Copigments in the blueing of sepal colour of Hydrangea macrophylla

From blue sepals of Hydrangea macrophylla, copigments which show a blueing effect on the hydrangea anthocyanin were isolated and identified as 3-p-coumaroylquinic acid and 3-caffeoylquinic acid. 5-Caffeoylquinic acid (chlorogenic acid) which was also found in the blue sepals, however, did not show such a blueing effect though it acted as a copigment. Likewise, the 4-esters of p-coumaroyl- and caffeoylquinic acids (not found in sepals) produced purple rather than blue colours. The facts suggest that the stereostructures of 3-p-coumaroyl- and 3-caffeoylquinic acids are effective for molecular interaction between the p-coumaroyl or caffeoyl residue in the compounds and the anthocyanin. The anthocyanin in red and blue sepals of hydrangea was confirmed to be delphinidin 3-monoglucoside.     

On estimating diversity in species-rich fish assemblages: an example with coral-reef fishes of eastern Indonesia

A new procedure for estimating fish species richness in open or semi-open habitats is presented with unpublished data on the coral-reef fish assemblages of Raja Ampat, eastern Indonesia, known as the centre of marine biodiversity in the western Pacific.     

A productive NADP+ binding mode of ferredoxin-NADP + reductase revealed by protein engineering and crystallographic studies.

The flavoenzyme ferredoxin-NADP+ reductase (FNR) catalyzes the production of NADPH during photosynthesis. Whereas the structures of FNRs from spinach leaf and a cyanobacterium as well as many of their homologs have been solved, none of these studies has yielded a productive geometry of the flavin-nicotinamide interaction. Here, we show that this failure occurs because nicotinamide binding to wild type FNR involves the energetically unfavorable displacement of the C-terminal Tyr side chain. We used mutants of this residue (Tyr 308) of pea FNR to obtain the structures of productive NADP+ and NADPH complexes. These structures reveal a unique NADP+ binding mode in which the nicotinamide ring is not parallel to the flavin isoalloxazine ring, but lies against it at an angle of approximately 30 degrees, with the C4 atom 3 A from the flavin N5 atom.     

Androgens rescue avian embryonic lumbar spinal motoneurons from injury‐induced but not naturally occurring cell death

The regulation of survival of spinal motoneurons (MNs) has been shown to depend during development and after injury on a variety of neurotrophic molecules produced by skeletal muscle target tissue. Increasing evidence also suggests that other sources of trophic support prevent MNs from undergoing naturally occurring or injury‐induced death. We have examined the role of endogenous and exogenous androgens on the survival of developing avian lumbar spinal MNs during their period of programmed cell death (PCD) between embryonic day (E)6 and E11 or after axotomy on E12. We found that although treatment with testosterone, dihydrotestosterone (DHT), or the androgen receptor antagonist flutamide (FL) failed to affect the number of these MNs during PCD, administration of DHT from E12 to E15 following axotomy on E12 significantly attenuated injury‐induced MN death. This effect was inhibited by cotreatment with FL, whereas treatment with FL alone did not affect MN survival. Finally, we examined the spinal cord at various times during development and following axotomy on E12 for the expression of androgen receptor using the polyclonal PG‐21 antibody. Our results suggest that exogenously applied androgens are capable of rescuing MNs from injury‐induced cell death and that they act directly on these cells via an androgen receptor‐mediated mechanism. By contrast, endogenous androgens do not appear to be involved in the regulation of normal PCD of developing avian MNs. © 1999 John Wiley & Sons, Inc. J Neurobiol 41: 585–595, 1999     

Quantitative and time-course analysis of microbial degradation of 1H,1H,2H,2H,8H,8H–perfluorododecanol in activated sludge

A methylene group in the fluorinated carbon backbone of 1H,1H,2H,2H,8H,8H–perfluorododecanol (degradable telomer fluoroalcohol, DTFA) renders the molecule cleavable by microbial degradation into two fluorinated carboxylic acids. Several biodegradation products of DTFA are known, but their rates of conversion and fates in the environment have not been determined. We used liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) to quantitatively investigate DTFA biodegradation by the microbial community in activated sludge in polyethylene terephthalate (PET) flasks, which we also determined here showed least adsorption of DTFA. A reduction in DTFA concentration in the medium was accompanied by rapid increases in the concentrations of 2H,2H,8H,8H–perfluorododecanoic acid (2H,2H,8H,8H–PFDoA), 2H,8H,8H-2-perfluorododecenoic acid (2H,8H,8H-2-PFUDoA), and 2H,2H,8H-7-perfluorododecenoic acid and 2H,2H,8H-8-perfluorododecenoic acid (2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA), which were in turn followed by an increase in 6H,6H–perfluorodecanoic acid (6H,6H–PFDeA) concentration, and decreases in 2H,2H,8H,8H–PFDoA, 2H,8H,8H-2-PFUDoA, and 2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA concentrations. Accumulation of perfluorobutanoic acid (PFBA), a presumed end product of DTFA degradation, was also detected. Our quantitative and time-course study of the concentrations of these compounds reveals main routes of DTFA biodegradation, and the presence of new biodegradation pathways.

     

Microhabitat selection in intertidal gobiid fishes: Species- and size-associated variation

Patterns of space use and the individual-based behaviour of microhabitat selection were investigated in three intertidal gobiid fishes, Bathygobius fuscus, Chaenogobius annularis and C. gulosus, from Kyushu, southern Japan. While the three species tended to occupy slightly different types of tidepool, their patterns of distribution largely overlapped in the field. Laboratory experiments involving choice of shelter (i.e. underneath a stone plate) and four different substrate types were conducted to examine size- and time-related variation in habitat selection. The shelter area was preferred by small- and large-sized C. gulosus (day and night), large C. annularis (day and night) and small C. annularis (daytime only), while no preference was evident in small B. fuscus (day and night) and small C. annularis (night). Patterns of substrate choice also differed among species, size groups and between day and night. Size differences in substrate use were evident in B. fuscus and C. gulosus but not in C. annularis, while diel differences were shown by all species groups except large B. fuscus. The gravel and sand substrates tended to be used more frequently than the bare rock substrate, but the strength of preference of a particular substrate type varied among individuals/species. Our results demonstrate that habitat selection by the three gobiid species is variable depending on species, body size and time of day, which must ultimately bear upon mitigating intra-/interspecific interactions in tidepool environments.     

Mitochondrial function in vivo: spectroscopy provides window on cellular energetics

Mitochondria integrate the key metabolic fluxes in the cell. This role places this organelle at the center of cellular energetics and, hence, mitochondrial dysfunction underlies a growing number of human disorders and age-related degenerative diseases. Here we present novel analytical and technical methods for evaluating mitochondrial metabolism and (dys)function in human muscle in vivo. Three innovations involving advances in optical spectroscopy (OS) and magnetic resonance spectroscopy (MRS) permit quantifying key compounds in energy metabolism to yield mitochondrial oxidation and phosphorylation fluxes. The first of these uses analytical methods applied to optical spectra to measure hemoglobin (Hb) and myoglobin (Mb) oxygenation states and relative contents ([Hb]/[Mb]) to determine mitochondrial respiration (O₂ uptake) in vivo. The second uses MRS methods to quantify key high-energy compounds (creatine phosphate, PCr, and adenosine triphosphate, ATP) to determine mitochondrial phosphorylation (ATP flux) in vivo. The third involves a functional test that combines these spectroscopic approaches to determine mitochondrial energy coupling (ATP/O₂), phosphorylation capacity (ATP_max) and oxidative capacity (O_2max) of muscle. These new developments in optical and MR tools allow us to determine the function and capacity of mitochondria noninvasively in order to identify specific defects in vivo that are associated with disease in human and animal muscle. The clinical implication of this unique diagnostic probe is the insight into the nature and extent of dysfunction in metabolic and degenerative disorders, as well as the ability to follow the impact of interventions designed to reverse these disorders.     

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning

Background  

We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment.