Revisiting the relationship between tumour volume and diameter in advanced NSCLC patients: An exercise to maximize the utility of each measure to assess response to therapy.

AIM: To revisit the presumed relationship between tumour diameter and volume in advanced non-small-cell lung cancer (NSCLC) patients, and determine whether the measured volume using volume-analysis software and its proportional changes during therapy matches with the calculated volume obtained from the presumed relationship and results in concordant response assessment. MATERIALS AND METHODS: Twenty-three patients with stage IIIB/IV NSCLC with a total of 53 measurable lung lesions, treated in a phase II trial of erlotinib, were studied with institutional review board approval. Tumour volume and diameter were measured at baseline and at the first follow-up computed tomography (CT) examination using volume-analysis software. Using the measured diameter (2r) and the equation, calculated volume was obtained as (4/3)πr(3) at baseline and at the follow-up. Percent volume change was obtained by comparing to baseline for measured and calculated volumes, and response assessment was assigned. RESULTS: The measured volume was significantly smaller than the calculated volume at baseline (median 11,488.9 mm(3) versus 17,148.6 mm(3); p < 0.0001), with a concordance correlation coefficient (CCC) of 0.7022. At follow-up, the measured volume was once again significantly smaller than the calculated volume (median 6573.5 mm(3) versus 9198.1 mm(3); p = 0.0022), with a CCC of 0.7408. Response assessment by calculated versus measured volume changes had only moderate agreement (weighted κ = 0.545), with discordant assessment results in 20% (8/40) of lesions. CONCLUSION: Calculated volume based on the presumed relationship significantly differed from the measured volume in advanced NSCLC patients, with only moderate concordance in response assessment, indicating the limitations of presumed relationship.

Nomogram to predict the presence of EGFR activating mutation in lung adenocarcinoma.

Epidermal growth factor receptor (EGFR) tumour genotyping is crucial to guide treatment decisions regarding the use of EGFR tyrosine kinase inhibitors in nonsmall cell lung cancer (NSCLC). However, some patients may not be able to obtain tumour testing, either because tissue is limited and/or tests are not routinely offered. Here, we aimed to build a model-based nomogram to allow for prediction of the presence of EGFR mutations in NSCLC. We retrospectively collected clinical and pathological data on 3,006 patients with NSCLC who had their tumours genotyped for EGFR mutations at five institutions worldwide. Variables of interest were integrated in a multivariate logistic regression model. In the 2,392 non-Asian patients with lung adenocarcinomas, the most important predictors of harbouring EGFR mutation were: lower tobacco smoking exposure (OR 0.41, 95% CI 0.37-0.46), longer time interval between smoking cessation and diagnosis (OR 2.19, 95% CI 1.71-2.80), advanced stage (OR 1.58, 95% CI 1.18-2.13), and papillary (OR 4.57, 95% CI 3.14-6.66) or bronchioloalveolar (OR 2.84, 95% CI 1.98-4.06) histologically predominant subtype. A nomogram was established and showed excellent discriminating accuracy: the concordance index on an independent validation dataset was 0.84. As clinical practices transition to incorporating genotyping as part of routine care, this nomogram could be highly useful to predict the presence of EGFR mutations in lung adenocarcinoma in non-Asian patients when mutational profiling is not available or possible.

Characterisation of troponin-T from salmonid fish.

Five major troponin-T isoforms were isolated from the myotomal muscles of Atlantic salmon: three from fast muscle (Tn-T1F, Tn-T2F and Tn-T3F) and two from slow muscle (Tn-T1S and Tn-T2S). In addition to their presence in troponin preparations, these proteins were also recognised to be Tn-T on the basis of immunoreaction with anti-troponin-T antibodies and partial amino acid sequence. The electrophoretic mobility in the presence of SDS of the various Tn-Ts increases in the order: 1S < 1F < 2S < 2F < or = 3F. Compositional analysis shows that the higher M(r) forms (1F and 1S) contain considerably more proline, glutamic acid and alanine than the lower-M(r) forms (2F, 3F and 2S). Every isoform lacks cysteine and phosphoserine is present only in isoforms 2F and 3F. All of the Tn-Ts, with the exception of isoform 1F, are N-terminally blocked. CNBr fragments from same cell type Tn-Ts yield identical sequences over at least fifteen Edman cycles. Two full-length cDNA sequences, presumed to represent 1S and 3F, or isoforms that are highly similar, are reported. As documented for higher vertebrate Tn-Ts, the predicted primary structures display a non-uniform distribution of charged amino acids and greater divergence at each end than in the central section. The most striking difference between the two salmonid proteins is the presence of a N-terminal (proline-, glutamic acid- and alanine-rich) extension of about fifty amino acids in Tn-T1s (278 amino acids) that is missing from the fast muscle Tn-T (223 amino acids). The sequences also differ in that 1S lacks the known phosphorylation site while the fast-type isoform contains serine next to the initiating methionine. Of the two, the slow isoform has accumulated the greater number of substitutions.

Heterogeneity of Atlantic salmon troponin-I.

Three non-identical, full length troponin-I (Tn-I) clones were isolated from an Atlantic salmon myotomal (trunk) muscle cDNA library. The primary structures, which are predicted to range from 172 to 180 amino acids in length, exhibit similar percent identity scores when compared with fast, slow and cardiac specific Tn-Is from higher vertebrates. When the sequence data are considered along with the results of Western blotting it is evident that Tn-I is more heterogeneous in Atlantic salmon than has been previously shown in higher vertebrates.

Further characterisation of fast, slow and cardiac muscle tropomyosins from salmonid fish.

Separate cDNA libraries were constructed from cardiac muscle and slow myotomal muscle of mature brown trout (Salmo trutta). The complete sequence of tropomyosin (TM) that is specific to these muscles was determined from full-length transcripts isolated from the corresponding library. The identity of the sequences was supported by protein data. When compared to the sequence of Atlantic salmon fast myotomal TM [Heeley, D. H., Bieger, T., Waddleton, D. M., Hong, C., Jackman, D. M., McGowan, C., Davidson, W. S. & Beavis, R. C. (1995) Characterisation of fast, slow and cardiac muscle tropomyosins from salmonid fish, Eur. J. Biochem. 232, 226-234], the main difference in the N- and C-terminal sequences comprising the site of end-to-end overlap occurs at residue 276 where an asparagine in fast TM is replaced by a histidine in both cardiac and slow TM. Trout cardiac TM exhibited greatest similarity to chicken cardiac TM while trout slow TM exhibited greatest similarity to skeletal alpha-TMs. Thus, none of the three salmonid TM sequences corresponds to a beta-type TM. In calorimetry experiments (0.1 M salt, pH 7.00, t = 10-60 degrees C), in the presence of dithiothreitol, differences were observed in the thermal unfolding profiles of the purified isoforms. A single endotherm (tm = 39.5 degrees C) was noted for cardiac TM. Two endotherms were observed for fast TM [tm = 26.5 degrees C and 39.8 degrees C (main)] and slow TM [tm = 37.4 degrees C and 46.9 degrees C (main)]. Fast TM was cloned and over expressed in the bacterial cell lines JM105 and BL21. Upon cell lysis, recombinant TM (rc TM) made in JM105 was rapidly and quantitatively cleaved between residues 6 and 7. Intact rc TM was produced by using BL21, as shown by Edman-based sequencing, carboxypeptidase digestion and mass analysis. In viscometry assays, performed at low ionic strength (pH 7.00, t = 5 degrees C) the full-length rc TM exhibited markedly lower relative viscosity values than the corresponding wild type.

Characterization of a nitrogen-fixation (nif) gene cluster from Anabaena azollae 1a shows that closely related cyanobacteria have highly variable but structured intergenic regions.

The exact identity of cyanobacteria that have been cultured from symbiotic associations with the water fern Azolla spp., whether they are required in the symbiotic process, and their relationship to the symbiotic species, is a matter of some debate. We have characterized a 6 kb region containing the nifB operon and the nifH gene from cyanobacterium Anabaena azollae 1a, a putative symbiont of Azolla caroliniana. Five complete open reading frames have been sequenced. All are very highly conserved when compared with the corresponding regions of Anabaena sp. PCC 7120, with 93% to 97% identity at the nucleotide level and 93% to almost 100% at the amino-acid level. The intergenic regions, however, are not highly conserved (53-89% identity) when compared to the corresponding regions of Anabaena 7120: the A. azollae genome contains both more copies and more types of short tandemly repeated repetitive sequences than Anabaena 7120. The start points of transcription for both the nifB and nifH operons were mapped and found to be the same as those in Anabaena 7120. It was not possible to discern an improved consensus nif promoter sequence, but it was possible to define the likely extent of the promoter to within 40 bases upstream of the transcription start-point.

Characterisation of fast, slow and cardiac muscle tropomyosins from salmonid fish.

Tropomyosin (TM) has been isolated from the cardiac muscle, and fast and slow trunk (myotomal) muscles of the mature salmonid fish Atlantic salmon (Salmo salar) and rainbow trout (Salmo gairdneri). When examined electrophoretically, isoforms of TM were detected which were specific, and exclusive, to each type of muscle. Cardiac and fast muscles contained single and distinct isoforms, while slow muscle contained two distinct isoforms, closely related in terms of apparent M(r), and pI. There was no detectable difference between the same TM type from either salmon or trout. On a variety of gel systems, the cardiac and slow isoforms migrated in close proximity to each other and to rabbit alpha-TM. The fast isoform comigrated with rabbit beta-TM. In developing salmon fry, a more acidic (unphosphorylated) variant of TM was present in addition to, and of similar M(r) to, the fast adult isoform. This TM declined in steady-state level during maturation and was virtually undetected in adult muscle. All of the isolated TMs contained little or no covalently bound phosphate and were blocked at the N-terminus. The amino acids released by carboxypeptidase A, when ordered to give maximal similarity to other muscle TMs, were consistent with the following sequences: fast (LDNALNDMTSI) and cardiac (LDHALNDMTSL). The C-terminal region of the slow TM contained His but was heterogeneous. In viscosity measurements, performed as a function of increasing protein concentration, at low ionic strength (t = 5 degrees C, pH 7.00), fast TM exhibited the highest relative viscosity values. Lower and equivalent levels of polymerisation occurred with the cardiac and slow TMs. Polymerisation of all three isoforms was temperature-dependent, with cardiac TM being least sensitive and fast TM being most sensitive. Determination of the complete coding sequence of adult fast TM confirmed the findings of the carboxypeptidase analysis, but the remainder of the sequence more closely resembled alpha-type TMs than beta-type TMs. Overall, salmon fast TM contains 20 (mostly conservative) substitutions compared to rabbit striated muscle alpha-TM and 40 (mostly conservative) substitutions compared to rabbit striated muscle beta-TM. This demonstrates that electrophoretic mobility is not, in all instances, a suitable method to assess the isomorphic nature of striated muscle TMs.

Heterocyst-forming filamentous cyanobacteria encode proteins that resemble eukaryotic RNA-binding proteins of the RNP family.

Heterocyst-forming cyanobacteria have multiple genes encoding proteins that are similar to the RNP family of eukaryotic RNA-binding proteins. Three genes from two strains of cyanobacteria (Anabaena and Chlorogloeopsis) have been sequenced. All three putative gene products contain a single RNA Recognition Motif (RRM) that includes the highly conserved RNP1 and RNP2 regions and all three have an auxiliary motif consisting either of a short glycine-rich carboxy-terminal tail or a carboxy-terminal tail rich in both asparagine and glycine. RNA-binding protein genes are abundant in heterocyst-forming filamentous cyanobacteria but are not abundant in non-heterocyst-forming filamentous or unicellular cyanobacteria suggesting that the cyanobacterial proteins may play a role in gene expression during heterocyst differentiation. The cyanobacterial gene products share a significant degree of similarity with the RNP family of RNA-binding proteins which includes snRNP proteins, hnRNP proteins, nucleolins, as well as some regulatory proteins and some plant chloroplast proteins. Although the exact function of the cyanobacterial gene products is not yet known, their similarity to eukaryotic proteins suggests that they may play a role in RNA processing and metabolism. Finally, the presence of these genes in cyanobacteria has implications for the evolution of RNA binding proteins and RNA processing.

Cloning and nucleotide sequence of the gene for dinitrogenase reductase (nifH) from the heterocyst-forming cyanobacterium Anabaena sp. L31.

The nucleotide sequence of an 1655 base pair segment from Anabaena sp. L31 containing the 3' half of the nifU gene, the complete sequence of the nifH gene and the 5' end of the nifD gene is presented. nifH is very highly conserved with the same gene from Anabaena sp. PCC 7120 (91% identical at the nucleotide level; 94% identical at the amino acid level) as are nifU and nifD. The intergenic regions are less well conserved.

Nucleotide sequence and expression of the gene for the 9 kDa FA/FB component of photosystem I from the cyanobacterium Anabaena sp. PCC7120.

The nucleotide sequence of an 813 bp Ssp I-Hinc II fragment containing the psaC gene from Anabaena sp. PCC 7120 is reported. The gene encodes a polypeptide of 81 amino acids, has a single transcript of size approximately 480 nucleotides and a single startpoint of transcription. It is flanked by a ribosome binding site on the 5' end and a potential transcription terminator on the 3' end. Comparison of the amino acid sequences of the psaC gene product from sixteen organisms shows that cyanobacteria group as a cluster distinct from monocotyledonous and dicotyledonous plants and that individual amino acids are diagnostic of each cluster.

Susceptibility of psychrotrophic pseudomonads of milk origin to psychrotrophic bacteriophages.

A total of 47 psychrotrophic pseudomonads isolated from raw milk came from Newfoundland (19 isolates), British Columbia (6 isolates), Ontario (19 isolates), and Cork, Ireland (3 isolates). The susceptibility of these was tested against 30 bacteriophages isolated from cold-storage beef. Distinct lysotypes were observed with isolates representing different geographic regions. Phages as agents in the control of bacterial populations in milk is discussed.

Physicochemical Properties of Heat-Stable Proteases from Psychrotrophic Pseudomonads.

Four purified heat-stable proteases from psychrotrophic pseudomonads were characterized and compared with other similar purified proteases. Amino acid compositions, hydrophobicities, Difference Index (DI) values, heat-stabilities, metal ion contents and N-terminal amino acids of these proteases were examined. Some similarities as well as differences in their amino acid compositions were observed. All were inactivated by EDTA-treatment and the apoenzymes were reactivated with either Ca, Mg or Mn ions. Proteases T25, T20, T16 and T13 contained 16, 8, 4 and 5 g atom per mol of Ca, respectively. Except for protease T20 which showed 4 g atom per mol of Mg, the other proteases showed less than 1 g atom per mol of the element. The Mn content of the proteases was negligible (less than 0.1 g atom per mol). The presence of exogenous Ca afforded protection to the protease activity in the partially purified enzymes when subjected to heat treatment. Heated samples of proteases when stored in cold regained activity indicating renaturation of the proteins. Threonine was tentatively identified as the N-terminal amino acid in the four purified proteases. Similarities and differences observed between purified proteases are discussed.

Heat-stable protease from Pseudomonas fluorescens T16: purification by affinity column chromatography and characterization.

A heat-stable extracellular protease from Pseudomonas fluorescens T16, a psychrotroph, was purified by affinity column chromatography on a carbobenzoxy-D-phenylalanine-triethylene tetramine-Sepharose-4B column. The purified enzyme is a monomer with a molecular weight of 38,905 +/- 2,000. In an analytical ultracentrifuge, the Schlieren profile revealed a single symmetrical peak. The sedimentation coefficient was estimated to be 3.93S. Alpha-casein was the preferred substrate, with a Km of 0.05 mM. Heating crude enzyme and purified enzyme in buffer at 50, 90, and 120 degrees C resulted in a rapid initial loss of more than 50% of the initial activity followed by a gradual inactivation which exhibited first-order kinetics. The activation energy for the hydrolysis of casein was calculated to be 3.2 kcal/mol (13.4 kJ/mol).

Heat-stable proteases from psychrotrophic pseudomonads: comparison of immunological properties.

A heat-stable extracellular protease from Pseudomonas fluorescens was purified by chromatography on a DEAE-cellulose column and gel filtration on a Sephadex G100 column. The homogeneous enzyme preparation was used to prepare antiserum in rabbits. The rabbit antiserum was used to study the antigenic relatedness of proteases from 19 psychrotrophic pseudomonads isolated from raw milk. The inhibition of the proteases by the antiserum and the gel precipitin reactions revealed similar antigenic determinants in proteases from different isolates. Rabbit antiserum to the purified protease gave precipitin bands with antigens (proteases) from 10 different isolates. However, the same antiserum did not inhibit the protease activity in cell extracts of isolates T10, T13, and T24. By determining serological cross-reactions, proteases from psychrotrophic pseudomonads were shown to be different from one another.