Biomedical subjects

Wen Liu

Publications and source records attributed to Wen Liu.

At least 19 recordsLinked to original sources

PubMed2026

Transcriptomic insights into exogenous fatty acid-enhanced halotolerance in Zygosaccharomyces rouxii.

BACKGROUND: High salinity restricts microbial growth during brine-based food fermentation. Although exogenous unsaturated fatty acids improve the salt tolerance of Zygosaccharomyces rouxii, the associated transcriptional mechanisms remain unclear. This study investigated the transcriptomic response of Z. rouxii CGMCC 3791 to palmitoleic acid (C16:1) under high salt conditions. RESULTS: Cells were cultured in yeast extract peptone dextrose (YPD) containing 120 g L-1 NaCl, with or without 20 μg mL-1 C16:1. They were analyzed by RNA sequencing. Principal component analysis clearly separated the two treatments. Using q < 0.05 and |log2 fold change| > 1, 23 differentially expressed genes were identified - three upregulated and 20 downregulated. INO1, MLS1, POX1, MEP2, and SOD5 were among the major responsive genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that peroxisome-associated functions, lipid metabolism, oxidative stress responses, nitrogen utilization, and mitogen-activated protein kinase (MAPK) signaling were the principal C16:1-responsive processes. CONCLUSION: Exogenous C16:1 elicited a focused transcriptional adjustment rather than broad transcriptome-wide reprogramming in salt-stressed Z. rouxii. The results indicated that peroxisome-linked lipid processes and redox regulation were candidate mechanisms underlying fatty-acid-associated halotolerance and provided targets for improving the robustness of high-salt food fermentation. © 2026 Society of Chemical Industry.

Zygosaccharomyces rouxii↗

PubMed2026

Identifying potential drug targets for physical and cognitive frailty: an integrative analysis of CHARLS cohort, mendelian randomization, and gene colocalization.

With the aging of the population, frailty has become a common syndrome that severely affects the quality of life of older adults. This study aims to analyze the correlation between cognition and frailty, physical activity and frailty, and elucidate the potential pharmacological targets of cognitive frailty and physical frailty.We conducted logistic regression analyses using data from the China Health and Retirement Longitudinal Study (CHARLS) to examine the associations between total cognition and frailty, physical activity and frailty. Furthermore, summary-data-based Mendelian randomization (SMR) and two-sample Mendelian randomization (TSMR) were employed to explore potential pharmacological targets for frailty. Genes associated with physical frailty and cognitive frailty were identified, followed by analysis via colocalization analysis, phenome-wide association studies (PheWAS), and DsigDB drug prediction. Cross-sectional analysis of CHARLs revealed that total cognition(OR 0.93, 95% CI 0.92-0.95) and middle physical activity(OR 0.95, 95% CI 0.92-0.97) were negatively correlated with frailty. SMR identified 41 drug genes associated with frailty, and subsequent TSMR validation and co-localization analysis showed that 11 candidate genes exhibited strong colocalization (PP.H4 > 0.8). GRPEL 1, PABPC 4, and WBP 2NL were ultimately identified as potential drug targets associated with physical frailty, while LANCL1, LRPPRC, FADS1, and WBP2NL were identified as potential drug targets associated with cognitive frailty. Phenome-wide association analysis(PheWAS) did not reveal any significant associations between these genes and other phenotypes at the genome-wide significance threshold. Laudanosine, 25-hydroxycholesterol, and hexadecanal emerged as the top three candidate compounds for therapeutic intervention. We identified potential drug targets for physical frailty and cognitive frailty through comprehensive analysis and elucidated drugs associated with potentially relevant genetic markers, thereby laying the foundation for a deeper understanding of the mechanisms of frailty.

Humans↗

PubMed2025

A Swedish genome-wide haplotype association analysis identifies novel candidate loci associated with endometrial cancer risk.

Genome-wide association studies [GWAS] have identified a limited number of endometrial cancer risk loci by analyzing single nucleotide polymorphisms [SNPs]. We hypothesized that analyzing haplotypes rather than SNPs could provide novel and more detailed information on genetic cancer susceptibility loci. To examine the association of a SNP or haplotype with endometrial cancer risk we performed a two-stage haplotype GWAS. The discovery GWAS included a sub-cohort of 1,116 Swedish endometrial cancer cases and 5,021 controls from previously published GWAS data. A sliding window analysis was employed with window sizes of 1-25 SNPs using a logistic regression model. The Swedish haplotype analysis identified 15 novel candidate risk loci (2q31.1, 4p16.1, 4p15.31, 6q13, 7p21.1, 9p13.3, 10q26.3, 11q21, 12q13.11, 13q12.11, 15q13.3, 16q24.3, 19q13.32, 20p12.3 and 22q13.2) with OR ranging from 1.6 to 3.3 and p-values from 4.25 × 10-8 to 9.86 × 10-15. A second replication haplotype analysis of the Swedish novel loci was performed using two cohorts from Belgium and Germany. In spite of small sample sizes in the replication cohorts, there was still support for most loci with positive ORs. In addition, the findings in the two European cohorts motivates further studies to search for founder haplotypes. These novel findings suggested that endometrial cancer loci, identified through haplotype analysis, conferred a higher risk compared to previous single-variant GWAS.

Humans↗

PubMed2006

High performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-MS/ESI) method for simultaneous determination of venlafaxine and its three metabolites in human plasma.

A high-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-MS/ESI) method for simultaneous determination of venlafaxine (VEN) and its three metabolites O-desmethylvenlafaxine (ODV), N-desmethylvenlafaxine (NDV) and N,O-didesmethylvenlafaxine (DDV) in human plasma has been developed and validated. Estazolam was used as the internal standard. The compounds and internal standard were extracted from plasma by a liquid-liquid extraction. The HPLC separation of the analytes was performed on a Thermo BDS HYPERSIL C18 (250 mm x 4.6 mm, 5 microm, USA) column, using a gradient elution program with solvents constituted of water (ammonium acetate: 30 mmol/l, formic acid 2.6 mmol/l and trifluoroacetic acid 0.13 mmol/l) and acetonitrile (60:40, V/V) at a flow-rate of 1.0 ml/min. All of the analytes were eluted within 6 min. The compounds were ionized in the electrospray ionization (ESI) ion source of the mass spectrometer and were detected in the selected ion recording (SIR) mode. Calibration curves in spiked whole blood were linear from 4.0-700 ng/ml, 2.0-900 ng/ml, 3.0-800 ng/ml and 2.0-700 ng/ml for VEN, ODV, NDV and DDV, respectively, all of them with coefficients of determination above 0.9991. The average extraction recoveries for all the four analytes were above 77%. The methodology recoveries were higher than 91%. The limits of detection were 0.4, 0.2, 0.3, and 0.2 ng/ml for VEN, ODV, NDV and DDV, respectively. The intra- and inter-day variation coefficients were less than 11%. The method is accurate, sensitive and reliable for the pharmacokinetic study of venlafaxine as well as therapeutic drug monitoring (TDM).

Antidepressive Agents, Second-Generation↗

PubMed2006

The tumor metastasis suppressor gene Drg-1 down-regulates the expression of activating transcription factor 3 in prostate cancer.

The tumor metastasis suppressor gene Drg-1 has been shown to suppress metastasis without affecting tumorigenicity in immunodeficient mouse models of prostate and colon cancer. Expression of Drg-1 has also been found to have a significant inverse correlation with metastasis or invasiveness in various types of human cancer. However, how Drg-1 exerts its metastasis suppressor function remains unknown. In the present study, to elucidate the mechanism of action of the Drg-1 gene, we did a microarray analysis and found that induction of Drg-1 significantly inhibited the expression of activating transcription factor (ATF) 3, a member of the ATF/cyclic AMP-responsive element binding protein family of transcription factors. We also showed that Drg-1 attenuated the endogenous level of ATF3 mRNA and protein in prostate cancer cells, whereas Drg-1 small interfering RNA up-regulated the ATF3 expression. Furthermore, Drg-1 suppressed the promoter activity of the ATF3 gene, indicating that Drg-1 regulates ATF3 expression at the transcriptional level. Our immunohistochemical analysis on prostate cancer specimens revealed that nuclear expression of ATF3 was inversely correlated to Drg-1 expression and positively correlated to metastases. Consistently, we have found that ATF3 overexpression promoted invasiveness of prostate tumor cells in vitro, whereas Drg-1 suppressed the invasive ability of these cells. More importantly, overexpression of ATF3 in prostate cancer cells significantly enhanced spontaneous lung metastasis of these cells without affecting primary tumorigenicity in a severe combined immunodeficient mouse model. Taken together, our results strongly suggest that Drg-1 suppresses metastasis of prostate tumor cells, at least in part, by inhibiting the invasive ability of the cells via down-regulation of the expression of the ATF3 gene.

Activating Transcription Factor 3↗

PubMed2006

Simultaneous stereoselective analysis of venlafaxine and O-desmethylvenlafaxine enantiomers in human plasma by HPLC-ESI/MS using a vancomycin chiral column.

A high-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI/MS) method for simultaneous stereoselective analysis of venlafaxine (VEN) and its major metabolite O-desmethylvenlafaxine (ODV) enantiomers in human plasma has been developed and validated. Chiral chromatography is performed on the CHRIOBIOTIC V (5 microm, 250 mm x 4.6 mm) column with mobile phase constituted of 30 mmol/l ammonium acetate-methanol (15:85, pH 6.0) at a flow rate of 1.0 ml/min and a postcolumn splitting ratio of 3:1. The compounds were ionized in the electrospray ionization (ESI) ion source of the mass spectrometer and detected using the selected ion recording (SIR) mode. Calibration curves obtained from spiked plasma were linear in the range of 5.0-400 ng/ml for S-(+)-VEN and R-(-)-VEN, 4.0-280 ng/ml for S-(+)-ODV and R-(-)-ODV, respectively, with linear correlation coefficient all above 0.999. The average extraction recoveries for all the four analytes were above 76%. The methodology recoveries were higher than 92%. The limit of detection were 1.0 ng/ml for S-(+)-VEN and R-(-)-VEN, 1.5 ng/ml for S-(+)-ODV and R-(-)-ODV, respectively. The intra- and inter-day variation coefficients were less than 9%.

Chromatography, High Pressure Liquid↗

PubMed2006

SVRMHC prediction server for MHC-binding peptides.

BACKGROUND: The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. RESULTS: Recently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods. CONCLUSION: SVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers.

Amino Acid Sequence↗

PubMed2006

Production of recombinant orange-spotted grouper (Epinephelus coioides) luteinizing hormone in insect cells by the baculovirus expression system and its biological effect.

The cDNA sequence encoding orange-spotted grouper lhb (LHbeta) and cga (GTHalpha) subunits were cocloned into baculovirus transfer vectors and expressed in insect Sf9 cells. The results showed that two bands of 15.6 kDa and 11.4 kDa could be detected by SDS-PAGE and a band of 30 kDa could be detected by native PAGE. The recombinant grouper Lh (rgLh) could stimulate the secretion of testosterone (T) and estradiol-17beta (E2) from the gonad in a static incubation system in a time-dependent, but not a dose-dependent, manner. Using in vivo bioassay, the mRNA levels of two aromatases (cyp19a1a [P450aromA] and cyp19a1b [P450aromB]), gnrh (GnRH), lhb, and cga in the pituitary, gonad, and hypothalamus were determined in different groups of orange-spotted groupers treated respectively with rgLh, human chorionic gonadotropin (hCG), and a culture medium of insect cells transformed with an expression vector without lhb and cga subunits. The mRNA levels of cyp19a1a and cyp19a1b rose dramatically after injecting rgLh intraperitoneally, which was consistent with the secretion of sex steroid hormones. Interestingly, the mRNA levels of gnrh dropped in the pituitary, hypothalamus, and gonad, and the mRNA levels of lhb and cga in the pituitary of the experimental group expressed at a higher level than that of the hCG group. These results are in accord with the long positive feedback loop of Lh on gonad sex steroid hormones and the short negative feedback loop of Lh on gnrh mRNA levels. These results indicate that the rgLh is successfully expressed by the baculovirus-insect expression system and that the rgLh has biological activity.

Animals↗

PubMed2006

Unloading reaction to electrical stimulation at neutral and supinated ankle positions.

An unloading reaction has been characterized as a modified flexor reflex (FR), in which the standing subjects decrease the load on the stimulated foot and increase the load on the contralateral side, but, without withdrawal of the stimulated foot. Different behavioral circumstances have been shown to modulate this reflex. It is not known whether unloading reactions can be modulated with a loaded supinated ankle position, which, in excess, may result in an ankle sprain injury. Since ankle sprain depends on the load applied to a supinated foot, our premise is that unloading reactions may protect the ankle from a sprain injury. Therefore, this study investigated how the unloading reactions were modulated during a loaded supinated ankle condition. We delivered non-nociceptive and nociceptive electrical stimulations on the lateral aspect of the ankle in standing subjects with the foot in neutral and in a supinated position. The magnitude and latencies of reflex responses were registered using kinetic and kinematic analyses and subsequently compared among the conditions. The analysis demonstrated greater reactions for the supinated ankle condition. The individuals also moved their whole body downwards and shifted the body weight to the non-stimulated foot. Therefore, this study suggested that a modified type of the classic flexion reflex, i.e., unloading reaction, may be used as a strategy to unload a supinated ankle and potentially minimize the risk of ankle sprain injuries.

Adult↗

PubMed2006

Fetal central nervous system anomalies: comparison of magnetic resonance imaging and ultrasonography for diagnosis.

BACKGROUND: Evaluation of fetal central nervous system (CNS) agenesis by ultrasonography (US) is frequently limited, but magnetic resonance imaging (MRI) has its own advantages and is gaining popularity in displaying suspected fetal anomalies. The purpose of this study was to explore the value of MRI in detecting fetal CNS agenesis. METHODS: Thirty-four women (aged from 22 to 35 years, average 27 years) with complicated pregnancies (16 - 39 weeks of gestation, average 30 weeks) were examined with a 1.5 T superconductive MR unit within 24 hours after ultrasonography. Half-Fourier acquisition single-shot turbo spin-echo (HASTE) T(2)-weighted imaging (T(2)WI) sequence were performed in all patients, and fast low angle shot (FLASH) T(1)-weighted imaging (T(1)WI) sequence were applied sequentially in seven of them. Comparison of the results was made between the MRI and US findings as well as autopsy or postnatal follow-up MRI findings. RESULTS: The gyrus, sulcus, corpus callosum, thalamus, cerebellum, brainstem, and spinal cord of fetus were shown more clearly on T(2)-weighted MR images than on T(1)-weighted MR images. MRI corrected the diagnosis of US in 10 cases (10/34, 29.41%) and the diagnosis was missed only in 1 case (1/34, 2.94%). CONCLUSION: MRI has advantages to US in detecting fetal CNS anomalies and is a supplement to US in complicated pregnancies.

Adult↗

PubMed2006

Regulation of cation transport in the distal nephron by mechanical forces.

Thiazide and loop diuretics induce renal K(+) secretion, often leading to renal K(+) wasting and hypokalemia. This phenomenon has been proposed to reflect an increase in delivery to and reabsorption of Na(+) by the distal nephron, with a resultant increase in the driving force for passive K(+) efflux across the apical membrane. Recent studies suggest that cellular mechanisms that lead to enhanced rates of Na(+) reabsorption as well as K(+) secretion in response to increases tubular flow rates are more complex. Increases in tubular flow rates directly enhance the activity of apical membrane Na(+) channels and indirectly activate a class of K(+) channels, referred to as maxi-K, that are functionally inactive under low flow states. This review addresses the role of biomechanical forces, generated by variations in urinary flow rate and tubular fluid volume, in the regulation of transepithelial Na(+) and K(+) transport in the distal nephron. The question of why the distal nephron has evolved to include a component of flow-dependent K(+) secretion is also addressed.

Animals↗

PubMed2006

Effects of repeated daily treatments with a 5-HT3 receptor antagonist on dopamine neurotransmission and functional activity of 5-HT3 receptors within the nucleus accumbens of Wistar rats.

A previous study indicated that pretreatment with repeated daily injections of serotonin-3 (5-HT3) receptor antagonists subsequently reduced the effectiveness of the 5-HT3 antagonists to attenuate ethanol intake under 24-h free-choice conditions; one possibility to account for this is that the functional activity of the 5-HT3 receptor may have been altered by prior treatment with the antagonists. The present experiments were conducted to examine the effects of local perfusion of the 5-HT3 agonist 1-(m-chlorophenyl)-biguanide (CPBG) on the extracellular levels of dopamine (DA) in the nucleus accumbens (ACB) and ventral tegmental area (VTA) of adult male Wistar rats that had received repeated daily injections of the 5-HT3 antagonist, MDL 72222 (MDL). In vivo microdialysis was used to test the hypothesis that alterations in 5-HT3 receptor function have occurred with repeated antagonist injections. One group was given daily injections of MDL (1 mg/kg, s.c.) for 10 consecutive days (MDL group), and the other group was administered saline for 10 days (saline group). On the day after the last treatment, rats were implanted with a unilateral guide cannula aimed at either the ACB or VTA. Two days later, the microdialysis probe was inserted into the guide cannula; on the next day, microdialysis experiments were conducted to determine the extracellular levels of DA in the ACB or VTA. Local perfusion of CPBG (17.5, 35, 70 microM) in the ACB significantly stimulated DA release in the saline- and MDL-treated animals. In terms of percent baseline, the CPBG-stimulated DA release was higher in the MDL-treated group than in the saline-treated group in both the ACB and VTA; however, on the basis of the extracellular concentration, there were no significant differences in the ACB between the two groups. Using the no-net-flux microdialysis, it was determine that the basal extracellular concentration of DA in the ACB was approximately 60% lower in the MDL group than saline group; there was no difference between the groups in the extraction fraction (clearance). Overall, the results suggest that repeated daily treatments with MDL decreased basal DA neurotransmission in the ACB and did not have a clear effect on functional activity of 5-HT3 receptors in the ACB.

Animals↗

PubMed2006

The DNA sequence, annotation and analysis of human chromosome 3.

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

Animals↗

PubMed2006

Cloning and characterization of a bacterial iterative type I polyketide synthase gene encoding the 6-methylsalicyclic acid synthase.

Unusual polyketide synthases (PKSs), that are structurally type I but act in an iterative manner for aromatic polyketide biosynthesis, are a new family found in bacteria. Here we report the cloning of the iterative type I PKS gene chlB1 from the chlorothricin (CHL) producer Streptomyces antibioticus DSM 40725 by a rapid PCR approach, and characterization of the function of the gene product as a 6-methylsalicyclic acid synthase (6-MSAS). Sequence analysis of various iterative type I PKSs suggests that the resulting aromatic or aliphatic structure of the products might be intrinsically determined by a catalytic feature of the paired KR-DH domains in the control of the double bond geometry. The finding of ChlB1 as a 6-MSAS not only enriches the current knowledge of aromatic polyketide biosynthesis in bacteria, but will also contribute to the generation of novel polyketide analogs via combinatorial biosynthesis with engineered PKSs.

Acyltransferases↗

PubMed2006

Mechanism underlying flow stimulation of sodium absorption in the mammalian collecting duct.

Vectorial Na(+) absorption across the aldosterone-sensitive distal nephron plays a key role in the regulation of extracellular fluid volume and blood pressure. Within this nephron segment, Na(+) diffuses from the urinary fluid into principal cells through an apical, amiloride-sensitive, epithelial Na(+) channel (ENaC), which is considered to be the rate-limiting step for Na(+) absorption. We have reported that increases in tubular flow rate in microperfused rabbit cortical collecting ducts (CCDs) lead to increases in net Na(+) absorption and that increases in laminar shear stress activate ENaC expressed in oocytes by increasing channel open probability. We therefore examined whether flow stimulates net Na(+) absorption (J(Na)) in CCDs by increasing channel open probability or by increasing the number of channels at the apical membrane. Both baseline and flow-stimulated J(Na) in CCDs were mediated by ENaC, as J(Na) was inhibited by benzamil. Flow-dependent increases in J(Na) were observed following treatment of tubules with reagents that altered membrane trafficking by disrupting microtubules (colchicine) or Golgi (brefeldin A). Furthermore, reducing luminal Ca(2+) concentration ([Ca(2+)]) or chelating intracellular [Ca(2+)] with BAPTA did not prevent the flow-dependent increase in J(Na). Extracellular trypsin has been shown to activate ENaC by increasing channel open probability, and we observed that trypsin significantly enhanced J(Na) when tubules were perfused at a slow flow rate. However, trypsin did not further enhance J(Na) in CCDs perfused at fast flow rates. Similarly, the shear-induced increase in benzamil-sensitive J(Na) in oocytes expressing protease resistance ENaC mutants was similar to that of controls. Our results suggest the rise in J(Na) accompanying increases in luminal flow rates reflects an increase in channel open probability.

Amiloride↗

PubMed2006

Hypericum sampsonii induces apoptosis and nuclear export of retinoid X receptor-alpha.

Natural products derived from plants provide a rich source for development of new anticancer drugs. Recent studies suggest that modulation of subcellular localization of retinoid X receptor-alpha (RXRalpha) represents a potential approach for inducing cancer cell apoptosis. In this study, we screened a herbal library for inducing translocation of RXRalpha from the nucleus to the cytoplasm. Our results revealed that the extract of Hypericum sampsonii, a member of the genus Hypericum, had remarkable effect on RXRalpha subcellular localization in various cancer cells. Treatment of NIH-H460 human lung cancer cells with H. sampsonii extract resulted in relocalization of RXRalpha from the nucleus to the cytoplasm. Cytoplasmic RXRalpha induced by H. sampsonii was associated with mitochondria, accompanied with cytochrome c release and apoptosis. H. sampsonii extract effectively inhibited the growth of various cancer cell lines, including NIH-H460 lung cancer, MGC-803 stomach cancer and SMMC7721 liver cancer cells. The growth inhibitory effect of H. sampsonii extract depended on levels of RXRalpha, as it failed to inhibit the growth of CV-1 cells lacking detectable RXRalpha, whereas transfection of RXRalpha into CV-1 cells restored its apoptotic response to H. sampsonii. Furthermore, the apoptotic effect of H. sampsonii was significantly enhanced when RXRalpha was overexpressed in NIH-H460 cells. Together, our results demonstrate that H. sampsonii contains ingredient(s) that induce apoptosis of cancer cells by modulating subcellular localization of RXRalpha.

Active Transport, Cell Nucleus↗

PubMed2006

Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models.

BACKGROUND: The binding between peptide epitopes and major histocompatibility complex proteins (MHCs) is an important event in the cellular immune response. Accurate prediction of the binding between short peptides and the MHC molecules has long been a principal challenge for immunoinformatics. Recently, the modeling of MHC-peptide binding has come to emphasize quantitative predictions: instead of categorizing peptides as "binders" or "non-binders" or as "strong binders" and "weak binders", recent methods seek to make predictions about precise binding affinities. RESULTS: We developed a quantitative support vector machine regression (SVR) approach, called SVRMHC, to model peptide-MHC binding affinities. As a non-linear method, SVRMHC was able to generate models that out-performed existing linear models, such as the "additive method". By adopting a new "11-factor encoding" scheme, SVRMHC takes into account similarities in the physicochemical properties of the amino acids constituting the input peptides. When applied to MHC-peptide binding data for three mouse class I MHC alleles, the SVRMHC models produced more accurate predictions than those produced previously. Furthermore, comparisons based on Receiver Operating Characteristic (ROC) analysis indicated that SVRMHC was able to out-perform several prominent methods in identifying strongly binding peptides. CONCLUSION: As a method with demonstrated performance in the quantitative modeling of MHC-peptide binding and in identifying strong binders, SVRMHC is a promising immunoinformatics tool with not inconsiderable future potential.

Algorithms↗

PubMed2006

The finished DNA sequence of human chromosome 12.

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

Animals↗