Measuring Biodiversity

'Biodiversity' is all to often used as a buzz-word, with no clearly defined meaning, let alone a strict procedure to measure it. This article proposes a logical procedure, based on a similar approach in socio-economics (to measure income inequality). Every element in our logical procedure is known. Bringing it all together as presented is new, as far as we know.     

Circadian organization of a subarctic rodent, the northern red-backed vole (Clethrionomys rutilus)

Arctic and subarctic environments are exposed to extreme light: dark (LD) regimes, including periods of constant light (LL) and constant dark (DD) and large daily changes in day length, but very little is known about circadian rhythms of mammals at high latitudes. The authors investigated the circadian rhythms of a subarctic population of northern red-backed voles (Clethrionomys rutilus). Both wild-caught and third-generation laboratory-bred animals showed predominantly nocturnal patterns of wheel running when exposed to a 16:8 LD cycle. In LL and DD conditions, animals displayed large phenotypic variation in circadian rhythms. Compared to wheel-running rhythms under a 16:8 LD cycle, the robustness of circadian activity rhythms decreased among all animals tested in LL and DD (i.e., decreased chi-squared periodogram waveform amplitude). A large segment of the population became noncircadian (60% in DD, 72% in LL) within 8 weeks of exposure to constant lighting conditions, of which the majority became ultradian, with a few individuals becoming arrhythmic, indicating highly labile circadian organization. Wild-caught and laboratory-bred animals that remained circadian in wheel running displayed free-running periods between 23.3 and 24.8 h. A phase-response curve to light pulses in DD showed significant phase delays at circadian times 12 and 15, indicating the capacity to entrain to rapidly changing day lengths at high latitudes. Whether this phenotypic variation in circadian organization, with circadian, ultradian, and arrhythmic wheel-running activity patterns in constant lighting conditions, is a novel adaptation to life in the arctic remains to be elucidated.     

Involvement of protein radical, protein aggregation, and effects on NO metabolism in the hypochlorite-mediated oxidation of mitochondrial cytochrome c

Cytochrome c (cyt c)-derived protein radicals, radical adduct aggregates, and protein tyrosine nitration have been implicated in the pro-apoptotic event connecting inflammation to the development of diseases. During inflammation, one of the reactive oxygen species metabolized via neutrophil activation is hypochlorite (HOCl); destruction of the mitochondrial electron transport chain by hypochlorite is considered to be a damaging factor. Previous study has shown that HOCl induces the site-specific oxidation of cyt c at met-80. In this work, we have assessed the hypothesis that exposure of cyt c to physiologically relevant concentrations of HOCl leads to protein-derived radical and consequent protein aggregation, which subsequently affects cyt c's regulation of nitric oxide metabolism. Reaction intermediates, chemical pathways available for protein aggregation, and protein nitration were examined. A weak ESR signal for immobilized nitroxide derived from the protein was detected when a high concentration of cyt c was reacted with hypochlorite in the presence of the nitroso spin trap 2-methyl-2-nitrosopropane. When a low concentration of cyt c was exposed to the physiologically relevant levels of HOCl in the presence of 5,5-dimethyl-pyrroline N-oxide (DMPO), we detected DMPO nitrone adducts derived from both protein and protein aggregate radicals as assessed by Western blot using an antibody raised against the DMPO nitrone adduct. The cyt c-derived protein radicals formed by HOCl were located on lysine and tyrosine residues, with lysine predominating. Cyt c-derived protein aggregates induced by HOCl involved primarily lysine residues and hydrophobic interaction. In addition, HOCl-oxidized cyt c (HOCl-cyt c) exhibited a higher affinity for NO and enhancement of nonenzymatic NO synthesis from nitrite reduction. Furthermore, HOCl-mediated cyt c oxidation also resulted in a significant elevation of cyt c nitration derived from either NO trapping of the cyt c-derived tyrosyl radical or cyt c-catalyzed one-electron oxidation of nitrite.     

Dipolar assisted rotational resonance NMR of tryptophan and tyrosine in rhodopsin

Two dimensional (2D) solid-state (13)C.(13)C dipolar recoupling experiments are performed on a series of model compounds and on the visual pigment rhodopsin to establish the most effective method for long range distance measurements in reconstituted membrane proteins. The effects of uniform labeling, inhomogeneous B(1) fields, relaxation and dipolar truncation on cross peak intensity are investigated through NMR measurements of simple amino acid and peptide model compounds. We first show that dipolar assisted rotational resonance (DARR) is more effective than RFDR in recoupling long-range dipolar interactions in these model systems. We then use DARR to establish (13)C-(13)C correlations in rhodopsin. In rhodopsin containing 4'-(13)C-Tyr and 8,19-(13)C retinal, we observe two distinct tyrosine-to-retinal correlations in the DARR spectrum. The most intense cross peak arises from a correlation between Tyr268 and the retinal 19-(13)CH(3), which are 4.8 A apart in the rhodopsin crystal structure. A second cross peak arises from a correlation between Tyr191 and the retinal 19-(13)CH(3), which are 5.5 A apart in the crystal structure. These data demonstrate that long range (13)C em leader (13)C correlations can be obtained in non-crystalline integral membrane proteins reconstituted into lipid membranes containing less than 150 nmoles of protein. In rhodopsin containing 2-(13)C Gly121 and U-(13)C Trp265, we do not observe a Trp-Gly cross peak in the DARR spectrum despite their close proximity (3.6 A) in the crystal structure. Based on model compounds, the absence of a (13)C em leader (13)C cross peak is due to loss of intensity in the diagonal Trp resonances rather than to dipolar truncation.     

Modes and balance of energy in the piezoelectric cochlear outer hair cell wall

Here, we analyze energy transformations in the outer hair cell and its effectiveness as a piezoelectric-type actuator in the cochlea. The major modes of energy are introduced, and a method to estimate the coefficients of their tension-dependence is proposed. Next, we derive balance of the mechanical and electrical parts of energy, and show two forms of the active energy associated with the motors driving electromotility. The two forms of the active energy, stored mechanical energy, and external electrical work are then introduced as functions of voltage and applied force. We use the energy balance to introduce and estimate the effectiveness of the cell's electromotile response.     

3-Hydroxy-4-arylsulfonyltetrahydropyranyl-3-hydroxamic acids are novel inhibitors of MMP-13 and aggrecanase

N-Hydroxy-3-hydroxy-4-arylsulfonyltetrahydropyranyl-3-carboxamides were designed as novel inhibitors of MMP-13 and aggrecanase based on known endocyclic hydroxamate inhibitors of matrix metalloproteinases. These compounds offer favorable physicochemical properties and low metabolic clearance. Synthesis and structure-activity relationships are reported.     

A thallium-sensitive, fluorescence-based assay for detecting and characterizing potassium channel modulators in mammalian cells

Potassium channels have been identified as targets for a large number of therapeutic indications. The ability to use a high-throughput functional assay for the detection and characterization of small-molecule modulators of potassium channels is very desirable. However, present techniques capable of screening very large chemical libraries are limited in terms of data quality, temporal resolution, ease of use, and requirements for specialized instrumentation. To address these issues, the authors have developed a fluorescence-based thallium flux assay. This assay is capable of detecting modulators of both voltage and ligand-gated potassium channels expressed in mammalian cells. The thallium flux assay can use instruments standard to most high-throughput screening laboratories, and using such equipment has been successfully employed to screen large chemical libraries consisting of hundreds of thousands of compounds.