Science and Sentiment: Grinnell’s Fact-Based Philosophy of Biodiversity Conservation

At the beginning of the twentieth century, the biologist Joseph Grinnell made a distinction between science and sentiment for producing fact-based generalizations on how to conserve biodiversity. We are inspired by Grinnellian science, which successfully produced a century-long impact on studying and conserving biodiversity that runs orthogonal to some familiar philosophical distinctions such as fact versus value, emotion versus reason and basic versus applied science. According to Grinnell, unlike sentiment-based generalizations, a fact-based generalization traces its diverse commitments and thus becomes tractable for its audience. We argue that foregrounding tractability better explains Grinnell’s practice in the context of his time as well as in the context of current discourse among scientists over the political “biases” of biodiversity research and its problem of “reproducibility.”     

Genetic variation in the genus Bufo I. An extreme degree of transferrin and albumin polymorphism in a population of the American toad (Bufo americanus)

A population of Bufo americanus from southwestern Ohio exhibited an extreme degree of transferrin and albumin polymorphism. One hundred and eighty-five individuals were collected from this population, and their transferrin and albumin phenotypes were determined by vertical acrylamide gel electrophoresis. Thirteen transferrin alleles were present in 36 phenotypes, and 11 albumin alleles were present in 29 phenotypes. A deficiency of heterozygotes occurred at both protein loci. The possible mechanisms responsible for the polymorphism and deficiency of heterozygotes are discussed.This work was supported by grants from the following agencies to the Senior author: NSF GB23601, Society of the Sigma Xi, and the American Philosophical Society. Miami University contributed the computer and audiovisual services.     

Anticomplementary Activity of Antitumour Polysaccharides

THE polysaccharides obtained from some basidiomycetes, Pleurotus ostreatus (Jacq. ex Fr.) Quel.¹, Flammulina velutipes (Curt, ex Fr.) Sing.², Lentinus edodes (Berk.) Sing.^2–4, Polia cocos, Wolf (Bukuryo)⁵ and Schizophyllum commune Fr.⁷, strongly inhibit the growth of sarcoma 180 and their anti-tumour activity is host-mediated^8,9.     

Interplay between recombinant Hsp70 and proteasomes: proteasome activity modulation and ubiquitin-independent cleavage of Hsp70

The heat shock protein 70 (Hsp70, human HSPA1A) plays indispensable roles in cellular stress responses and protein quality control (PQC). In the framework of PQC, it cooperates with the ubiquitin-proteasome system (UPS) to clear damaged and dysfunctional proteins in the cell. Moreover, Hsp70 itself is rapidly degraded following the recovery from stress. It was demonstrated that its fast turnover is mediated via ubiquitination and subsequent degradation by the 26S proteasome. At the same time, the effect of Hsp70 on the functional state of proteasomes has been insufficiently investigated. Here, we characterized the direct effect of recombinant Hsp70 on the activity of 20S and 26S proteasomes and studied Hsp70 degradation by the 20S proteasome in vitro. We have shown that the activity of purified 20S proteasomes is decreased following incubation with recombinant human Hsp70. On the other hand, high concentrations of Hsp70 activated 26S proteasomes. Finally, we obtained evidence that in addition to previously reported ubiquitin-dependent degradation, Hsp70 could be cleaved independent of ubiquitination by the 20S proteasome. The results obtained reveal novel aspects of the interplay between Hsp70 and proteasomes.     

Apoptosis in fresh and cryopreserved cardiac valves of pig samples

To analyse the influence of cold ischemic time (CIT) (2–24 h) and of cryopreservation (liquid phase) on the viability of the valvular fibroblasts and in the presence of apoptosis. Cardiac valves from 10 pigs were evaluated by anatomo-pathological study of the wall, muscle and leaflet. At the same time, the presence of cellular death due to apoptosis was investigated in two ways; directly on tissue by Apodetec system and by two-colour flow cytometry assay analyzing a suspension of fibroblast from valve leaflets using Anexina V and propidium iodure (PI). We established three groups of samples to compare different experimental conditions: 2 h of ischemia (group 1), 24 h of ischemia (group 2), and a programme of cryopreservation (−1°C/min) after 2 h of ischemia, followed by storage in liquid nitrogen during a week and thawing was performed (group 3). The analysis of viabilities showed slight differences between all three groups. The results indicated CIT of 24 h undergoing more structural affectation than CIT of 2 h. Flow cytometry analysis did not show important differences between groups; however cryopreserved samples (group 3) slightly less viability and a higher percentage of death by apoptosis than group 1 and 2 using flow cytometry. Apoptosis was confirmed on tissue from all valves but mainly in samples of group 2 and group 3. In summary, the viability of the valves in the case of ischemic times of 2 h, 24 h or after cryopreservation/thawing differs slightly. The death of the cells is mainly mediated by necrosis and not by apoptosis.     

Calcium spikes in a leech nonspiking neuron

The NS neurons are nonspiking cells, present as pairs in each midbody ganglion of the leech nervous system, which display a very extensive arborization. They were shown to regulate the coactivation of motoneurons. Here we have investigated the electrophysiological properties of these neurons under the hypothesis that transmission along the extensive neurites requires the aid of voltage-dependent conductances. The results indicate that NS neurons respond to electrical stimulation with a spike-like event, which was not an all-or-none but rather a graded phenomenon that depended on the intensity and duration of the electrical stimulus. The spike-like response was activated at a membrane potential of approximately −50 mV; its amplitude was a logarithmic function of the extracellular Ca²⁺ concentration and was unaffected by a broad range of changes in the extracellular Na⁺ concentration; intracellular application of tetraethylammonium (TEA) caused a large increase in its amplitude and duration. These data indicate that NS neurons bear voltage-dependent low-threshold Ca²⁺ and TEA-sensitive K⁺ conductances that could contribute to shaping synaptic signals, or transmission along the extensive neuritic tree.     

Seizing the Opportunity: Subordinate Male Fowl Respond Rapidly to Variation in Social Context

Dominance affects mating and reproductive success in many group-living species. Potential mechanisms include subordinates being inherently less attractive and social constraints imposed by dominant individuals. To test the former possibility, we measured morphology in 45 male fowl, Gallus gallus , prior to group formation. Males were then assigned to social groups (three males and three females in each). None of the measured traits predicted subsequent social status, suggesting that subordinates were not inherently unattractive. We then manipulated social constraints in each group to test if subordinates were socially constrained. We removed either the alpha (experimental) or the gamma male (control) for 40 min and observed the effect on the beta male's reproductive behavior. Controls accounted for putative group size and disturbance effects, and ensured that the only difference between treatments was the relative dominance of the remaining male. In each trial, we measured the beta male's courtship effort and his mating success, as well as his proximity to females and to the remaining male. Results show that social context did not affect mating success, but had a significant impact on courtship behavior. Beta males courted significantly more often when they had exclusive access to a female, as opposed to when another male was nearby. Furthermore, their courtship effort was higher if the nearby male was a fellow subordinate, as opposed to the dominant male. We conclude that both the proximity and social status of nearby males affects, either directly or indirectly, the courtship efforts of subordinate male fowl.     

A new method for class prediction based on signed-rank algorithms applied to Affymetrix<Superscript>®</Superscript> microarray experiments

Background

The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types for class prediction of limited sample populations. Affymetrix^® technology provides both a quantitative fluorescence signal and a decision (detection call: absent or present) based on signed-rank algorithms applied to several hybridization repeats of each gene, with a per-chip normalization. We developed a new prediction method for class belonging based on the detection call only from recent Affymetrix chip type. Biological data were obtained by hybridization on U133A, U133B and U133Plus 2.0 microarrays of purified normal B cells and cells from three independent groups of multiple myeloma (MM) patients.

Results

After a call-based data reduction step to filter out non class-discriminative probe sets, the gene list obtained was reduced to a predictor with correction for multiple testing by iterative deletion of probe sets that sequentially improve inter-class comparisons and their significance. The error rate of the method was determined using leave-one-out and 5-fold cross-validation. It was successfully applied to (i) determine a sex predictor with the normal donor group classifying gender with no error in all patient groups except for male MM samples with a Y chromosome deletion, (ii) predict the immunoglobulin light and heavy chains expressed by the malignant myeloma clones of the validation group and (iii) predict sex, light and heavy chain nature for every new patient. Finally, this method was shown powerful when compared to the popular classification method Prediction Analysis of Microarray (PAM).

Conclusion

This normalization-free method is routinely used for quality control and correction of collection errors in patient reports to clinicians. It can be easily extended to multiple class prediction suitable with clinical groups, and looks particularly promising through international cooperative projects like the "Microarray Quality Control project of US FDA" MAQC as a predictive classifier for diagnostic, prognostic and response to treatment. Finally, it can be used as a powerful tool to mine published data generated on Affymetrix systems and more generally classify samples with binary feature values.

     

Dual targeting of organellar seryl-tRNA synthetase to maize mitochondria and chloroplasts

Aminoacyl-tRNA synthetases (AARSs) play a critical role in translation and are thus required in three plant protein-synthesizing compartments: cytosol, mitochondria and plastids. A systematic study had previously shown extensive sharing of organellar AARSs from Arabidopsis thaliana, mostly between mitochondria and chloroplasts. However, distribution of AARSs from monocot species, such as maize, has never been experimentally investigated. Here we demonstrate dual targeting of maize seryl-tRNA synthetase, SerZMo, into both mitochondria and chloroplasts using combination of complementary methods, including in vitro import assay, transient expression analysis of green fluorescent protein (GFP) fusions and immunodetection. We also show that SerZMo dual localization is established by the virtue of an ambiguous targeting peptide. Full-length SerZMo protein fused to GFP is targeted to chloroplast stromules, indicating that SerZMo protein performs its function in plastid stroma. The deletion mutant lacking N-terminal region of the ambiguous SerZMo targeting peptide was neither targeted into mitochondria nor chloroplasts, indicating the importance of this region in both mitochondrial and chloroplastic import.