Preparing the biochemistry laboratory for the next outbreak: lessons from SARS in Singapore

Severe acute respiratory syndrome (SARS) is an emerging disease characterised by fever and atypical pneumonia and caused by a novel coronavirus. Singapore was affected by the global pandemic in early 2003, with 238 cases and 33 deaths. Samples sent to the biochemistry laboratory made up the majority (69%) of all SARS samples, yet remained a minority (29%) of total biochemistry workload. This paper describes the problems encountered and solutions adopted by the biochemistry laboratory at the designated SARS hospital in coping with this epidemic. It provides practical advice for laboratories planning for the handling of samples from future outbreaks.     

A variance-stabilizing transformation for gene-expression microarray data

MOTIVATION: Standard statistical techniques often assume that data are normally distributed, with constant variance not depending on the mean of the data. Data that violate these assumptions can often be brought in line with the assumptions by application of a transformation. Gene-expression microarray data have a complicated error structure, with a variance that changes with the mean in a non-linear fashion. Log transformations, which are often applied to microarray data, can inflate the variance of observations near background. RESULTS: We introduce a transformation that stabilizes the variance of microarray data across the full range of expression. Simulation studies also suggest that this transformation approximately symmetrizes microarray data.     

The human serum albumin gene: structure of a unique locus

The entire gene for human serum albumin (HSA) has been isolated from a genomic DNA library, carried in the lambda Charon 4A vector. Six independent isolates have been found to hybridize to a cloned HSA cDNA probe, and all six clones share restriction site sequence homology in the overlapping portion of their DNA. These results seem to indicate that the albumin gene is single-copy, or unique, within the human haploid genome. Measuring from the "CAP" site to the "poly(A)" addition site, albumin gene comprises 16.5 kb of DNA.     

Grazing dynamics in intertidal rockpools: Connectivity of microhabitats

Differences between rockpool and emergent rock communities are often attributed to their contrasting physical conditions. However, differences in grazing pressure between rockpools and open rock could also exert an important structuring role. Greater densities and/or the lack of tidal constraints on foraging may allow grazing intensity to be greater in rockpools. Here, wax discs were deployed to compare grazing intensity between rockpool and emergent rock habitats at each of three tidal heights on a moderately exposed shore in SW England. Grazing intensity was then examined in relation to herbivore density. Grazing intensity in pools was twice that on emergent rock, despite a lower density of herbivores in the rockpools. Of these herbivores, patellid limpets are the dominant grazers on rocky shores throughout the NE Atlantic and are recognised to have a major role in structuring intertidal communities. Thus, subsequent experiments focussed on the influence of limpets in determining the differences in consumer pressure between rockpools and emergent rock. Three alternative explanations were considered: (1) the effect of continuous immersion on grazing intensity in rockpools; (2) differences in limpet species abundance between the two habitats; (3) movement of limpets from emergent rock into pools to feed. The level of grazing pressure exerted by Patella ulyssiponensis (Gmelin), the predominant species living constantly immersed in rockpools, was similar to that of P. vulgata (Linnaeus) which is predominantly found on emergent rock. P. vulgata were observed moving from emergent rock into rockpools during high tide. Manipulative experiments confirmed that these foraging excursions resulted in a 2-fold increase in grazing intensity in the pools. Grazing activity of P. vulgata in rockpools was not consistent between sites and may be influenced by differences in wave exposure and/or the abundance of microbial resources. Elevated consumer pressure in rockpools may be an important factor influencing algal assemblages and probably explains the predominance of grazer resistant-species in these pools.     

Distribution of HLA A,B and C antigens in an Australian population

Summary HLA A and B antigens have been determined in 2740 adult responders to a population health survey in Busselton, Western Australia. HLA A B and C antigens have been determined in 481 schoolchildren. The antigen frequencies are generally close to those obtained elsewhere for subjects of British origin, but there are some differences from the frequencies found in North American Caucasians. The frequencies were not affected by the inclusion of genetically related individuals in the sample. Seventeen HLA A-B haplotypes, six A-C haplotypes and six B-C haplotypes had frequencies above 1%. A total of 1071 distinct phenotypes were identified out of the 5069 which are theoretically possible for the HLAA-B model used in the study. The most frequent phenotype was A2, B12 which occurred in 2.5% of the sample.     

Selection of phage antibodies by binding affinity. Mimicking affinity maturation.

We describe a process, based on display of antibodies on the surface of filamentous bacteriophage, for selecting antibodies either by their affinity for antigen or by their kinetics of dissociation (off-rate) from antigen. For affinity selection, phage are mixed with small amounts of soluble biotinylated antigen (less than 1 microgram) such that the antigen is in excess over phage but with the concentration of antigen lower than the dissociation constant (Kd) of the antibody. Those phage bound to antigen are then selected using streptavidin-coated paramagnetic beads. The process can distinguish between antibodies with closely related affinities. For off-rate selection, antibodies are preloaded with biotinylated antigen and diluted into excess unlabelled antigen for variable times prior to capture on streptavidin-coated paramagnetic beads. To mimic the affinity maturation process of the immune system, we introduced random mutations into the antibody genes in vitro using an error-prone polymerase, and used affinity selection to isolate mutants with improved affinity. Starting with a small library (40,000 clones) of mutants (average 1.7 base changes per VH gene) of the mouse antibody B1.8, and using several rounds of affinity selection, we isolated a mutant with a fourfold improved affinity to the hapten 4-hydroxy-5-iodo-3-nitrophenacetyl-(NIP)-caproic acid (mutant Kd = 9.4(+/- 0.3) nM compared with B1.8 Kd = 41.9(+/- 1.6) nm). The relative increase in affinity of the mutant is comparable to the increase seen in the anti-4-hydroxy-3-nitrophenylacetyl/NIP-caproic acid murine secondary immune response.     

Regulation of alternative splicing by SRrp86 and its interacting proteins

SRrp86 is a unique member of the SR protein superfamily containing one RNA recognition motif and two serine-arginine (SR)-rich domains separated by an unusual glutamic acid-lysine (EK)-rich region. Previously, we showed that SRrp86 could regulate alternative splicing by both positively and negatively modulating the activity of other SR proteins and that the unique EK domain could inhibit both constitutive and alternative splicing. These functions were most consistent with the model in which SRrp86 functions by interacting with and thereby modulating the activity of target proteins. To identify the specific proteins that interact with SRrp86, we used a yeast two-hybrid library screen and immunoprecipitation coupled to mass spectrometry. We show that SRrp86 interacts with all of the core SR proteins, as well as a subset of other splicing regulatory proteins, including SAF-B, hnRNP G, YB-1, and p72. In contrast to previous results that showed activation of SRp20 by SRrp86, we now show that SAF-B, hnRNP G, and 9G8 all antagonize the activity of SRrp86. Overall, we conclude that not only does SRrp86 regulate SR protein activity but that it is, in turn, regulated by other splicing factors to control alternative splice site selection.