Biomedical subjects

Liang Feng

Publications and source records attributed to Liang Feng.

At least 19 recordsLinked to original sources

PubMed2021

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

Circulating Tumor DNA↗

PubMed2007

Relationship between mRNA stability and intron presence.

Introns were found to enhance almost every steps of gene expression except increasing mRNA stability. By analyzing the genome-wide data of mRNA stability published by someone previously, we found that human intron-containing genes have more stable mRNAs than intronless genes, and the Arabidopsis thaliana genes with the most unstable mRNAs have fewer introns than other genes in the genome. After controlling for mRNA length, we found mRNA stability is still positively correlated with intron number in human intron-containing genes. But in yeast Saccharomyces cerevisiae, two different datasets on mRNA half-life gave conflicting results. The components of messenger ribonucleoprotein particles recruited during intron splicing may be retained in cytoplasmic mRNPs and act as signals of mRNA stability or simply insulators to avoid mRNA degradation.

Arabidopsis↗

PubMed2007

Relationship between mRNA stability and length: an old question with a new twist.

The half-life of individual mRNA plays a central role in controlling the level of gene expression. However, the determinants of mRNA stability have not yet been well defined. Most previous studies suggest that mRNA length does not affect its stability. Here, we show significant negative correlations between mRNA length and stability in human and Escherichia coli, but not in Saccharomyces cerevisiae or Bacillus subtilis. This finding suggests the possibility that endonucleolytic attacks by RNA endonuclease and/or mechanical damage may strongly influence mRNA stability in both prokaryotes and eukaryotes.

Bacillus subtilis↗

PubMed2006

Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry.

Intramembrane proteolysis regulates diverse biological processes. Cleavage of substrate peptide bonds within the membrane bilayer is catalyzed by integral membrane proteases. Here we report the crystal structure of the transmembrane core domain of GlpG, a rhomboid-family intramembrane serine protease from Escherichia coli. The protein contains six transmembrane helices, with the catalytic Ser201 located at the N terminus of helix alpha4 approximately 10 A below the membrane surface. Access to water molecules is provided by a central cavity that opens to the extracellular region and converges on Ser201. One of the two GlpG molecules in the asymmetric unit has an open conformation at the active site, with the transmembrane helix alpha5 bent away from the rest of the molecule. Structural analysis suggests that substrate entry to the active site is probably gated by the movement of helix alpha5.

Amino Acid Sequence↗

PubMed2006

Requirement for Bhlhb5 in the specification of amacrine and cone bipolar subtypes in mouse retina.

The mammalian retina comprises six major neuronal cell types and one glial type that are further classified into multiple subtypes based on their anatomical and functional differences. Nevertheless, how these subtypes arise remains largely unknown at the molecular level. Here, we demonstrate that the expression of Bhlhb5, a bHLH transcription factor of the Olig family, is tightly associated with the generation of selective GABAergic amacrine and Type 2 OFF-cone bipolar subtypes throughout retinogenesis. Targeted deletion of Bhlhb5 results in a significant reduction in the generation of these selective bipolar and amacrine subtypes. Furthermore, although a Bhlhb5-null mutation has no effect on the expression of bHLH-class retinogenic genes, Bhlhb5 expression overlaps with that of the pan-amacrine factor NeuroD and the expression of Bhlhb5 and NeuroD is negatively regulated by ganglion cell-competence factor Math5. Our results reveal that a bHLH transcription factor cascade is involved in regulating retinal cell differentiation and imply that Bhlhb5 functions downstream of retinogenic factors to specify bipolar and amacrine subtypes.

Amacrine Cells↗

PubMed2006

Structural basis of RNA-dependent recruitment of glutamine to the genetic code.

Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.

Acylation↗

PubMed2006

Expression of the basic helix-loop-factor Olig2 in the developing retina: Olig2 as a new marker for retinal progenitors and late-born cells.

In this study, we examined the spatiotemporal expression patterns of Olig2, a basic helix-loop-helix transcription factor, in the developing mouse retina. Expression of Olig2 was initially detected on embryonic day 12.5 (E12.5). The majority of Olig2-positive cells were identified as retinal progenitor cells throughout embryogenesis. During later embryonic stages, the number of Olig2-positive retinal progenitor cells increased, and Olig2-positive cells were confined only to the neuroblast layer (NBL). Olig2 expression was not observed in the ganglion cell layer (GCL) nor in the inner nuclear layer (INL) that contain the differentiated retinal cell types, indicating that Olig2 is not expressed in differentiated cells in prenatal retina. In later postnatal stages, Olig2 expression was retained in mature neurons and glial cells, namely retinal ganglion cells (RGCs), amacrine cells (ACs), horizontal cells, bipolar cells and Müller glial cells. Thus, Olig2 is an marker both for retinal progenitor cells during embryonic stages, and also for differentiated retinal subpopulations within the GCL and INL during postnatal stages.

Animals↗

PubMed2006

Psychiatric morbidity and acute hospitalization in elderly people.

BACKGROUND: Few studies have investigated the association of psychiatric morbidity with acute hospitalization risk in elderly people. METHOD: We examined this association using population-based data for 1092 older adults aged > or =60 years in Singapore, including subjects who reported at least one acute hospitalization from any medical condition(s) in the 12 months prior to interview (N = 136). Psychiatric morbid/comorbid disorders were diagnosed using the Geriatric Mental State examination. RESULTS: In a multivariate analysis, comorbid psychiatric disorders were independently associated with hospitalization [adjusted odds ratio 2.76, 95% confidence interval 1.20-6.33], after controlling for age, ethnicity, employment status, number of medical comorbidities, number of activities of daily living limitations, hearing and visual impairment, SF-12 Physical and Mental Component Summary scores, social, productive, fitness and health activities, and regular visits to health-care providers. Neither dementia diagnosis nor cognitive impairment measured by the Mini-mental State Examination was associated with increased hospitalization risk. CONCLUSION: Psychiatric morbidity in old age was significantly associated with increased hospitalization risk. This finding underlines the importance of treating psychiatric illness to reduce the risk of acute hospitalization in elderly patients.

Activities of Daily Living↗

PubMed2006

Acoustic backward-wave negative refractions in the second band of a sonic crystal.

Acoustic negative refractions with backward-wave (BW) effects were both theoretically and experimentally established in the second band of a two-dimensional (2D) triangular sonic crystal (SC). Intense Bragg scatterings result in the extreme deformation of the second band equifrequency surface (EFS) into two classes: one around the K point and the other around the point of the reduced Brillouin zone. The two classes can lead to BW negative refractions (BWNRs) but with reverse negative refraction dependences on frequencies and incident angles. Not only BWNR but BW positive refraction can be present at EFSs around the K point, so it is possible to enhance the resolution of acoustic waves with a subdiffraction limit regardless of refractions, which is no analogy in both left-handed material and SCs' first band. These abundant characters make refractions in the second band distinguished.

Journal Article↗

PubMed2006

[Solitary necrotic nodule of the liver].

Explore the source record for details and available documents.

Adenocarcinoma↗

PubMed2005

Structure of oxidized alpha-haemoglobin bound to AHSP reveals a protective mechanism for haem.

The synthesis of haemoglobin A (HbA) is exquisitely coordinated during erythrocyte development to prevent damaging effects from individual alpha- and beta-subunits. The alpha-haemoglobin-stabilizing protein (AHSP) binds alpha-haemoglobin (alphaHb), inhibits the ability of alphaHb to generate reactive oxygen species and prevents its precipitation on exposure to oxidant stress. The structure of AHSP bound to ferrous alphaHb is thought to represent a transitional complex through which alphaHb is converted to a non-reactive, hexacoordinate ferric form. Here we report the crystal structure of this ferric alphaHb-AHSP complex at 2.4 A resolution. Our findings reveal a striking bis-histidyl configuration in which both the proximal and the distal histidines coordinate the haem iron atom. To attain this unusual conformation, segments of alphaHb undergo drastic structural rearrangements, including the repositioning of several alpha-helices. Moreover, conversion to the ferric bis-histidine configuration strongly and specifically inhibits redox chemistry catalysis and haem loss from alphaHb. The observed structural changes, which impair the chemical reactivity of haem iron, explain how AHSP stabilizes alphaHb and prevents its damaging effects in cells.

Blood Proteins↗

PubMed2005

The fabrication and characterization of a formaldehyde odor sensor using molecularly imprinted polymers.

The fabrication and characterization of odor sensors based on molecularly imprinted polymers is reported as the first case of imprinting formaldehyde. A quartz crystal microbalance is employed as a sensitive apparatus of a sensor for the determination of odor formaldehyde. An equation is deduced to characterize the interaction between molecularly imprinted films and the template. A linear relationship between the frequency shifts and the concentration of analyte in the range of 1.25 to 14.25 microM is found. The detection limit is about 20.5 microM. The sensor can selectively distinguish gaseous formaldehyde. It is envisaged that this novel and handy method could be employed to determine formaldehyde gas in the atmosphere.

Air Pollution↗

PubMed2005

Aspartyl-tRNA synthetase requires a conserved proline in the anticodon-binding loop for tRNA(Asn) recognition in vivo.

Most prokaryotes require Asp-tRNA(Asn) for the synthesis of Asn-tRNA(Asn). This misacylated tRNA species is synthesized by a non-discriminating aspartyl-tRNA synthetase (AspRS) that acylates both tRNA(Asp) and tRNA(Asn) with aspartate. In contrast, a discriminating AspRS forms only Asp-tRNA(Asp). Here we show that a conserved proline (position 77) in the L1 loop of the non-discriminating Deinococcus radiodurans AspRS2 is required for tRNA(Asn) recognition in vivo. Escherichia coli trpA34 was transformed with DNA from a library of D. radiodurans aspS2 genes with a randomized codon 77 and then subjected to in vivo selection for Asp-tRNA(Asn) formation by growth in minimal medium. Only proline codons were found at position 77 in the aspS2 genes isolated from 21 of the resulting viable colonies. However, when the aspS temperature-sensitive E. coli strain CS89 was transformed with the same DNA library and then screened for Asp-tRNA(Asp) formation in vivo by growth at the non-permissive temperature, codons for seven other amino acids besides proline were identified at position 77 in the isolates examined. Thus, replacement of proline 77 by cysteine, isoleucine, leucine, lysine, phenylalanine, serine, or valine resulted in mutant D. radiodurans AspRS2 enzymes still capable of forming Asp-tRNA(Asp) but unable to recognize tRNA(Asn). This strongly suggests that proline 77 is responsible for the non-discriminatory tRNA recognition properties of this enzyme.

Acylation↗

PubMed2005

Functional equivalence of Brn3 POU-domain transcription factors in mouse retinal neurogenesis.

POU-domain transcription factors play essential roles in cell proliferation and differentiation. Previous studies have shown that targeted deletion of each of the three POU-domain Brn3 factors in mice leads to the developmental failure and apoptosis of a unique set of sensory neurons in retina, dorsal root ganglia, trigeminal ganglia and inner ear. The specific defects associated with the removal of each Brn3 gene closely reflect their characteristic spatiotemporal expression patterns. Nevertheless, it remains elusive whether Brn3 factors are functionally equivalent and act through a common molecular mechanism to regulate the development and survival of these sensory neurons. By knocking-in Brn3a (Brn3aki) into the Brn3b locus, we showed here that Brn3aki was expressed in a spatiotemporal manner identical to that of endogenous Brn3b. In addition, Brn3aki functionally restored the normal development and survival of retinal ganglion cells (RGCs) in the absence of Brn3b and fully reinstated the early developmental expression profiles of Brn3b downstream target genes in retina. These results indicate that Brn3 factors are functionally equal and that their unique roles in neurogenesis are determined by the distinctive Brn3 spatiotemporal expression patterns.

Animals↗

PubMed2005

Epidemiological survey of Tourette syndrome in children and adolescents in Wenzhou of P.R. China.

An epidemiological survey on Tourette syndrome (TS) in a developing country is relatively scarce. This study was conducted to investigate the prevalence and distribution of TS in children and juveniles aged 7-16 years in Wenzhou of P.R. China. A total of 9742 children and adolescents were included in this survey. Cross-sectional study with stratified-cluster sampling method was used. The prevalence of TS among school-age children was estimated to be an average of 0.43%. The ratio of male to female was 10.6 to 1 (0.74% for males and 0.07% for females). Pupils in the age range of 7-16 years are more likely to have comorbid disorders. The mean age at onset of TS was 7.7+/-2.7 years, with 45.2% of them at the age of 6-7. The rate of delayed diagnosis, misdiagnosis and misclassification of the syndrome were 78.6, 42.9 and 23.8%, respectively. This survey supports that TS is a common disease prevalent amongst children and juveniles in Wenzhou area of P.R. China, and its incidence was correlated with age and sex and often misdiagnosed and misclassified.

Adolescent↗

PubMed2005

Simple bioseparations using self-cleaving elastin-like polypeptide tags.

We introduce a new method for the purification of recombinant proteins expressed in Escherichia coli using self-cleaving elastin-like polypeptide (ELP) fusion tags without the need for affinity chromatography or proteolytic tag removal. Using this method we obtained high purity, activity and reasonable yields for ten diverse target proteins.

Chemical Fractionation↗

PubMed2005

Role of alpha-hemoglobin-stabilizing protein in normal erythropoiesis and beta-thalassemia.

Hemoglobin (Hb) synthesis is coordinated by homeostatic mechanisms to limit the accumulation of free alpha or beta subunits, which are cytotoxic. Alpha hemoglobin-stabilizing protein (AHSP) is an abundant erythroid protein that specifically binds free alphaHb, stabilizes its structure, and limits its ability to participate in chemical reactions that generate reactive oxygen species. Gene ablation studies in mice demonstrate that AHSP is required for normal erythropoiesis. AHSP-null erythrocytes are short-lived, contain Hb precipitates, and exhibit signs of oxidative damage. Loss of AHSP exacerbates beta-thalassemia in mice, indicating that altered AHSP expression or function could modify thalassemia phenotypes in humans, a topic that is beginning to be explored in clinical studies. We used biochemical, spectroscopic, and crystallographic methods to examine how AHSP stabilizes alphaHb. AHSP binds the G and H helices of alphaHb on a surface that largely overlaps with the alpha1-beta1 interface of HbA. This result explains previous findings that betaHb can competitively displace AHSP from alphaHb to form HbA tetramer. Remarkably, binding of AHSP to oxygenated alphaHb induces dramatic conformational changes and converts the heme-bound iron to an oxidized hemichrome state in which all six coordinate positions are occupied. This structure limits the reactivity of heme iron, providing a mechanism by which AHSP stabilizes alphaHb. These findings suggest a biochemical pathway through which AHSP might participate in normal Hb synthesis and modulate the severity of thalassemias. Moreover, understanding how AHSP stabilizes alphaHb provides a theoretical basis for new strategies to inhibit the damaging effects of free alphaHb that accumulates in beta-thalassemia.

Animals↗

PubMed2004

Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.

Gln-tRNA(Gln) is synthesized from Glu-tRNA(Gln) in most microorganisms by a tRNA-dependent amidotransferase in a reaction requiring ATP and an amide donor such as glutamine. GatDE is a heterodimeric amidotransferase that is ubiquitous in Archaea. GatD resembles bacterial asparaginases and is expected to function in amide donor hydrolysis. We show here that Methanothermobacter thermautotrophicus GatD acts as a glutaminase but only in the presence of both Glu-tRNA(Gln) and the other subunit, GatE. The fact that only Glu-tRNA(Gln) but not tRNA(Gln) could activate the glutaminase activity of GatD suggests that glutamine hydrolysis is coupled tightly to transamidation. M. thermautotrophicus GatDE enzymes that were mutated in GatD at each of the four critical asparaginase-active site residues lost the ability to hydrolyze glutamine and were unable to convert Glu-tRNA(Gln) to Gln-tRNA(Gln) when glutamine was the amide donor. However, ammonium chloride rescued the activities of these mutants, suggesting that the integrity of the ATPase and the transferase activities in the mutant GatDE enzymes was maintained. In addition, pyroglutamyl-tRNA(Gln) accumulated during the reaction catalyzed by the glutaminase-deficient mutants or by GatE alone. The pyroglutamyl-tRNA is most likely a cyclized by-product derived from gamma-phosphoryl-Glu-tRNA(Gln), the proposed high energy intermediate in Glu-tRNA(Gln) transamidation. That GatE alone could form the intermediate indicates that GatE is a Glu-tRNA(Gln) kinase. The activation of Glu-tRNA(Gln) via gamma-phosphorylation bears a similarity to the mechanism used by glutamine synthetase, which may point to an ancient link between glutamine synthesized for metabolism and translation.

Adenosine Triphosphate↗