A simple method for quantification of interferon- &alfa;2b through surface plasmon resonance technique

A rapid and efficient immunoassay method for quantification of interferon-2b using surface plasmon resonance was developed with BIAcore 3000 as a sensor. Two different levels of anti-interferon monoclonal antibody were immobilized onto a CM5 chip using an amine coupling method. Similarbinding ratio was observed for both the ligand densities. There was no steric hindrance and loss of antibody activity even at higher ligand density (> 22,000 RU). The sensitivity of the assay was increased up to 45% with the increment in ligand density from 15,400 to 22,360 RU. The binding betweeninterferon-2b and anti-interferon monoclonal antibody was predominantly controlled by mass transfer rate and the relationship was found linear, ranged from 5 to 400 ng/mL. Total cycle time per analysis was less than 8 min and required only 5 L of sample injection

Production and optimization of alkalostable lipase by alkalophilic Burkholderia cenocepacia ST8

A superior lipase-producing bacterium was isolated from forest soil samples in Setapak, Malaysia and it was identified as Burkholderia cenocepacia with 16S rRNA sequencing technique. Multifactor experimental design based on ‘change-one-factor-at-a-time’ approach was employed to optimize the production of Bukholderia lipase with submerged fermentation technique. Effects of carbon and nitrogen sources, metal ions as well as initial pH of medium on lipase production were extensively investigated. Optimal lipase activity was achieved in medium using combination of sunflower oil and Tween 80 (1% v/v each) as carbon sources. Simple sugars such as glucose and fructose, however, did not promote the production of lipase. Peptone (from meat) at 0.33% (w/v) was the most suitable nitrogen source for lipase production by this Gram-negative bacterium. The presence of Ca2+ in the cultivation medium possessed significant effect on lipase production while Mg2+, Mn2+, Na+, Fe2+, Cu2+ and Co2+ exhibited inhibitory effect towards the enzyme production. Initial culture pH in the range of 5 to 11 were found suitable for lipase production, with the maximum level of lipase activity recorded in the medium with initial culture pH of 9.0.Key words: Alkalostable lipase, alkalophilic Burkholderia cenocepacia, optimization, multifactor experimental design

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

biological space

EL2 deep donor state in semi-insulating GaAs revealed by frequency dependent positron mobility measurements

Positron mobility measurements carried out on semi-insulating GaAs, using the Doppler shift in annihilation radiation technique, show a sharp transition from a high mobility value ∼120 cm2 V-1 s-1 to a lower value ∼45 V-1 s-1 just below room temperature. The temperature of the transition is found to be dependent on the frequency of the applied AC bias. We show that this effect is an artifact due to the thermal ionization of the EL2 deep donor state, which in its ionized state forms a positive space charge that causes the positron to experience large electric fields. This observation suggests a new positron annihilation-based deep-level transient technique applicable to semi-insulating materials. © 1994 The American Physical Society.published_or_final_versio

Application of a high density adsorbent in expanded bed adsorption of lipase from Burkholderia pseudomallei

The application of STREAMLINE Direct HST adsorbent in expanded bed adsorption of lipase from Burkholderia pseudomallei was explored in this study. Scouting of optimum binding and elution condition was performed in batch binding mode. The addition of 0.2 M salt in acetate buffer (pH 5)during adsorption has increased the specificity and quantity of lipase binding onto the adsorbent. The addition of 0.4 M salt in phosphate buffer (pH 7) achieved the highest purification fold (2.5) in elution. The high density of the adsorbent allowed the EBA to be operated at linear velocity as high as 657 cm/h with feedstock containing 4.5% (w/v) wet biomass. The Richardson-Zaki correlation obtained for this EBA system at the presence of 4.5% (w/v) wet biomass is 5.14, a value closed to the laminar flow regime of 4.8, demonstrated that a stable bed is achieved under this operating condition. Meanwhile, a flow velocity of 343 cm/h with bed expansion of 3.2 gave highest dynamic binding capacity (4979.28 U/ml)and productivity (61.52 U/ml.min) for this EBA operation. It also demonstrated that biomass concentration up to 4.5% (w/v) wet weight showed slightly drop of sorption efficiency (0.82) compared to lower biomass concentration (0.94). Further increase of biomass concentration above 4.5% (w/v) wet weight has greatly decreased the equilibrium and dynamic capacity. Application of high density adsorbent tolerated to high density and biomass has reduced the processing time and increased theproductivity

Effect of promoter strength and signal sequence on the periplasmic expression of human interferon- &#9452b in Escherichia coli

Two plasmids, pFLAG-ATS and pET 26b(+), were studied for the periplasmic expression of recombinant human interferon-2b (IFN-2b) in Escherichia coli. The pFLAG-ATS contains ompA signal sequence and tac promoter while pET 26b(+) contains pelB signal sequence and T7lac promoter. It was observedthat periplasmic expression of IFN-2b from pET 26b(+) was around 3000 times higher than pFLAGATS. Difference in the expression level was attributed to the difference in the promoters and the signal sequences. In silico analysis of mRNA secondary structures were analyzed using Vienna RNA packageand MFOLD. The results suggested that the increase of expression would mainly due to the difference in the translation initiation associated with secondary structure of mRNA transcribed by both plasmids

Outcome of index upper gastrointestinal endoscopy in patients presenting with dysphagia in a tertiary care hospital-A 10 years review

<p>Abstract</p> <p>Background</p> <p>Patients with malignant tumours of the upper gastrointestinal tract tumours exhibit important alarm symptoms such as dysphagia that warrant clinical investigations. An endoscopic examination of the upper gastrointestinal tract will be required in most cases. This study evaluates the diagnostic potential of index endoscopy in a random population of patients with dysphagia.</p> <p>Methods</p> <p>This is a retrospective analysis of prospectively collected data over 10 years. Patients with previous endoscopic evaluation or upper gastrointestinal pathology were excluded from the study. Data was analysed to see the number and frequency of abnormal findings in upper gastrointestinal tract, and their significance in relation to the presenting symptoms.</p> <p>Results</p> <p>Total number of index endoscopies was 13, 881. 913 patients were included in the study including 465 males (age range: 17–92 years, median: 55 years) and 448 females (age range: 18–100, median: 59 years), with male to female ratio of 1.04: 1. Oesophagus was abnormal in 678 cases (74%) and biopsies were taken in 428 patients (47%). Superficial oesophagitis, Barrett's oesophagus, oesophageal cancer, and oesophageal ulcer were main histological findings. Age more than 50 years and weight loss were significant predictors of oesophageal cancer (p < 0.0001). Male gender, heartburn, epigastric pain, weight loss and vomiting were significantly related to Barrett's oesophagus. A total of 486 gastric and 56 duodenal biopsies were also taken. There were 20 cases of gastric adenocarcinoma.</p> <p>Conclusion</p> <p>OGD is an effective initial investigation to assess patients with dysphagia, especially males above the age of 50 years. Patients may be started on treatment or referred for further investigations, for example, a barium meal in the absence of any anatomical abnormality.</p

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization

Structure and mechanism of human DNA polymerase η

The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase eta (Pol eta), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol eta at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol eta acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol eta orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Pol eta missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol eta in replicating through D loop and DNA fragile sites