Correction to: ThalPred: a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia.

Following publication of the original article [1], the authors reported an error in one of the authors' names. In this Correction the incorrect and correct author name are shown. The original publication of this article has been corrected.

ThalPred: a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia.

BACKGROUND: The hypochromic microcytic anemia (HMA) commonly found in Thailand are iron deficiency anemia (IDA) and thalassemia trait (TT). Accurate discrimination between IDA and TT is an important issue and better methods are urgently needed. Although considerable RBC formulas and indices with various optimal cut-off values have been developed, distinguishing between IDA and TT is still a challenging problem due to the diversity of various anemic populations. To address this problem, it is desirable to develop an improved and automated prediction model for discriminating IDA from TT. METHODS: We retrospectively collected laboratory data of HMA found in Thai adults. Five machine learnings, including k-nearest neighbor (k-NN), decision tree, random forest (RF), artificial neural network (ANN) and support vector machine (SVM), were applied to construct a discriminant model. Performance was assessed and compared with thirteen existing discriminant formulas and indices. RESULTS: The data of 186 patients (146 patients with TT and 40 with IDA) were enrolled. The interpretable rules derived from the RF model were proposed to demonstrate the combination of RBC indices for discriminating IDA from TT. A web-based tool 'ThalPred' was implemented using an SVM model based on seven RBC parameters. ThalPred achieved prediction results with an external accuracy, MCC and AUC of 95.59, 0.87 and 0.98, respectively. CONCLUSION: ThalPred and an interpretable rule were provided for distinguishing IDA from TT. For the convenience of health care team experimental scientists, a web-based tool has been established at http://codes.bio/thalpred/ by which users can easily get their desired screening test result without the need to go through the underlying mathematical and computational details.

Large-scale classification of P-glycoprotein inhibitors using SMILES-based descriptors.

P-glycoprotein (Pgp) inhibition has been considered as an effective strategy towards combating multidrug-resistant cancers. Owing to the substrate promiscuity of Pgp, the classification of its interacting ligands is not an easy task and is an ongoing issue of debate. Chemical structures can be represented by the simplified molecular input line entry system (SMILES) in the form of linear string of symbols. In this study, the SMILES notations of 2254 Pgp inhibitors including 1341 active, and 913 inactive compounds were used for the construction of a SMILE-based classification model using CORrelation And Logic (CORAL) software. The model provided an acceptable predictive performance as observed from statistical parameters consisting of accuracy, sensitivity and specificity that afforded values greater than 70% and MCC value greater than 0.6 for training, calibration and validation sets. In addition, the CORAL method highlighted chemical features that may contribute to increased and decreased Pgp inhibitory activities. This study highlights the potential of CORAL software for rapid screening of prospective compounds from a large chemical space and provides information that could aid in the design and development of potential Pgp inhibitors.

Revelation of staphylococcal cassette chromosome mec types in methicillin-resistant Staphylococcus aureus isolates from Thailand and Vietnam.

Methicillin resistant Staphylococcus aureus (MRSA) is highly prevalent, and its typing plays a crucial role in epidemiology and evolution in both health and community settings. Multiplex PCR and staphylococcal cassette chromosome mec (SCCmec) typing based on mec complexes and cassette chromosome recombinase (ccr) allotypes have been developed for MRSA identification. The first of these procedures can identify 4 mec classes (A, B, C1, and E) and 2 ccr allotypes (B2 and B4) in one tube, and the second can identify mecA, mec class C2, and 3 allotypes (A1, A3, and C). Our method offers a novel means to further differentiate between the main SCCmec types I through XI and is both highly sensitive (detectable up to 0.3ηg DNA) and specific (100%). Several SCCmec types (I, III, IV, V and a non-typeable group) were found in 66 MRSA isolates obtained from Ho Chi Minh City, Vietnam and Nakhon Pathom, Thailand. SCCmec type III was highly predominant in both regions. The designed assay is rapid, convenient, flexible, and reliable. Therefore, this assay is suitable for the high-throughput screening of the main SCCmec types of MRSA isolates.

Lipid-membrane affinity of chimeric metal-binding green fluorescent protein.

The Green Fluorescent Protein (GFP) is a useful marker to trace the expression of cellular proteins. However, little is known about changes in protein interaction properties after fusion to GFP. In this study, we present evidence for a binding affinity of chimeric cadmium-binding green fluorescent proteins to lipid membrane. This affinity has been observed in both cellular membranes and artificial lipid monolayers and bilayers. At the cellular level, the presence of Cd-binding peptide promoted the association of the chimeric GFP onto the lipid membrane, which declined the fluorescence emission of the engineered cells. Binding affinity to lipid membranes was further investigated using artificial lipid bilayers and monolayers. Small amounts of the chimeric GFP were found to incorporate into the lipid vesicles due to the high surface pressure of bilayer lipids. At low interfacial pressure of the lipid monolayer, incorporation of the chimeric Cd-binding GFP onto the lipid monolayer was revealed. From the measured lipid isotherms, we conclude that Cd-binding GFP mediates an increase in membrane fluidity and an expansion of the surface area of the lipid film. This evidence was strongly supported by epifluorescence microscopy, showing that the chimeric Cd-binding GFP preferentially binds to fluid-phase areas and defect parts of the lipid monolayer. All these findings demonstrate the hydrophobicity of the GFP constructs is mainly influenced by the fusion partner. Thus, the example of a metal-binding unit used here shines new light on the biophysical properties of GFP constructs.

Purification and characterization of a beta-lactamase from Haemophilus ducreyi in Escherichia coli.

A pCb plasmid encoding a beta-lactamase from Haemophilus ducreyi was transferred to Escherichia coli, purified, and characterized. The beta-lactamase could be isolated from a culture filtrate and further purified by ammonium sulfate and chelating Sepharose fast flow loaded with Zn(2+). The purified enzyme resulted in a major band at approximately 30-kDa on SDS-PAGE and its pI was determined to be 5.4. The beta-lactamase could hydrolyze both penicillin antibiotics including ampicillin, benzylpenicillin, and carbenicillin as well as cephalosporin antibiotics including nitrocefin, cephalothin, cephaloridine, and cefoperazone. However, benzylpenicillin was the best substrate. The enzyme activity was inhibited by clavulanic acid but not by boric acid, cefotaxime, ethylenediaminetetraacetic acid, or phenylmethylsulfonyl fluoride. The sequence of the beta-lactamase gene was also determined. It confirmed that the enzyme belonged to a class A beta-lactamase which had 99% identity to the ampicillin resistance transposon Tn3 of pBR322. Two nucleotides were different between the E. coli (Tn3) and H. ducreyi (pCb) genes that affected the amino-acid sequence. The valine at position 82 (ABL 84) was changed to isoleucine and the alanine at position 182 (ABL 184) was changed to valine. Genetic homogeneity among beta-lactamases is remarkable. Amino acid sequencing of some beta-lactamases has shown that substitution of only a few amino acids in the bla gene leads to high-level resistance against specific cephalosporins.

TPA-activated transcription of the human MnSOD gene: role of transcription factors Sp-1 and Egr-1.

Induction of manganese superoxide dismutase (MnSOD) in response to oxidative stress has been well established in animals, tissues, and cell culture. However, the role of the human MnSOD (hMnSOD) promoter in stimulus-dependent activation of transcription is unknown. The hMnSOD promoter lacks both a TATA and a CAAT box but possesses several GC motifs. In a previous study, we showed that the basal promoter contains multiple Sp1 and AP-2 binding sites and that Sp1 is essential for the constitutive expression of the hMnSOD gene. In this study, we identified an Egr-1 binding site in the basal promoter of hMnSOD. We also found that the basal promoter is responsive to 12-O-tetradecanoylphorbol-13-acetate (TPA)-activated hMnSOD transcription in the human hepatocarcinoma cell line HepG2. The contributions of these binding sites and the roles of the transcription factors Egr-1, AP-2, and Sp1 in the activation of hMnSOD transcription by TPA were investigated by site-directed mutation analysis, Western blotting, and overexpression of transcription factors. The results showed that Sp1 plays a positive role for both basal and TPA-activated hMnSOD transcription, whereas overexpression of Egr-1 has a negative role in the basal promoter activity without any effect on TPA-mediated activation of hMnSOD transcription.

Calorimetric analysis of cephalosporins using an immobilized TEM-1 beta-lactamase on Ni2+ chelating sepharose fast flow.

Two beta-lactamases, penicillinase type I from Bacillus cereus and TEM-1 beta-lactamase from Haemophilus ducreyi, were immobilized on a Chelating Sepharose Fast Flow column loaded with Ni2+ in an active form. Flow-injection analysis of beta-lactams was performed by using an enzyme column reactor fitted into the enzyme thermistor. With both enzymes it was possible to monitor both penicillins and cephalosporins. Moreover, Michaelis constants of the TEM-1 beta-lactamase were markedly increased upon immobilization for all substrates, especially carbenicillin, cephaloridine, and cefoperazone.

Episome profiles and mobilizable beta-lactamase plasmid in Haemophilus ducreyi.

Chancroid caused by Haemophilus ducreyi has been described as a significantly predisposing factor of HIV heterosexual transmission in an endemic region of both diseases. The fastidious, H. ducreyi has been reported world wide with various antimicrobial susceptibility patterns. A high tendency of drug resistances has generally been found among isolates derived in Thailand. In this study, the plasmids of H. ducreyi were isolated and analysed from 63 clinically derived organisms. Twenty-nine out of 63 isolates (46%) revealed the same plasmid profiles. Plasmid DNA was further cloned into Escherichia coli and transformants were selected. A 3.6 kb plasmid (pCb) carrying ampicillin resistance was subsequently identified. The pCb conferred resistance to various beta-lactam antibiotics including penicillin G, carbenicillin, piperacillin, cefazolin, cefoperazone, ampicillin-sulbactam, and amoxicillin-clavulanate but not to cefoxitin. Co-resistance to streptomycin, chloramphenicol and tetracycline was not detected. Beta-lactamase gene was located on the major pCb fragment of EcoRI and AatII cutting.

Constituents and bioactivity of the tubers of Euphorbia sessiliflora.

The diterpene ent-12-hydroxy-12[R]-abieta-8(14),13(15)-dien-16,12-olide was isolated from the tubers of Euphorbia sessiliflora Roxb., together with four known ent-abietadienolides, four known cycloartane triterpenes and ellagic acid-beta-D-glucopyranoside. Two of these metabolates displayed moderate antibacterial activities.

Zinc ions bound to chimeric His4/lactate dehydrogenase facilitate decarboxylation of oxaloacetate.

A chemically synthesized DNA linker coding for a peptide fragment that contains four histidines was fused in-frame to the 5'-end of the Bacillus stearothermophilus lactate dehydrogenase gene. The gene product, His4/lactate dehydrogenase, could be purified to homogeneity using either immobilized metal (Zn2+)-affinity chromatography or affinity chromatography on oxamate agarose. The stability against heat and urea for the modified enzymes was decreased as compared to the native lactate dehydrogenase but could be increased if zinc ions were present during the denaturation. In the presence of zinc ions the His4/lactate dehydrogenase could catalyse the sequential reaction from oxaloacetate to L-lactate, hence operating as a semi-synthetic bifunctional enzyme. A small increase in the apparent second-order rate constant (kcat/Km) of the coupled reaction was observed as compared to a corresponding system with native lactate dehydrogenase.

Isolation and characterization of RNA of Entamoeba histolytica.

RNAs were isolated from Entamoeba histolytica with a high salt sodium dodecylsulfate-diethylpyrocarbonate technique. Majority species of 25 S, 17 S and 4 S RNAs were detected after sucrose gradient centrifugation. An additional 5 S RNA was detected by polyacrylamide gel electrophoresis. The molecular weights of these RNAs as determined by completely denaturing polyacrylamide gel electrophoresis were 1.31 X 10(6) (25 S), 0.803 X 10(6) (17 S), 4.0 X 10(4) (5 S) and 2.5 X 10(4) (4 S). The 25 S RNA was labile and dissociated under mild denaturing conditions (between 37 degrees C and 55 degrees C) into 17 S and 16 S RNAs with molecular weights of 0.700 X 10(6) and 0.614 X 10(6), respectively; under completely denaturing conditions an additional 5.8 S RNA with a molecular weight of 4.8 X 10(4) was detected. Evidence is presented which suggests that the lability of the 25 S RNA is the result of an in vivo cleavage rather than one which is generated during RNA isolation.