On plotting species abundance distributions

1. There has been a revival of interest in species abundance distribution (SAD) models, stimulated by the claim that the log-normal distribution gave an underestimate of the observed numbers of rare species in species-rich assemblages. This led to the development of the neutral Zero Sum Multinomial distribution (ZSM) to better fit the observed data. 2. Yet plots of SADs, purportedly of the same data, showed differences in frequencies of species and of statistical fits to the ZSM and log-normal models due to the use of different binning methods. 3. We plot six different binning methods for the Barro Colorado Island (BCI) tropical tree data. The appearances of the curves are very different for the different binning methods. Consequently, the fits to different models may vary depending on the binning system used. 4. There is no agreed binning method for SAD plots. Our analysis suggests that a simple doubling of the number of individuals per species in each bin is perhaps the most practical one for illustrative purposes. Alternatively rank-abundance plots should be used. 5. For fitting and testing models exact methods have been developed and application of these does not require binning of data. Errors are introduced unnecessarily if data are binned before testing goodness-of-fit to models.     

Nanosecond pulsed electric fields cause melanomas to self-destruct

We have discovered a new, drug-free therapy for treating solid skin tumors. Pulsed electric fields greater than 20 kV/cm with rise times of 30 ns and durations of 300 ns penetrate into the interior of tumor cells and cause tumor cell nuclei to rapidly shrink and tumor blood flow to stop. Melanomas shrink by 90% within two weeks following a cumulative field exposure time of 120 micros. A second treatment at this time can result in complete remission. This new technique provides a highly localized targeting of tumor cells with only minor effects on overlying skin. Each pulse deposits 0.2 J and 100 pulses increase the temperature of the treated region by only 3 degrees C, ten degrees lower than the minimum temperature for hyperthermia effects.     

C-terminal ladder sequencing of peptides using an alternative nucleophile in carboxypeptidase Y digests

A method for improved sequence coverage in C-terminal sequencing of peptides, based on carboxypeptidase digestion, is described. In conventional carboxypeptidase digestions, the peptide substrate is usually extensively degraded and a full amino acid sequence cannot be obtained due to the lack of a complete peptide ladder. In the presented method, a protecting group is introduced at the C terminus of a fraction of the peptide fragments formed in the digest, and thereby further degradation of the C-terminally modified peptides are slowed down. The protecting group was attached to the C-terminal amino acid through a carboxypeptidase-catalyzed reaction with an alternative nucleophile, 2-pyridylmethylamine, added to the aqueous digestion buffer. Six peptides were digested by carboxypeptidase Y with and without 2-pyridylmethylamine present in the digest buffer, and the resulting fragments subsequently were analyzed with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Comparison of the two digestion methods showed that the probability of successful ladder sequencing increased, by more than 50% using 2-pyridylmethylamine as a competing nucleophile in carboxypeptidase Y digests.     

Effects of Morris water maze testing on the neuroendocrine stress response and intrahypothalamic release of vasopressin and oxytocin in the rat

Adult male Wistar rats were trained in the Morris water maze (MWM) on 3 consecutive days to find a visible platform. Concomitantly, microdialysis samples from the hypothalamic paraventricular (PVN) and supraoptic (SON) nuclei were collected in order to monitor local release of the neuropeptides vasopressin (AVP) and oxytocin (OXT), respectively, during controllable swim stress. Additionally, a separate set of animals was equipped with chronic jugular venous catheters to collect blood samples for analyzing plasma concentrations of corticotropin (ACTH) and corticosterone during training in the MWM. As measured by microdialysis, swimming in the MWM caused a significantly increased release of AVP within the PVN and of OXT within the SON on each of the 3 test sessions. In contrast to OXT in the SON, basal AVP concentrations in the PVN tended to rise from day to day. Plasma ACTH and corticosterone were found to be similarly elevated in response to MWM exposure on each of the test sessions. Taken together, these data demonstrate that testing in the MWM is not only associated with a significant activation of the hypothalamo-pituitary-adrenal axis but also with an intrahypothalamic release of AVP and OXT. If compared with findings using repeated forced swimming as an uncontrollable stressor (Wotjak, C.T., Ganster, J., Kohl, G., Holsboer, F., Landgraf, R., Engelmann, M., 1998. Dissociated central and peripheral release of vasopressin, but not oxytocin, in response to repeated swim stress: new insights into the secretory capacities of peptidergic neurons. Neuroscience 85, 1209-1222), the present results suggest that (1) similarities in the release profiles of AVP in the PVN and plasma hormone levels are fairly independent from the controllability of the stressor and seem, thus, to primarily relate to the physical demands of the task, whereas (2) the different intra-SON OXT release profiles might be linked to the controllability of the stressor.     

Parameters influencing the accuracy and practical applicability of UV indicator cards.

In order to evaluate the potential hazard for the skin and the eye presented by solar ultraviolet radiation, and to take appropriate precautions, it is necessary to characterise the biological effective irradiance or dose. Recently, inexpensive UV indicator cards became available that in principle would provide an attractive means to roughly indicate the local level of erythemal solar UV irradiance. We have characterised the properties of a number of different types of UV indicator cards. Several parameters which may influence the colour of the cards were examined with both outdoor trials under solar UV as well as indoor trials using a filtered xenon arc lamp. Our findings show that the tested cards do not give an appropriate estimation of the effective irradiance due to their spectral sensitivity and their temperature dependence. The application area of the tested UV indicator cards is therefore limited to certain temperature ranges and to seasons where a certain ratio between solar UV-A and solar UV-B occurs.     

Motion and twisting of magnetic particles ingested by alveolar macrophages in the human lung: effect of smoking and disease

Background

Magnetic microparticles being ingested by alveolar macrophages can be used as a monitor for intracellular phagosome motions and cytoskeletal mechanical properties. These studies can be performed in the human lung after voluntary inhalation. The influence of cigarette smoking and lung diseases on cytoskeleton dependent functions was studied.

Methods

Spherical 1.3 μm diameter ferrimagnetic iron oxide particles were inhaled by 17 healthy volunteers (40 – 65 years), 15 patients with sarcoidosis (SAR), 12 patients with idiopathic pulmonary fibrosis (IPF), and 18 patients with chronic obstructive bronchitis (COB). The retained particles were magnetized and aligned in an external 100 mT magnetic field. All magnetized particles induce a weak magnetic field of the lung, which was detected by a sensitive SQUID (superconducting quantum interference device) sensor. Cytoskeletal reorganizations within macrophages and intracellular transport cause stochastic magnetic dipole rotations, which are reflected in a decay of the magnetic lung field, called relaxation. Directed phagosome motion was induced in a weak magnetic twisting field. The resistance of the cytoplasm to particle twisting was characterized by the viscosity and the stiffness (ratio between stress to strain) of the cytoskeleton.

Results

One week after particle inhalation and later macrophage motility (relaxation) and cytoskeletal stiffness was not influenced by cigarette smoking, neither in healthy subjects, nor in the patients. Patients with IPF showed in tendency a faster relaxation (p = 0.06). Particle twisting revealed a non-Newtonian viscosity with a pure viscous and a viscoelastic compartment. The viscous shear was dominant, and only 27% of the shear recoiled and reflected viscoelastic properties. In patients with IPF, the stiffness was reduced by 60% (p < 0.02). An analysis of the shear rate and stress dependence of particle twisting allows correlating the rheological compartments to cytoskeletal subunits, in which microtubules mediate the pure viscous (non-recoverable) shear and microfilaments mediate the viscoelastic (recoverable) behavior. The missing correlation between relaxation and particle twisting shows that both stochastic and directed phagosome motion reflect different cytoskeletal mechanisms.

Conclusion

Faster relaxation and a soft cytoskeleton in patients with IPF indicate alterations in cytoskeleton dependent functions of alveolar macrophages, which may cause dysfunction's in the alveolar defense, like a slower migration, a retarded phagocytosis, a disturbed phagosome lysosome fusion and an impaired clearance.

     

Highbrow proteasome in high-throughput technology

Proteasome is a major protease of the ubiquitin-proteasome pathway involved in the regulation of practically all intracellular biochemical processes. The enzyme core is created by a heteromultimer of complex architecture built with multiple subunits arranged into a tube-like structure. The multiple active sites of diverse peptidase specificity are hidden inside the tube. Access to the interior is guarded by a gate formed by the N-termini of specialized subunits and by the attachment of additional multisubunit protein complexes controlling the enzymatic capabilities of the core. Proteasome, due to its Byzantine molecular architecture and equally sophisticated enzymatic mechanism, is by itself a fascinating biophysical object. Recently, the position of the protease advanced from an academically remarkable protein processor to a providential anticancer drug target and futuristic nanomachine. Proteomics studies actively shape our current understanding of the protease and direct the future applications of the proteasome in medicine.     

Bacterial adhesion to sulcular epithelium in periodontitis

The purpose of this study was to investigate, by electron microscopy, the type of bacterial attachment to the sulcular epithelium in periodontitis. Gingiva biopsies were observed in a transmission electron microscope using cytochemical staining with ruthenium red for glycocalyx visualisation. In addition, subgingival plaque samples and biopsies from the sulcular epithelium in periodontitis from the patients were estimated microbiologically. Aerobic bacteria only were estimated in the subgingival plaque and both aerobic and anaerobic bacteria in the gingival biopsies. No bacterial internalisation could be observed. Fimbria-mediated adhesion as the only type of bacterial attachment and a large diversity of bacterial glycocalyces were detected. As the fimbrial adhesins of putative periodontal pathogens are able in vitro to induce inflammation and bone resorption via stimulation of the proinflammatory cytokine production, the demonstrated fimbrial adhesins suggest the significant role of bacterial adhesion to sulcular epithelium in periodontitis.