Data pattern analysis for the individualised pretherapeutic identification of high-risk diffuse large B-cell lymphoma (DLBCL) patients by cytomics.

BACKGROUND: Clinical outcome predictions in phase III studies are mostly derived for patient groups, but not for individual patients, although individualised predictions are an ultimate goal to permit a personalised fine tuning of therapy. This may permit earlier application of target therapies, minimise general damage to the organism, and result in improved complete remission rates in malignant diseases. METHODS: In this study, Lymphochip cDNA microarray gene expression results of DLBCL patients, from a published prospective meta-analysis study on the prediction of group prognosis, were analysed for individualised predictions using a nonstatistical data pattern classification approach. The training set was comprised of the same 160 DLBCL patients as in the prognosis study, with the validation set of 80 patients remaining unknown to the learning process. This permits the assessment of prospective classifier performance towards unknown patients. RESULTS: Pretherapeutic predictions for the training and validation set patients were correct in 98.1% and 78.3% of the cases for nonsurvival and in 67.3% and 45.3% for survival. The discriminatory data pattern consisted of 14 known and 10 unknown gene products. CONCLUSIONS: The better than 95% correct pretherapeutic prediction for about one-half of the ultimately nonsurviving high-risk patients of the training set is promising for clinical considerations about individualised therapy in such cases. Reliable individualised survival predictions are not possible with the information content of the present dataset. It seems necessary to investigate additional gene products, since survival may significantly depend on non-lymphocyte-associated genes that escape to the lymphocyte-oriented Lymphochip gene activation analysis.     

Regeneration of plants from hypocotyl protoplasts of rapessed (Brassica napus L. var. oleifera) cultivars

Protoplast cultures were prepared from hypocotyls of ten spring rapeseed cultivars. Protoplasts from all genotypes tested formed calli, and shoots were regenerated from calli of nine of the genotypes at frequencies varying from 15 to 76%. The regenerating cultivars fell into a high regenerating group (>60% and a low regenerating group <25%).     

Artificial dimers of native actin: Preparation and properties in biological functions

With the aid of tartryl-bis--aminocaprylazide artificial dimers were produced from F actin from rabbit striated muscle. These derivatives will not polymerize by themselves but are able to copolymerize fully with native G actin. By modification of a single side chain per dimer, this copolymerization was completely inhibited. The dimers are able to activate subfragment I ATPase of myosin and bind to DNase I with inactivation of the enzyme in the same manner as native G actin. Within the dimer, one ADP is immobilized and will exchange against ATP extremely slowly. The dimers do not bind to the mushroom toxin phalloidin.     

Acquisition of embryogenic potential in carrot cell-suspension cultures

Embryogenic suspension cultures of domesticated carrot (Daucus carota L.) are characterized by the presence of proembryogenic masses (PEMs) from which somatic embryos develop under conditions of low cell density in the absence of phytohormones. A culture system, referred to as starting cultures, was developed that allowed analysis of the emergence of PEMs in newly initiated hypocotyl-derived suspension cultures. Embryogenic potential, reflected by the number of FEMs present, slowly increased in starting cultures over a period of six weeks. Addition of excreted, high-molecular-weight, heat-labile cell factors from an established embryogenic culture considerably accelerated the acquisition of embryogenic potential in starting cultures. Analysis of [³⁵S]methionine-labeled proteins excreted into the medium revealed distinct changes concomitant with the acquisition of embryogenic potential in these cultures. Analysis of the pattern of gene expression by in-vitro translation of total cellular mRNA from starting cultures with different embryogenic potential and subsequent separation of the [³⁵S]methionine-labeled products by two-dimensional polyacrylamide gel electrophoresis demonstrated a small number of abundant in-vitro-translation products to be present in somatic embryos and in embryogenic cells but absent in nonembryogenic cells. Several other in-vitro-translation products were present in explants, non-embryogenic and embryogenic cells but were absent in somatic embryos. Hybridization of an embryoregulated complementary-DNA sequence, Dc3, to RNA extracted from starting cultures showed that the corresponding gene is expressed in somatic embryos and PEMs but not in non-embryogenic cells.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - cDNA complementary DNA - PAGE polyacrylamide gel electrophoresis - PEM proembryogenic mass     

Bacteria associated with a marine planktonic copepod in culture. I. Bacterial genera in seawater, body surface, intestines and fecal pellets and succession during fecal pellet degradation

In laboratory experiments, the bacterial flora of the zooplanktonmicrobial environments seawater, fecal pellets and associatedwith the external and internal surfaces of the copepod Acartiatonsa(Dana) were examined. The bacteria associated with fecal pelletswere dominated by Bacillus spp., Cytophaga/Flavobacterium spp.,Vibrio spp. and Pseudomonas spp. The same genera were foundin the seawater (0.22 7mu;m filtered) in which the pellets wereincubated. The bacteria showed a characteristic growth succession,and the abundance increased several orders of magnitude in theseawater during incubation of the pellets, indicating growthand proliferation based on the disintegrating/degrading fecalpellets. A carbon budget calculation revealed that organic matterfrom degrading fecal pellets could cover the carbon demand forthe growing bacterioplankton. The composition of the bacterialcommunity in the seawater and the fecal pellets also indicateda colonization of the pellets from bacterioplankton. The compositionof the bacteria associated with the copepods showed that bacterialgenera characterized as surface associated were preferentiallyassociated with fecal pellets, animal surfaces and intestines.This suggests a specific intestinal flora in the cultivatedcopepods composed of 10³ culturable bacteria per intestine (colony-formingunits, c.f.u.) or 10⁵ bacteria per intestine (acridine orangedirect counts, AODC), possibly colonizing the intestine passivelyduring filtration of algae. The activity of the bacterial communitieswas examined by the numencal ratio c.f.u.:AODC, where 1–19%of the bacteria were found active, with no significant differencebetween microbial environments.     

The effect of homocysteine thiolactone and its alpha methylated derivative on bone matrix in the mouse

Summary Homocysteine (HC) is a radiation protector but toxic to bone. Its derivative homocysteine thiolactone (HCTL) and the alpha-alkylated analogue (A-methyl-HCTL) was fed to mice for a period of six weeks in a daily dose of 50 mg/kg body weight. Parameters for bone matrix as collagen content, acid solubility of bone collagen, urinary bone collagen cross links (pyridinolines) and urinary acid glycosaminoglycans were determined. Urinary acid glycosaminoglycans were significantly reduced in the HCTL treated group but not in the alpha-methyl-homocysteine thiolactone (A-methyl-HCTL) group (controls: 45 ± 7 mg/mmol creatinine, homocysteine thiolactone 38 ± 5 mg/mmol creatinine, A-methyl HCTL 45 ± 6 mg/mmol creatinine).No differences were found for the parameters of bone collagen between the groups. The potent radiation protecting methylated derivative therefore did not change bone matrix and should be a candidate for further toxicological studies.     

The effect of ovariectomy on phenylalanine and tyrosine metabolism

Summary Although the regulatory activity of steroid hormones on amino acid metabolism has been described, no information is published on the effect of ovariectomy. We studied the influence of ovariectomy in Wistar rats determining the amino acids phenylalanine and tyrosine in liver, kidney, plasma and urine. 32 animals were used in the study, 12 animals were sham operated, 9 animals were ovariectomized and 11 rats were ovariectomized and supplemented with estradiol. No quantitative changes were detected comparing liver and kidney phenylalanine and tyrosine between the groups (sham operated rats liver phenylalanine 2,53nM/mg ± 1,07; liver tyrosine 1.95nM/mg ± 0.92; kidney phenylalanine 2.16nM/mg ± 0.53; kidney tyrosine 1.80nM/mg ± 0.39. Ovariectomized rats showed liver phenylalanine 3.07nM/mg ± 1.14; liver tyrosine 2.63nM/mg ± 1.01; kidney phenylalanine 2.30 nM/mg ± 0.74; kidney tyrosine 1.93nM/mg ± 0.63. Ovariectomized and estradiol supplemented rats presented with liver phenylalanine 2.84nM/mg ± 1.40; liver tyrosine 2.35nM/mg ± 1.28; kidney phenylalanine 1.91nM/mg ± 0.26, kidney tyrosine 1.67nM/mg ± 0.23.). When, however, the phenylalanine/tyrosine ratio in the liver was evaluated, ovariectomized rats showed a significant decrease of the quotient (p = 0.001). The phenylalanine/tyrosine ratio was restored by estradiol replacement. Our findings show that phenylalanine and tyrosine metabolism is under estradiol control. The effect on the metabolic changes could be mediated by enzyme systems as phenylalanine hydroxylase, tyrosine hydroxylase and tyrosine aminotransferase. Our results would be compatible with previous reports on the stimulatory effect of estradiol on these enzymes. The kidney phenylalanine/tyrosine ratio was unaffected by ovariectomy and/or estradiol replacement which can be easily explained by different pools, enzyme activities, filtration/reabsorption effects, etc.The urinary P/T ratio was decreased by ovariectomy and restored by estradiol replacement indicating endocrine control of renal reabsorption and secretion mechanisms.     

The effect of ovariectomy of serum amino acids and cholesterol in the rat

Summary As steroid hormones are known to influence amino acid metabolism we tested the hypothesis that ovariectomy should lead to significant changes in this system.We found that after ovariectomy serum alanine was significantly decreased (p = 0.0006) in contrast to serum glycine and branched chain amino acids (BCAA). The ratio of glycine/BCAA, a parameter for anabolism or catabolism was not changed after ovariectomy. If, however, the amino acid alanine as the link to carbohydrate and lipid metabolism was introduced the alanine/BCAA ratio was significantly altered (p = 0.01).Although serum cholesterol was altered as well (increased,p = 0.03), no significant correlation with alanine was found. We can therefore assume that there are two independent mechanisms for lipid and amino acid changes after ovariectomy.The most prominent finding was that estradiol replacement after ovariectomy restored increased cholesterol levels but did not restore alanine levels. Other ovarial hormones must be incriminated for the regulation of alanine metabolism. The anabolic effects of estradiol as decreasing glycine and BCAA were noticed which rules out insufficient estradiol replacement.