Airborne bacterial assemblage in a zero carbon building: A case study.

Currently, there is little information pertaining to the airborne bacterial communities of green buildings. In this case study, the air bacterial community of a zero carbon building (ZCB) in Hong Kong was characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment dominated the indoor airborne bacterial assemblage, with a modest contribution from bacteria associated with human skin. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties were detected, which may have been driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighted UniFrac distances) differed depending on the season and sampling location. A Bayesian source-tracking approach further supported the importance of adjacent outdoor air bacterial assemblage in sourcing the ZCB indoor bioaerosol. Despite the unique building attributes, the ZCB microbial assemblage detected and its temporal characteristics were not dissimilar to that of conventional built environments investigated previously. Future controlled experiments and microbial assemblage investigations of other ZCBs will undoubtedly uncover additional knowledge related to how airborne bacteria in green buildings may be influenced by their distinctive architectural attributes.

In silico prediction of the granzyme B degradome.

BACKGROUND: Granzyme B is a serine protease which cleaves at unique tetrapeptide sequences. It is involved in several signaling cross-talks with caspases and functions as a pivotal mediator in a broad range of cellular processes such as apoptosis and inflammation. The granzyme B degradome constitutes proteins from a myriad of functional classes with many more expected to be discovered. However, the experimental discovery and validation of bona fide granzyme B substrates require time consuming and laborious efforts. As such, computational methods for the prediction of substrates would be immensely helpful. RESULTS: We have compiled a dataset of 580 experimentally verified granzyme B cleavage sites and found distinctive patterns of residue conservation and position-specific residue propensities which could be useful for in silico prediction using machine learning algorithms. We trained a series of support vector machines (SVM) classifiers employing Bayes Feature Extraction to predict cleavage sites using sequence windows of diverse lengths and compositions. The SVM classifiers achieved accuracy and AROC scores between 71.00% to 86.50% and 0.78 to 0.94 respectively on independent test sets. We have applied our prediction method on the Chikungunya viral proteome and identified several regulatory domains of viral proteins to be potential sites of granzyme B cleavage, suggesting direct antiviral activity of granzyme B during host-viral innate immune responses. CONCLUSIONS: We have compiled a comprehensive dataset of granzyme B cleavage sites and developed an accurate SVM-based prediction method utilizing Bayes Feature Extraction to identify novel substrates of granzyme B in silico. The prediction server is available online, together with reference datasets and supplementary materials.

Lacrimal drainage obstruction and dacryocystorhinostomy in children.

PURPOSE: To determine the outcome of dacryocystorhinostomy (DCR) for nasolacrimal duct obstruction (NLDO) in children. METHODS: A review of medical records of 104 cases (82 patients) of paediatric DCR who underwent DCR at the Sydney Eye Hospital from 1995 to 2004. The main outcome measures included post-operative symptomatic relief of presenting symptoms, complications, subjective visibility of any scar, and general satisfaction. Statistical methods included chi(2) tests, and Student's t-tests for the comparison of variables among groups. RESULTS: Ninety-four external, 10 endoscopic primary procedures, and five revision procedures were included. Fifty-six of the cases were primary NLDO, and 48 were secondary NLDO. The mean follow-up was 1.44 years. Average age at surgery was 6.6+/-4.2 years (mean+/-SD). Ninety-one eyes needed DCR for the involvement of the lower lacrimal outflow system, and 13 eyes were NLDO associated with congenital punctual/canalicular dysgenesis.Most of the complications of external DCR were related to Jones tube placement. Five cases (4.8%) needed DCR revision. There was a significantly higher incidence of revision surgery in the non-stented group (P<0.01), and the Jones tube group (P<0.001) as compared with the silicone intubation stent group. CONCLUSIONS: External DCRs have acceptable long-term clinical and cosmetic results, and low post-operative complication rate. Cases with punctal stenosis or those requiring Jones tube insertion are associated with a higher complication rate. Silicone intubation is associated with a lower need for operative revision.

Conformational epitopes on the diabetes autoantigen GAD65 identified by peptide phage display and molecular modeling.

The major diabetes autoantigen, glutamic acid decarboxylase (GAD65), contains a region of sequence similarity, including six identical residues PEVKEK, to the P2C protein of coxsackie B virus, suggesting that cross-reactivity between coxsackie B virus and GAD65 can initiate autoimmune diabetes. We used the human islet cell mAbs MICA3 and MICA4 to identify the Ab epitopes of GAD65 by screening phage-displayed random peptide libraries. The identified peptide sequences could be mapped to a homology model of the pyridoxal phosphate (PLP) binding domain of GAD65. For MICA3, a surface loop containing the sequence PEVKEK and two adjacent exposed helixes were identified in the PLP binding domain as well as a region of the C terminus of GAD65 that has previously been identified as critical for MICA3 binding. To confirm that the loop containing the PEVKEK sequence contributes to the MICA3 epitope, this loop was deleted by mutagenesis. This reduced binding of MICA3 by 70%. Peptide sequences selected using MICA4 were rich in basic or hydroxyl-containing amino acids, and the surface of the GAD65 PLP-binding domain surrounding Lys358, which is known to be critical for MICA4 binding, was likewise rich in these amino acids. Also, the two phage most reactive with MICA4 encoded the motif VALxG, and the reverse of this sequence, LAV, was located in this same region. Thus, we have defined the MICA3 and MICA4 epitopes on GAD65 using the combination of phage display, molecular modeling, and mutagenesis and have provided compelling evidence for the involvement of the PEVKEK loop in the MICA3 epitope.

V92A mutation altered the folding propensity of chicken apocytochrome c and its interaction with phospholipids.

Chicken apocytochrome c has been shown to possess a much stronger tendency to fold spontaneously in aqueous solution than the equivalent enzyme from other species. In the present work, the amino acid that determines its folding ability was elucidated by site-directed mutagenesis. Wild-type chicken apocytochrome c and three mutants V92A, S103A, and V92A/S103A were expressed in Escherichia coli. The wild-type apoprotein and S103A exhibited the same folding property during dialysis renaturation processes as that chemically prepared from chicken cytochrome c, while those containing V92A mutation did not. Quantitative studies by 2,2,2-trifluoroethanol (TFE) and sodium perchlorate (NaClO4) titration demonstrated that the V92A mutation decreased the helix content that could be induced and confirmed that valine 92 is the major determinant of the folding propensity of chicken apocytochrome c. Furthermore, CD spectra, turbidity measurements, and a translocation assay on a model membrane system showed that the V92A mutation also drastically altered the conformation of apocytochrome c after being incorporated into lipid bilayer and decreased the aggregation of phospholipid vesicles after association of the apoprotein, thus rendering the molecule more competent for translocation across the membrane. Our results showed that a single amino acid substitution could radically alter the folding propensity of an unfolded polypeptide chain and thus influence the conformation following its insertion into phospholipid bilayer.

Hydrophobic interaction and folding propensity of chicken heart apocytochrome c.

In contrast to horse heart apocytochrome c, the chicken one showed quite different folding propensity as titrated by NaCl at different pH. At pH 2.0, folding behaviour of both apocytochrome c are essentially similar; while at pH higher than 4.0, chicken heart apocytochrome c has much enhanced propensity to fold and aggregate, as was shown by circular dichroism spectra, intrinsic fluorescence and non-denatured polyacrylamide gel electrophoresis. Hydrophobic chromatography demonstrated much higher hydrophobicity of chicken heart apocytochrome c, thus strongly suggested that it is the hydrophobic interaction that stabilize the 'Molten Globule' like, partially-folded structure of chicken heart apocytochrome c at neutral pH.

Cloning and high-level expression of chicken apocytochrome c gene in Escherichia coli.

Chicken apocytochrome c gene with correct reading frame was easily cloned through excision by polymerase chain reaction of the intron in the genomic clone of chicken cytochrome c gene, and was successfully overexpressed in Escherichia coli by cloning into expression vector pET-3d under the control of T7 promoter. Expressed protein can amount to as high as 40% of the total protein and mainly presents as inclusion body. Purification of chicken apocytochrome c from the inclusion body and characterization by SDS-PAGE, isoelectric focusing electrophoresis, and amino acid analysis showed that the purified apocytochrome c is identical to that prepared from chicken heart cytochrome c by chemically depletion of heme.

Correlation between unfolded states of apocytochrome c and its ability to pass lipid bilayer.

In contrast to the horse heart apocytochrome c, the chicken heart apocytochrome c underwent a conformational change from random coil to partial folding during a renaturation process. When the apocytochrome horse heart and that of chicken heart c were subjected to a translocation assay in vitro using large trypsin-enclosed unilamellar vesicles from soybean phospholipids, the ability of the chicken heart apocytochrome c to penetrate into the liposomes was found to decrease markedly with the renaturation procedure, while that of horse heart apocytochrome c remained relatively constant. Observations from circular dichroism measurement on the induction of secondary folding of these two species of apocytochrome c upon interaction with soybean phospholipid vesicles suggested that a more flexible structure of apocytochrome c embedded in the lipid matrix be required for its efficient translocation across the bilayer.

Study on the translocation of chicken heart apocytochrome C with different unfolded states.

Chemically-prepared chicken heart apocytochrome c with different unfolded states could be obtained during the renaturation process. They exhibited distinct circular dichroism patterns designated as Apo C1 (random coiled), Apo C2 (less ordered) and Apo C3 (more ordered). This characteristic is unique to chicken heart apocytochrome c while compared with its counterparts from Candida krusei, tuna heart or horse heart and promises the emergence of much more detail of correlation of translocation with unfolded states of apocytochrome c. When chicken heart apocytochrome c was subjected to a translocation assay in vitro using trypsin-enclosed large unilamellar vesicles from soybean phospholipids, the ability of the protein to penetrate into the liposomes was found to follow the order of Apo C1 > Apo C2 > Apo C3. Conformational alterations of Apo C1, Apo C2 and Apo C3 in association with soybean phospholipid vesicles shown by circular dichroism measurement demonstrated that Apo C1 bound to phospholipids existed in a more loosely folded conformation than Apo C2 and Apo C3. We propose that a more flexible structure of apocytochrome c following the interaction with phospholipids is required for its efficient translocation across the bilayer.