed their fishes with feces of domestic animals and humans. All these factors of unhealthy behaviors, poor knowledge, inappropriate farming/fishery practices, and eating raw fish have made the prevalence of clonorchiasis increase in humans in the Shenzhen area. It is urgent to perform a control program, including health education, environmental modification, reform of traditional farming/fishery practice, mass screening, and chemotherapy for humans, and the management of domestic animals to decrease C. sinensis infection in the human population in Shenzhen.

Adolescent↗

PubMed2006

Glutathione peroxidase-1 inhibits UVA-induced AP-2alpha expression in human keratinocytes.

In this study, we found a role for H(2)O(2) in UVA-induced AP-2alpha expression in the HaCaT human keratinocyte cell line. UVA irradiation not only increased AP-2alpha, but also caused accumulation of H(2)O(2) in the cell culture media, and H(2)O(2) by itself could induce the expression of AP-2alpha. By catalyzing the removal of H(2)O(2) from cells through over-expression of GPx-1, induction of AP-2alpha expression by UVA was abolished. Induction of transcription factor AP-2alpha by UVA had been previously shown to be mediated through the second messenger ceramide. We found that not only UVA irradiation, but also H(2)O(2) by itself caused increases of ceramide in HaCaT cells, and C2-ceramide added to cells induced the AP-2alpha signaling pathway. Finally, forced expression of GPx-1 eliminated UVA-induced ceramide accumulation as well as AP-2alpha expression. Taken together, these findings suggest that GPx-1 inhibits UVA-induced AP-2alpha expression by suppressing the accumulation of H(2)O(2).

Ceramides↗

PubMed2006

Ionic liquid high-temperature gas sensor array.

A novel sensor array using seven room-temperature ionic liquids (ILs) as sensing materials and a quartz crystal microbalance (QCM) as a transducer was developed for the detection of organic vapors at ambient and elevated temperatures. Ethanol, dichloromethane, benzene, and heptane were selected as representative gas analytes for various kinds of environmental pollutants and common industrial solvents. The QCM/IL sensors responded proportionately and reversibly to the organic vapor concentrations (i.e., ethanol, heptane, and benzene) in the gas phase from 0 to 100% saturation at room and elevated temperatures (e.g., 120 degrees C) but deviated from this linear relationship at high concentrations for dichloromethane, a highly volatile compound. Linear discriminant analysis was used to analyze the sensing patterns. Excellent classifications were obtained for both known and unknown concentrations of vapor samples. The correct classifications were 100% for known concentration samples and 96% for samples with unknown concentrations. Thermodynamics and ATR-FT-IR studies were conducted to understand specific molecular interactions, the strength of the interaction between ILs and organic vapors, and the degree of ordering that takes place upon dissolution of the vapors in ILs. The different response intensity of the QCM/IL sensors to the organic vapors depends on the different solubilities of organic vapors in ILs and varying molecular/ion interactions between each organic vapor and IL. The diverse set of IL studied showed selective responses due to structural differences. Therefore, a sensor array of ILs would be able to effectively differentiate different vapors in pattern recognitions, facilitating discrimination by their distinctive patterns in response to organic vapors in both room and high temperatures.

Hot Temperature↗

PubMed2006

[A case report of simultaneous liver, pancreas-duodenum, and kidney transplantation in a patient with post-hepatitic cirrhosis combined with uremia and insulin-dependent diabetes related to chronic pancreatitis].

OBJECTIVE: To study the effect of triple organ transplantation (liver, kidney, and pancreas) in patient of end-stage liver disease with renal failure and diabetes, and to explore the optimal surgical procedure. METHODS: Simultaneous piggyback orthotopic heterotopic liver, pancreas-duodenum, and kidney transplantation was performed on a 43-year-old male patient with exocrine pancreatic insufficiency and insulin-dependent diabetes related to chronic pancreatitis (CP) who developed hepatic and renal failure. The pancreatic exocrine secretions were drained enterically to the jejunum. Prednisone, tacrolimus, mycophenolate mofetil, and ATG were used as immunosuppression therapy. RESULTS: Good liver and pancreas allograft function recovery was achieved within 7 days after the operation. And the recovery of renal allograft function was delayed. The renal allograft was removed because of break-down of renal blood flow 16 days after the transplantation. A new renal transplantation was performed at the same position. The second kidney graft recovered its normal function 3 days later. Up to the writing of this paper no acute rejection of organs and such complications as pancreatitis, thrombosis, and localized infection occurred. The patient became insulin independent with normal liver and renal function. CONCLUSION: Simultaneous piggyback orthotopic heterotopic liver, pancreas-duodenum, and kidney transplantation can be a good method for the patients with exocrine pancreatic insufficiency and insulin-dependent diabetes combined with hepatic and renal failure.

Adult↗

PubMed2006

SNAP-25 in hippocampal CA3 region is required for long-term memory formation.

SNAP-25 is a synaptosomal protein of 25 kDa, a key component of synaptic vesicle-docking/fusion machinery, and plays a critical role in exocytosis and neurotransmitter release. We previously reported that SNAP-25 in the hippocampal CA1 region is involved in consolidation of contextual fear memory and water-maze spatial memory (Hou et al. European J Neuroscience, 20: 1593-1603, 2004). SNAP-25 is expressed not only in the CA1 region, but also in the CA3 region, and the SNAP-25 mRNA level in the CA3 region is higher than in the CA1 region. Here, we provide evidence that SNAP-25 in the CA3 region is also involved in learning/memory. Intra-CA3 infusion of SNAP-25 antisense oligonucleotide impaired both long-term contextual fear memory and water-maze spatial memory, with short-term memory intact. Furthermore, the SNAP-25 antisense oligonucleotide suppressed the long-term potentiation (LTP) of field excitatory post-synaptic potential (fEPSP) in the mossy-fiber pathway (DG-CA3 pathway), with no effect on paired-pulse facilitation of the fEPSP. These results are consistent with the notion that SNAP-25 in the hippocampal CA3 region is required for long-term memory formation.

Animals↗

PubMed2006

Investigation of N-terminal glutamate cyclization of recombinant monoclonal antibody in formulation development.

The N-terminal glutamic acid (Glu) can be cyclized to form pyroglutamate (pGlu). Recent studies have suggested that N-terminal pGlu formation is an important posttranslational or co-translational event and is greatly facilitated by the enzyme glutaminyl cyclase, although the impact of the N-terminal cyclization on the potency and overall stability of mAbs is not been well known. Since most recombinant monoclonal antibodies (mAbs) contain glutamic acid and/or glutamine at their N-terminus, understanding the cyclization mechanisms may shed light on the factors that control the pGlu formation in therapeutic mAb development. Here, two mass spectrometry-based techniques were developed to investigate N-pyroglutamyl formation and the high conversion rate to pGlu at the N-terminus of the mAb was reported in the formulation development. The pGlu formation is favored at pH 4 and 8, but is less common at the neutral pH that is optimum for the enzymatic Glu conversion. These observations suggest that pGlu formation can proceed non-enzymatically at mild conditions and that this cyclization is not driven by glutaminyl cyclase in non-physiological conditions. We also calculate the half-lives of the N-terminal Glu at different pH and temperatures from the kinetics data, which would be very helpful for predicting pGlu formation and for selecting proper formulation and storage conditions.

Amino Acid Sequence↗

PubMed2006

Inhibition of CD147 expression reduces tumor cell invasion in human prostate cancer cell line via RNA interference.

CD147, also named extracelluar matrix metalloproteinase inducer (EMMPRIN), has been proved to be involved in the invasion and metastasis processes of tumor cells in many types of cancers. To determine the role of CD147 in the invasiveness properties of prostate cancer, we successfully downregulated CD147 by RNA interference (RNAi) technology, in PC-3 cell line at high level of CD147 expression. PC-3 cells were transfected with a pSilencer 4.1-CMV neo Vector coding for an RNA composed of two identical 19-nucleotide sequence motifs in an inverted orientation, separated by a 9-bp spacer to form a hairpin dsRNA capable of mediating target CD147 inhibition. Gelatin zymography was employed to determine the effect on reducing secretions of MMP-2 and MMP-9 of the transfected cells. Matrigel invasion assay was performed to evaluate the invasion ability of PC-3 cells in vitro. Our results showed that CD147 expression was significantly inhibited by small interfering RNAs (siRNA) transfectants in PC-3 cells at mRNA and protein levels, which resulted in dramatic reduction of invasion ability in tumor cells. Moreover, downregulation of CD147 resulted in reducing secretions of MMP-2, MMP-9. Taken together, CD147 downregulation by RNAi technology decreases the invasive capability of prostate cancer cells, demonstrating that stable expression of siRNA CD147 could potentially be an experimental approach for prostate cancer gene therapy.

Antigens, CD↗

PubMed2006

Limbic and HPA axis function in an animal model of chronic neuropathic pain.

Chronic pain can be considered a form of chronic stress, and chronic pain patients often have disturbances of the hypothalamic-pituitary-adrenal (HPA) axis, including abnormal cortisol levels. In addition, chronic pain patients have an increased incidence of depression and anxiety, stress-related disorders that are frequently accompanied by disturbances in the limbic system (e.g. hippocampus and amygdala) and the HPA axis. Despite the fact that the literature supports a strong link between chronic pain, stress disorders, and limbic dysfunction, the mechanisms underlying the effects of chronic pain on the HPA axis and limbic system are not understood. The current study employs a rodent neuropathic pain model (chronic constriction injury (CCI) of the sciatic nerve) to assess the long-term impact of chronic pain on the HPA axis and limbic system. Adult male rats received CCI or sham surgery; nociceptive behavioral testing confirmed CCI-induced neuropathic pain. Tests of HPA axis function at 13-23 days postsurgery demonstrated that CCI did not affect indices of basal or restraint stress-induced HPA axis activity. CCI increased the expression of corticotrophin releasing hormone mRNA in the central amygdala, and not the paraventricular nucleus of the hypothalamus or the bed nucleus of the stria terminalis. Moreover, glucocorticoid receptor mRNA expression in CCI rats was increased in the medial and central amygdala, unaffected in the paraventricular nucleus, and decreased in the hippocampus. These results suggest that increased nociceptive sensitivity during chronic pain is associated with alterations in the limbic system, but is dissociated from HPA axis activation.

Adrenocorticotropic Hormone↗

PubMed2006

Paradoxical effects of very low dose MK-801.

Systemic injection of the noncompetitive NMDA (N-methyl-D-aspartate) receptor antagonist MK-801 (dizocilpine maleate) is known to cause increased locomotion and various stereotypic behaviors in rodents. However, the MK-801 dose ranges commonly examined usually begin at tenth of mg/kg and going higher, with the implicit assumption of lower doses being ineffective. We report here that very low dose MK-801, well below the commonly studied doses, exert distinct effects on rodent behaviors. In C57BL/6 mice, very low dose MK-801 (0.02 mg/kg) has strikingly different effects than higher doses commonly reported in the literature. Locomotion, rearing, grooming, and other behaviors are strongly inhibited, replaced by periods of immobility. This is in contrast to the mobility-enhancing effect of MK-801 at commonly reported dose ranges. The effects of very low dose MK-801 are qualitatively similar to those observed with moderate doses (0.1-0.2 mg/kg) of the typical antipsychotic haloperidol. These results highlight the complexity of the dose-response relation for MK-801-induced behaviors.

Animals↗

PubMed2006

Carbohydrate-protein interactions by "clicked" carbohydrate self-assembled monolayers.

A Huisgen 1,3-dipolar cycloaddition "click chemistry" was employed to immobilize azido sugars (mannose, lactose, alpha-Gal) to fabricate carbohydrate self-assembled monolayers (SAMs) on gold. This fabrication was based on preformed SAM templates incorporated with alkyne terminal groups, which could further anchor the azido sugars to form well-packed, stable, and rigid sugar SAMs. The clicked mannose, lactose, and alpha-Gal trisaccharide SAMs were used in the analysis of specific carbohydrate-protein interactions (i.e., mannose-Con A; ECL-lactose, alpha-Gal-anti-Gal). The apparent affinity constant of Con A binding to mannose was (8.7 +/- 2.8) x 10(5) and (3.9 +/- 0.2) x 10(6) M(-1) measured by QCM and SPR, respectively. The apparent affinity constants of lactose binding with ECL and alpha-Gal binding with polyclonal anti-Gal antibody were determined to be (4.6 +/- 2.4) x 10(6) and (6.7 +/- 3.3) x 10(6) M(-1), respectively by QCM. SPR, QCM, AFM, and electrochemistry studies confirmed that the carbohydrate SAM sensors maintained the specificity to their corresponding lectins and nonspecific adsorption on the clicked carbohydrate surface was negligible. This study showed that the clicked carbohydrate SAMs in concert with nonlabel QCM or SPR offered a potent platform for high-throughput characterization of carbohydrate-protein interactions. Such a combination should complement other methods such as ITC and ELISA in a favorable manner and provide insightful knowledge for the corresponding complex glycobiological processes.

Carbohydrates↗

PubMed2006

The negative cell cycle regulator, Tob (transducer of ErbB-2), is involved in motor skill learning.

Tob (transducer of ErbB-2) is a negative cell cycle regulator with anti-proliferative activity in peripheral tissues. Our previous study identified Tob as a protein involved in hippocampus-dependent memory consolidation (M.L. Jin, X.M. Wang, Y.Y. Tu, X.H. Zhang, X. Gao, N. Guo, Z.Q. Xie, G.P. Zhao, N.H. Jing, B.M. Li, Y.Yu, The negative cell cycle regulator, Tob (Transducer of ErbB-2), is a multifunctional protein involved in hippocampus-dependent learning and memory, Neuroscience 131 (2005) 647-659). Here, we provide evidence that Tob in the central nervous system is engaged in acquisition of motor skill. Tob has a relatively high expression in the cerebellum. Tob expression is up-regulated in the cerebellum after rats receive training on a rotarod-running task. Rats infused with Tob antisense oligonucleotides into the 4th ventricle exhibit a severe deficit in running on a rotating rod or walking across a horizontally elevated beam.

Animals↗

PubMed2006

Genotype and smoking history affect risk of levodopa-induced dyskinesias in Parkinson's disease.

Parkinson's disease (PD) patients vary widely in their response to levodopa treatment, and this variation may be partially genetic in origin. We determined whether particular dopamine and opioid receptor polymorphisms were associated with risk of earlier onset of dyskinesia side effects during levodopa therapy. Smoking status was also examined. The 92 subjects were recruited from the movement disorders clinic of a neurology practice associated with a medical school. All were adult-onset PD patients who had been taking levodopa at least 5 years and/or had developed levodopa-induced dyskinesia. Carrying the G-allele of the A118G single nucleotide coding region polymorphism of the mu opioid receptor, as well as a history of never smoking, were independently associated with increased risk of earlier onset of dyskinesia (P=0.05 and 0.02, respectively). One genotype of the D2 dopamine receptor intronic dinucleotide repeat polymorphism (14 repeats/15 repeats, with frequency of 6%) was also associated with earlier dyskinesia (P=0.003). History of smoking has previously been associated with reduced risk of developing PD. Our results suggest that smoking history may also influence the response to levodopa, with contribution comparable to those of individual genes including the mu opioid receptor and D2 dopamine receptor.

Adult↗

PubMed2006

Identification of N-terminal modification for recombinant monoclonal antibody light chain using partial reduction and quadrupole time-of-flight mass spectrometry.

Since most recombinant monoclonal antibodies (mAbs) contain glutamic acid or glutamate at their N-terminus, cyclization of these residues to form pyroglutamate is an important degradation pathway that often occurs in therapeutic mAb development. In this work, a rapid method was developed to determine pyroglutamate at the N-terminus of mAb light chain by liquid chromatography coupled with electrospray ionization on a quadrupole time-of-flight mass spectrometer (QTOF). High levels of pyroglutamate were found at the N-terminus of the light chain of a typical recombinant mAb. The quantitative results were comparable to those obtained with a more conventional peptide mapping method. The direct method outlined here can be used to evaluate the impact of N-terminal cyclization during the processing of recombinant mAbs.

Antibodies, Monoclonal↗