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Biomedical subjects

L Y Han

Publications and source records attributed to L Y Han.

At least 37 records · Page 2Linked to original sources
PubMed2004

MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids.

Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.

Computational Biology↗
PubMed2004

Enzyme family classification by support vector machines.

One approach for facilitating protein function prediction is to classify proteins into functional families. Recent studies on the classification of G-protein coupled receptors and other proteins suggest that a statistical learning method, Support vector machines (SVM), may be potentially useful for protein classification into functional families. In this work, SVM is applied and tested on the classification of enzymes into functional families defined by the Enzyme Nomenclature Committee of IUBMB. SVM classification system for each family is trained from representative enzymes of that family and seed proteins of Pfam curated protein families. The classification accuracy for enzymes from 46 families and for non-enzymes is in the range of 50.0% to 95.7% and 79.0% to 100% respectively. The corresponding Matthews correlation coefficient is in the range of 54.1% to 96.1%. Moreover, 80.3% of the 8,291 correctly classified enzymes are uniquely classified into a specific enzyme family by using a scoring function, indicating that SVM may have certain level of unique prediction capability. Testing results also suggest that SVM in some cases is capable of classification of distantly related enzymes and homologous enzymes of different functions. Effort is being made to use a more comprehensive set of enzymes as training sets and to incorporate multi-class SVM classification systems to further enhance the unique prediction accuracy. Our results suggest the potential of SVM for enzyme family classification and for facilitating protein function prediction. Our software is accessible at http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.

Amino Acid Sequence↗
PubMed2004

TRMP: a database of therapeutically relevant multiple pathways.

UNLABELLED: Disease processes often involve crosstalks between proteins in different pathways. Different proteins have been used as separate therapeutic targets for the same disease. Synergetic targeting of multiple targets has been explored in combination therapy of a number of diseases. Potential harmful interactions of multiple targeting have also been closely studied. To facilitate mechanistic study of drug actions and a more comprehensive understanding the relationship between different targets of the same disease, it is useful to develop a database of known therapeutically relevant multiple pathways (TRMPs). Information about non-target proteins and natural small molecules involved in these pathways also provides useful hint for searching new therapeutic targets and facilitate the understanding of how therapeutic targets interact with other molecules in performing specific tasks. The TRMPs database is designed to provide information about such multiple pathways along with related therapeutic targets, corresponding drugs/ligands, targeted disease conditions, constituent individual pathways, structural and functional information about each protein in the pathways. Cross links to other databases are also introduced to facilitate the access of information about individual pathways and proteins. AVAILABILITY: This database can be accessed at http://bidd.nus.edu.sg/group/trmp/trmp.asp and it currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions together with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. SUPPLEMENTARY INFORMATION: http://bidd.nus.edu.sg/group/trmp/sm.pdf

Biomarkers↗
PubMed2003

SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence.

Prediction of protein function is of significance in studying biological processes. One approach for function prediction is to classify a protein into functional family. Support vector machine (SVM) is a useful method for such classification, which may involve proteins with diverse sequence distribution. We have developed a web-based software, SVMProt, for SVM classification of a protein into functional family from its primary sequence. SVMProt classification system is trained from representative proteins of a number of functional families and seed proteins of Pfam curated protein families. It currently covers 54 functional families and additional families will be added in the near future. The computed accuracy for protein family classification is found to be in the range of 69.1-99.6%. SVMProt shows a certain degree of capability for the classification of distantly related proteins and homologous proteins of different function and thus may be used as a protein function prediction tool that complements sequence alignment methods. SVMProt can be accessed at http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.

Amino Acid Sequence↗
PubMed2003

KDBI: Kinetic Data of Bio-molecular Interactions database.

Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. Databases of interacting molecules, pathways and related chemical reaction equations have been developed. The kinetic data for these interactions, which is important for mechanistic investigation, quantitative study and simulation of cellular processes and events, is not provided in the existing databases. We introduce a new database of Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules (name, synonyms, molecular formula, classification, SWISS-PROT AC or CAS number), binding or reaction equation, kinetic data and related references. The kinetic data is in terms of one or a combination of the following quantities as given in the literature of a particular event: association/dissociation or on/off rate constant, first/second/third/. order rate constant, equilibrium rate constant, catalytic rate constant, equilibrium association/dissociation constant, inhibition constant and binding affinity constant. Each entry can be retrieved through protein or nucleic acid or ligand name, SWISS-PROT AC number, ligand CAS number and full-text search of a binding or reaction event. KDBI currently contains 8273 entries of biomolecular binding or reaction events involving 1380 proteins, 143 nucleic acids and 1395 small molecules. Hyperlinks are provided for accessing references in Medline and available 3D structures in PDB and NDB. This database can be accessed at http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp.

DNA↗
PubMed2001

Dysregulation of olfactory receptor neuron lineage in schizophrenia.

BACKGROUND: Growing evidence implicates abnormal neurodevelopment in schizophrenia. While neuron birth and differentiation is largely completed by the end of gestation, the olfactory epithelium (OE) is a unique part of the central nervous system that undergoes regeneration throughout life, thus offering an opportunity to investigate cellular and molecular events of neurogenesis and development postmortem. We hypothesized that OE neurons exhibit deviant progress through neurodevelopment in schizophrenia characterized by an increase in immature neurons. METHODS: Olfactory epithelium was removed at autopsy from 13 prospectively assessed elderly subjects who had schizophrenia and 10 nonpsychiatric control subjects. Sections were immunolabeled with antibodies that distinguish OE neurons in different stages of development, including basal cells (low-affinity nerve growth factor receptor, p75NGFR), postmitotic immature neurons (growth-associated protein 43 [GAP43]), and mature olfactory receptor neurons (olfactory marker protein). Absolute and relative densities of each cell type were determined. RESULTS: We observed a significantly lower density of p75NGFR basal cells (37%) in schizophrenia and increases in GAP43 + postmitotic immature neurons (316%) and ratios of GAP43 + postmitotic immature neurons to p75NGFR + cells (665%) and olfactory marker protein + mature neurons to p75NGFR + basal cells (328%). Neuroleptic-free schizophrenia subjects exhibited the highest GAP43 + postmitotic immature neuron values. CONCLUSIONS: Abnormal densities and ratios of OE neurons at different stages of development indicate dysregulation of OE neuronal lineage in schizophrenia. This could be because of intrinsic factors controlling differentiation or an inability to gain trophic support from axonal targets in the olfactory bulb. While caution is necessary in extrapolating developmental findings in mature OE to early brain development, similarities in molecular events suggest that such studies may be instructive.

Aged↗
PubMed2000

Absence of neurodegeneration in the thalamus and caudate of elderly patients with schizophrenia.

The cognitive and functional deterioration observed in many 'poor-outcome' patients with schizophrenia suggests an ongoing neurodegenerative process. Diagnostic neuropathologic studies have excluded known neurodegenerative diseases as the cause of this dementia, and in a previous quantitative investigation of neurodegeneration and neural injury in this population we found no abnormalities in the cerebral cortex. However, it is possible that the deterioration observed in these patients could be due to subcortical neurodegenerative processes. Neurodegeneration and neural injury in the caudate nucleus and mediodorsal nucleus of the thalamus were investigated in a postmortem study of 11 prospectively accrued, clinically well-characterized elderly people with schizophrenia, 11 elderly control subjects with no neuropsychiatric illness, and 12 subjects with Alzheimer's disease. Traditional and immunohistochemical staining and unbiased computerized counting methods were used to quantify common markers of neurodegeneration and neural injury (neuron loss, neurofibrillary tangles, astrocytosis, microgliosis). No statistically significant differences were found between schizophrenia and control subjects for the densities of any markers. There is no evidence that abnormal neurodegeneration occurs in these two important subcortical structures.

Age Factors↗
PubMed2000

Novel method to quantify neuropil threads in brains from elders with or without cognitive impairment.

Pathological alterations in dendrites and axons (i.e., neuritic pathologies) occur in the normal aging brain as well as in brains from elders with mild cognitive impairment and neurodegenerative dementia. These alterations may correlate with clinical measures of cognitive abilities, but the contribution of neuropil threads (NTs), which constitute 85-90% of cortical tau pathology, has not been clear because of the lack of quantitative methodologies. We combined quantitative fractionation and image analysis to devise a strategy for measuring the burden of tau-rich NTs in the entorhinal and perirhinal cortex of brains from elders with and without cognitive impairment, including dementia due to Alzheimer's disease (AD). On the basis of data presented here using this novel strategy, we conclude that this quantitative imaging technique will facilitate efforts to determine the behavioral correlations of neuritic lesions in AD and other brain disorders.

Aged↗
PubMed1998

Absence of neurodegeneration and neural injury in the cerebral cortex in a sample of elderly patients with schizophrenia.

BACKGROUND: The cognitive and functional deterioration that is observed in many "poor-outcome" patients with schizophrenia suggests a neurodegenerative process extending into late life. Previous diagnostic studies have excluded known neurodegenerative diseases as explanations for this dementia. However, we hypothesized that relatively small accumulations of age- or disease-related neurodegenerative lesions occurring in an otherwise abnormal brain could result in deterioration in schizophrenia. METHODS: Postmortem studies were conducted using 23 prospectively accrued elderly persons with chronic schizophrenia for whom clinical ratings had been determined before death, 14 elderly control patients with no neuropsychiatric disease, and 10 control patients with Alzheimer disease. Immunohistochemistry and unbiased stereological counting methods were used to quantify common neurodegenerative lesions (ie, neurofibrillary tangles, amyloid plaques, and Lewy bodies) and cellular reactions to a variety of noxious stimuli (ubiquitinated dystrophic neurites, astrocytosis, and microglial infiltrates) in the ventromedial temporal lobe and the frontal and the calcarine (primary visual) cortices. RESULTS: No statistically significant differences were found between the patients with schizophrenia and the control patients without neuropsychiatric disease for the densities of any of the markers, while both groups exhibited fewer lesions than did the control group with Alzheimer disease. Correlation analyses in the schizophrenia sample failed to identify significant correlations between cognitive and psychiatric ratings and densities of any of the neuropathologic markers. CONCLUSIONS: No significant evidence of neurodegeneration or ongoing neural injury in the cerebral cortex was found in this sample of elderly persons with schizophrenia. Furthermore, the behavioral and cognitive deterioration observed in late life did not correlate with age-related degenerative phenomena.

Age Factors↗
PubMed1997

Further evidence of abnormal cytoarchitecture of the entorhinal cortex in schizophrenia using spatial point pattern analyses.

Previous studies have reported cytoarchitectural abnormalities in superficial laminae of rostral portions of the entorhinal cortex in schizophrenia, including decreased densities of neurons, poorly formed layer II neuron islands, and apparent displacement of layer II-type neurons deep into layer III; however, findings have been controversial, given the qualitative nature of the descriptions and the normal heterogeneity of cytoarchitecture of the region. The x, y coordinates of Nissl-stained neurons were mapped in layers II, III, and V of entorhinal subdivision ER in 8 prospectively accrued patients with schizophrenia and 8 nonneuropsychiatric controls. Indices of neuron dispersion, nearest neighbor distances, and effective radius were determined. An abnormally clustered dispersion of neurons in layer III was present in schizophrenics compared to controls along with a reduced neuron effective radius, whereas the mean nearest-neighbor distance was normal. In layer II, there was a significantly increased effective radius, whereas other indices were normal. No between-group differences were noted in layer V for any variable. These data provide further evidence for subtle aberrant cytoarchitecture in superficial laminae of the entorhinal cortex in schizophrenia and are consistent with neurodevelopmental models of abnormal neuronal pruning, "miswiring," and/or migration in the illness.

Aged↗
PubMed1997

Inositol 1,4,5-trisphosphate receptor expression in odontoblast cells.

The cellular distribution of inositol 1,4,5-trisphosphate receptors was examined in rodent maxillary incisor teeth. In situ hybridization studies with a transmembrane probe of type I inositol 1,4,5-trisphosphate receptor indicated that this receptor/channel was highly expressed in odontoblast cells of incisor teeth. In contrast, very low labeling was observed in dental pulp. Northern analysis showed a message size of approximately 9.5 kilobases for this receptor, and demonstrated that type III inositol 1,4,5-trisphosphate receptor was expressed in incisor teeth. Immunocytochemical studies confirmed that types I and III inositol 1,4,5-trisphosphate receptors were both highly expressed in odontoblasts while very low expression was detected in dental pulp. Finally, antibodies that recognized alpha subunits of the Gq class of GTP binding proteins also stained odontoblasts. These results indicate that receptor-mediated regulation of calcium release through inositol 1,4,5-trisphosphate receptors may occur in odontoblasts of rat incisor teeth. These findings also suggest that inositol 1,4,5-trisphosphate receptor/channels regulate calcium flux in odontoblasts during mineralization of dentin, or in growth and differentiation of incisor tissue.

Animals↗
PubMed1997

Inositol 1,4,5-trisphosphate receptor expression in mammalian olfactory tissue.

Two cDNAs encoding inositol 1,4,5-trisphosphate (IP3) receptors were amplified from rat olfactory tissue, and both exhibited 100% sequence identity to the short (Segment II - ) variant of type I IP3 receptor. Type III IP3 receptor was also expressed in olfactory tissue. The distribution of IP3 receptors included the olfactory epithelium, lamina propria, and glandular tissue. These results demonstrate the co-expression of multiple IP3 receptor subtypes in olfactory cells, and suggest multiple functions for IP3 receptors in this tissue.

Animals↗
PubMed1997

Ribonuclease H renaturation gel assay using a fluorescent-labeled substrate.

Ribonucleases H (RNases H) are enzymes that specifically degrade the RNA of RNA-DNA hybrids. These enzymes are involved in DNA replication, reverse transcription (RT) and antisense oligodeoxyribonucleotide-mediated arrest of translation. One of the most valuable tools for assaying RNase H activity is the renaturation gel assay with which such activities can be detected using purified protein preparations or crude extracts. Radioactive substrates [32P labeled poly(rA)-poly(dT) hybrid] are commonly used with exposure of the gel to X-ray film; this is possible at any time without disturbing the renaturation-degradation process. Here, we describe a method using fluorescent-labeled substrates. RNA-DNA substrates are synthesized by first transcribing DNA with T7 RNA polymerase using Bodipy-TR-14-UTP and the four normal nucleoside triphosphates. The run-off transcript is annealed to a short oligomeric DNA complementary to the 3'-end of the transcript, and the DNA portion of the hybrid is formed by RT. This RNA-DNA is added to the polyacrylamide mixture before polymerization, and SDS-PAGE is performed as usual. After various periods of renaturation, the gel is scanned to detect fluorescent substrate using the red-excited laser of a fluorescence scanner. This fluorescence method has all of the advantages of using radio-labeled substrates and none of its disadvantages, and the sensitivities of the two methods are comparable. In addition, we show that the sensitivity of this procedure can be increased if damaging chemicals remaining in the gel after polymerization are eliminated by simultaneous electrophoresis of the RNase H and a protein with higher mobility.

DNA↗
PubMed1995

Synaptic loss in the central nucleus of the inferior colliculus correlates with sensorineural hearing loss in the C57BL/6 mouse model of presbycusis.

Between 3 and 25 months of age, light and electron microscopic features of principal neurons in the central nucleus of the inferior colliculus of the C57BL/6 mouse were quantitated. This mouse strain has a genetic defect producing progressive sensorineural hearing loss which starts during young adulthood (2 months of age) with high-frequency sounds. During the second year of life, hearing is severely impaired, progressively involving all frequencies. The hearing loss was documented in the present study by auditory brainstem recordings of the mice at various ages. The cochleas from many of the same animals showed massive loss of both inner and outer hair cells beginning at the base (high-frequency region) and progressing with age along the entire length to the apex (low-frequency region). In the inferior colliculi, there was a significant decrease in the size of principal neurons in the central nucleus. There was a dramatic decrease in the number of synapses of all morphologic types on principal neuronal somas. The percentage of somatic membrane covered by synapses decreased by 67%. A ventral (high frequency) to dorsal (low frequency) gradient of synaptic loss could not be identified within the central nucleus. These synaptic changes may be related to the equally dramatic physiologic changes which have been noted in the central nucleus of the inferior colliculus, in which response properties of neurons normally sensitive to high-frequency sounds become more sensitive to low-frequency sounds. The synaptic loss noted in this study may be due to more than the loss of primary afferent pathways. It may represent alterations of the complex synaptic circuitry related to the central deficits of presbycusis.

Animals↗
PubMed1995

Cortical Lewy bodies in Alzheimer's disease.

Forty-eight cases of pathologically verified Alzheimer's disease were examined for the presence of ubiquitin-positive cortical Lewy bodies (CLBs). Thirty-four (71%) of 48 cases of Alzheimer's disease had CLBs compared with 4 (44%) of nine patients with idiopathic Parkinson's disease, and 2 (20%) of 10 patients with multi-infarct dementia. None of the 18 cognitively intact elderly controls we examined had CLBs. Among Alzheimer's disease patients, there was a strong correlation between CLBs and degenerative changes in the substantia nigra. We also found an association between the presence of CLBs and extrapyramidal symptoms. Among Alzheimer's disease patients, there was no association of CLBs with either senile plaques or neurons containing neurofibrillary tangles in hippocampus, neocortex, or ventral striatum. The incidence of CLBs among pathologically verified Alzheimer's disease cases is high when a careful search for these inclusions is performed with a sensitive method such as anti-ubiquitin immunocytochemistry.

Aged↗
PubMed1992

Radiological evidence of progression of bronchiectasis.

Radiological evidence of progression of bronchiectasis was sought in a group of 84 consecutive adult patients admitted to a tertiary unit with a particular interest in the disease. Methodical comparison for each patient of the earliest and most recent chest X-rays (n = 84), bronchograms (n = 1) and thoracic computed tomography (CT) scans (n = 32) was performed. Fifteen patients (18%) were considered to show radiological evidence of progression of bronchiectasis, 14 on chest X-ray, two of whom also showed progression on CT scans, and in one patient on bronchography alone. The likelihood of finding evidence of radiological progression increased the longer the interval between examinations. Serial radiology allows identification of patients with progression of disease and indicates the need to review management strategy.

Adolescent↗