Unexpected foraminiferal diversity revealed by small-subunit rDNA analysis of Antarctic sediment

Studies of benthic Foraminifera typically rely on the morphological identification of dried specimens. This approach can introduce sampling bias against small, delicate, or morphologically ambiguous forms. To overcome this limitation, we extracted total DNA from sediment followed by PCR using group- and species-specific primers. Phylogenetic analyses revealed that approximately ninety percent of the PCR products represented previously undescribed sequence types that group with undersampled members of the allogromiid Foraminifera. We also used a modification of this technique to track individual species in sediment fractions too fine for normal morphological identification, and to confirm species placement of morphologically ambiguous foraminiferans. We were able to identify the DNA of several large foraminiferal species in fine fractions in a seasonally-dependent manner, indicating that in some seasons the majority of the standing stock of these species exists as gametes/juveniles. The approach outlined here represents a powerful strategy for exploring the total diversity of benthic foraminiferal communities.     

Short-term low-carbohydrate diet dissociates lactate and ammonia thresholds in men

A low-carbohydrate (L-CHO) diet has been shown to shift the lactate threshold toward higher workloads. The aim of the present study was to examine the effect of an L-CHO diet on the ammonia threshold and to compare it with the lactate threshold in men. The plasma catecholamine threshold was also measured. Eight young, untrained men participated in the study. Two exercise tests with graded workload were performed. The workload was increased every 3 minutes by 40 W until volitional exhaustion. The first test was performed after 3 days of a controlled mixed diet. After the first test, the mixed diet was switched to a L-CHO diet. Three days later the same test was repeated. The blood concentration of lactate, ammonia, noradrenaline, and adrenaline was measured before and after each workload in both groups. It was found that the concentration of the examined compounds in the blood increases exponentially with graded workload after each kind of diet. This led us to calculate the blood ammonia, lactate, epinephrine, and norepinephrine thresholds. The thresholds were defined as points at which the concentration of a given compound starts to increase in a nonlinear fashion, which is calculated using 2 segmental linear regressions. After the mixed diet, the threshold for each compound occurs at the same workload. The L-CHO diet resulted in dissociation of the lactate threshold from the ammonia threshold: the lactate threshold was shifted toward a higher workload, whereas the ammonia threshold was shifted toward a lower workload. The norepinephrine threshold was also shifted toward a lower workload, and the epinephrine threshold remained unchanged. The results obtained indicate that an L-CHO diet accelerates production of ammonia and delays production of lactate during graded exercise, as well as that diet must be strictly controlled when ammonia and lactate thresholds are measured.     

How to decide whether small samples comply with an equidistribution

The decision whether a measured distribution complies with an equidistribution is a central element of many biostatistical methods. High throughput differential expression measurements, for instance, necessitate to judge possible over-representation of genes. The reliability of this judgement, however, is strongly affected when rarely expressed genes are pooled. We propose a method that can be applied to frequency ranked distributions and that yields a simple but efficient criterion to assess the hypothesis of equiprobable expression levels. By applying our technique to surrogate data we exemplify how the decision criterion can differentiate between a true equidistribution and a triangular distribution. The distinction succeeds even for small sample sizes where standard tests of significance (e.g. chi(2)) fail. Our method will have a major impact on several problems of computational biology where rare events baffle a reliable assessment of frequency distributions. The program package is available upon request from the authors.     

A Ca2+-induced mitochondrial permeability transition causes complete release of rat liver endonuclease G activity from its exclusive location within the mitochondrial intermembrane space. Identification of a novel endo-exonuclease activity residing within the mitochondrial matrix

Endonuclease G, a protein historically thought to be involved in mitochondrial DNA (mtDNA) replication, repair, recombination and degradation, has recently been reported to be involved in nuclear DNA degradation during the apoptotic process. As a result, its involvement in mtDNA homeostasis has been called into question and has necessitated detailed analyses of its precise location within the mitochondrion. Data is presented localizing rat liver endonuclease G activity exclusively to the mitochondrial intermembrane space with no activity associated with either the interior face of the inner mitochondrial membrane or with the mitochondrial matrix. Additionally, it is shown that endonuclease G can be selectively released from the mitochondrion via induction of a Ca²⁺-induced mitochondrial permeability transition and that, upon its release, a further nuclease activity loosely associated with the interior face of the inner mitochondrial membrane and distinct in its properties from that of endonuclease G can be detected.     

RNA-related tools on the Bielefeld Bioinformatics Server

We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison (including local structure alignment) and prediction of structures potentially containing a certain kind of pseudoknots. All are available via the Bielefeld University Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de).     

A basal membrane-like structure surrounding tumour nodules may prevent intraepithelial leucocyte infiltration in colorectal cancer

Epithelial tumours consist of an epithelial compartment and a stromal compartment, which are sometimes separated by a basal membrane-like structure. We sought to determine whether these factors have prognostic value in 84 curatively resected stage II and III colorectal cancer by immunohistochemically staining tumours for leucocytes (CD45) and extracellular matrix, and to assess the presence of a basal membrane-like structure. Leucocyte infiltration was also assessed in hematoxylin-eosin (HE) stained sections. Most leucocytes were located in the tumour stroma. A relatively high intraepithelial leucocyte infiltration was significantly correlated with a lower level of tumour recurrence (P=0.03) and a longer disease-free survival (P=0.05), whereas leucocytes located in the tumour stroma (P=0.92) or at the advancing margin (p=0.06) were not. Intraepithelial leucocyte infiltration was also significantly correlated with leucocyte infiltration in the tumour stroma (P=0.02) and at the advancing tumour margin (P=0.005), and as assessed in HE-stained tumour sections (P=0.05), but each of these parameters on its own did not have a prognostic value in predicting disease-free survival. Moreover, the presence of a basal membrane-like structure surrounding the tumour epithelium was inversely correlated with the number of intraepithelial leucocytes (P=0.05), suggesting that this membrane-like structure functions as a barrier to intraepithelial leucocyte infiltration. We conclude that leucocytes must be in the direct vicinity of tumour cells to affect tumour growth. The presence of an extracellular matrix barrier seems to prevent this interaction.     

Safety,biodistribution, pharmacokinetics,and immunogenicity of <Superscript>99m</Superscript>Tc-labeled humanized monoclonal antibody BIWA 4 (bivatuzumab) in patients with squamous cell carcinoma of the head and neck

Previous studies have shown the potential of murine and chimeric anti-CD44v6 monoclonal antibodies (MAbs) for radioimmunotherapy (RIT) of head and neck squamous cell carcinoma (HNSCC). A limitation of these MAbs, however, appeared to be their immunogenicity. Therefore, humanized monoclonal antibody BIWA 4 (bivatuzumab), with an intermediate affinity for CD44v6, was recently selected. As a prelude to RIT, we evaluated the safety, tumor-targeting potential, pharmacokinetics, and immunogenicity of technetium-99m-labeled BIWA 4 in patients undergoing operations for primary HNSCC in this study. Ten patients were treated at BIWA 4 dose levels of 25 mg (n=3), 50 mg (n=4), and 100 mg (n=3). Patients received 2 mg of 750 MBq 99mTc-BIWA 4, together with 23-, 48-, and 98-mg unlabeled BIWA 4, respectively. Radioimmunoscintigraphy (RIS) was performed within 1 h and after 21 h, and patients underwent surgery at 48 h after injection. Biodistribution of 99mTc-BIWA 4 was evaluated by radioactivity measurements in blood, bone marrow, and in biopsies of a surgical specimen obtained 48 h after injection. BIWA 4 concentration in blood was assessed by ELISA and high performance liquid chromatography and related to soluble CD44v6 levels in serum samples. The development of human anti-human antibody (HAHA) responses was determined. Administration of 99mTc-BIWA 4 was well tolerated by all patients and no HAHA responses were observed. A mean t1/2 in plasma of 54.8 +/- 11.5 h, 76.1 +/- 21.8 h, and 68.5 +/- 21.2 h was found for the 25-, 50-, and 100-mg dose group, respectively. No complex formation of BIWA 4 with soluble CD44v6 in blood was observed. RIS showed targeting of primary tumors and lymph node metastases in 8 of 10 and 1 of 5 patients, respectively. The highest tumor uptake and tumor to nontumor ratios were observed for the 50-mg dose group. Tumor uptake was 12.9 +/- 5.9, 26.2 +/- 3.1, and 15.4 +/- 1.9% of the injected dose (ID)/kg for the 25-, 50-, and 100-mg dose group, respectively, while the tumor to bone marrow ratios for these groups were 1.7 +/- 0.5, 3.2 +/- 1.1, and 2.0 +/- 0.6, respectively. CONCLUSION: 99mTc-BIWA 4 can safely be administered to patients with HNSCC, with absence of detectable HAHA responses. The 50-mg dose level showed the highest tumor uptake and tumor to nontumor ratios. These findings support the use of BIWA 4 for RIT studies in patients with HNSCC.