Energy-dispersive X-ray fluorescence analysis applied to biomonitoring on alps

Biological Trace Element Research - The results of a research in progress at the Istituto di Fisica Generale Applicata—University of Milan—on natural and anthropogenic elements'...     

1.56 Å structure of mature truncated human fibroblast collagenase

The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β-sheet and three α-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley-Liss, Inc.     

Identification of N-terminal helix capping boxes by means of 13C chemical shifts

Summary We have examined the ¹³C and ¹³C chemical shifts of a number of proteins and found that their values at the N-terminal end of a helix provide a good predictor for the presence of a capping box. A capping box consists of a hydrogen-bonded cycle of four amino acids in which the side chain of the N-cap residue forms a hydrogen bond with the backbone amide of the N3 residue, whose side chain in turn may accept a hydrogen bond from the amide of the N-cap residue. The N-cap residue exhibits characteristic values for its backbone torsion angles, with and clustering around 94±15° and 167±5°, respectively. This is manifested by a 1–2 ppm upfield shift of the ¹³C resonance and a 1–4 ppm downfield shift of the ¹³C resonance, relative to their random coil values, and is mainly associated with the unusually large value of . The residues following the N-cap residue exhibit downfield shifts of 1–3 ppm for the ¹³C resonances and small upfield shifts for the ¹³C ones, typical of an -helix.     

Biomarker indications for microbial contribution to Recent and Late Jurassic carbonate deposits

Summary Biomarker investigations were applied to the hydrocarbon fractions of three Recent (cyanobacterial mat, Lake Van microbialite and Lake Satonda microbialite) and two Late Jurassic carbonate samples obtained from sponge bioherms. The relative concentrations ofn-alkanes, monomethyl alkanes, acyclic isoprenoids, steroids and hopanoids in these samples are studied and their probable biological precursors are discussed. Normal alkanes with carbon chain lengths ranging from C₁₅ to C₃₄ and monomethyl alkanes ranging from C₁₇ to C₂₁ with a varying methyl branching pattern are found. The major hydrocarbons are low molecular weight (LMW)n-alkanes (C₁₅–C₂₁) with a slight to strong predominance ofn-heptadecane (C₁₇). High molecular weight (HMW)n-alkanes occur in low to moderate relative concentrations showing a preference of odd-carbon numbered compounds with a maximum at C₂₉. Within the acyclic isoprenoids, pristane, phytane/phytene, pentamethyl-eicosane, squalane and lycopane could be identified. Polycyclic terpenoids of the sterane and/or hopane type are present in all carbonate samples. The carbon numbers of these components range from 27 to 29 and 27 to 32, respectively. These organic compounds identified can be attributed to various source organisms such as cyanobacteria, archaebacteria, algae and vascular plants. All hydrocarbon fractions of the samples are characterized by moderate to high relative concentrations of compounds derived from cyanobacteria, signifying the role of these organisms as contributors to the Recent as well as to the Late Jurassic carbonate deposits.     

Fasciola hepatica: A secreted cathepsin L-like proteinase cleaves host immunoglobulin

Adult Fasciola hepatica secrete a cysteine proteinase capable of cleaving host IgG close to the papain cleaving site. The proteinase was separated by size permeation chromatography. Gelatinsubstrate polyacrylamide gel electrophoresis analysis revealed that the proteinase migrates as 6 proteolytic bands in the apparent molecular size range 60–90 kDa. Based on pH profiles of activity, inhibition studies using diethylpyrocarbonate and the diazomethylketone Z-phe-ala-CHN₂, and characterising the substrate specificity of the enzymes using fluorogenic peptide substrates we have shown that the 60–90-kDa proteinases are cathepsin L-Iike proteinases.     

Do independent processes control the activation and inactivation of potassium contracture tension in rat skeletal muscle?

Potassium (K⁺) contracture tension, measured in small bundles of rat soleus muscle fibers during maintained depolarization, increases to a peak value and then decays either to the baseline or to a pedestal level. We have tested the hypothesis that the rise and fall of tension are determined by independent activation and inactivation processes. If the “Independence” hypothesis is correct, tension during the decay of K⁺ contractures should equal tension predicted from the product of the activation and inactivation parameters determined from the same K⁺ contractures. Both the measured and predicted tensions decayed to a pedestal level that was increased in amplitude in the presence of perchlorate ions. However, the measured tensions in normal solutions and in the presence of perchlorate were three to five times smaller than the predicted tensions. This result indicates that the activation and inactivation of processes controlling the rise and decay of K⁺ contracture tension are not independent.     

Linkage analysis versus association analysis: distinguishing between two models that explain disease-marker associations.

Human genetics researchers have been intrigued for many years by weak-to-moderate associations between markers and diseases. However, in most cases of association, the cause of this phenomenon is still not known. Recently, interest has grown in pursuing association studies for complex diseases, either instead of or in addition to linkage studies. Hence, it is timely to reconsider what a disease-marker association, particularly in the weak-to-moderate range (relative risk < 10), can tell us about disease etiology. To this end, this study accomplishes three aims: (1) It formulates two different models explaining weak-to-moderate associations and derives the relationship between them. One is a linkage disequilibrium model, and the other is a "susceptibility," or pure association, model. The importance of drawing the distinction between these two models and the implications for our understanding of the genetics of human disease will also be discussed. It will be argued that the linkage disequilibrium model represents true linkage but that the susceptibility model does not. (2) It examines two family-based association tests proposed recently by Parsian et al. and Spielman et al. and derives formulas for their behavior under the two models described above. It demonstrates that these tests yield almost identical results under these two models. It shows that, whereas these tests can confirm an association, they cannot determine whether the association is caused by the linkage disequilibrium model or the susceptibility model. The study also characterizes the probabilities yielded by the family association tests in the presence of weak-to-moderate associations, which will aid researchers using these tests. (3) It proposes two approaches, both based on linkage analysis, which can distinguish between the two models described above. One approach involves a straightforward linkage analysis of the data; the other involves a partitioned association-linkage (PAL) test, as suggested by Greenberg. Formulas are derived for testing identity by descent in affected sib pairs by using both approaches. (4) Finally, the formulas and arguments are illustrated with two examples from the literature and one computer-simulated data set.     

Pyric Herbivory and the Nexus Between Forage,Fire and Native and Introduced Large Grazing Herbivores in Australian Tropical Savannas

Earth’s tropical savannas typically support high biomass of diverse grazing herbivores that depend on a highly fluctuating resource: high-quality forage. An annual wet–dry cycle, fire and herbivory combine to influence forage quality and availability throughout the year. In the savannas of northern Australia, a depauperate suite of large native (marsupial) herbivores (wallaroos [Osphranter spp.] and the agile wallaby [Notamacropus agilis]) compete for resources with non-native large herbivores introduced in the late nineteenth century, particularly bovines (feral and managed cattle [Bos spp.] and feral water buffalo [Bubalus bubalis]) that now dominate the landscape. Anecdotal reports of recent population declines of large macropods and negative impacts of bovines highlight the need to better understand the complex relationship between forage, fire and abundance of native and introduced large herbivores. The pyric herbivory conceptual model, which posits complex feedbacks between fire and herbivory and was developed outside Australia, predicts that native and introduced large herbivores will both respond positively to post-fire forage production in Australian savannas where they co-occur. We used grazing exclosures, forage biomass and nutrient analyses and motion-sensor camera-trapping to evaluate the overall robustness of the pyric herbivory model in the Australian context, specifically whether forage quantity and quality are impacted by herbivory, season and fire activity, and which forage attributes most influence large grazing herbivore abundance. Forage quantity, as measured by live, dead and total herbaceous biomass and proportion of biomass alive, was higher inside herbivore exclosures, even at relatively low densities of herbivores. Forage quality, as measured by fibre content, was not affected by herbivory, however, crude protein content of live herbaceous biomass was greater outside herbivore exclosures. Recent fire was an important predictor of all measures of forage quantity and quality. Recent fire occurrence decreased overall quantity (biomass) but increased quality (decreased fibre content and increased crude protein content); late dry season fires resulted in forage with the highest crude protein content. The predictions of the pyric herbivory conceptual model are consistent with observations of the feeding behaviour of introduced bovines and some large macropods in northern Australian savannas, lending support to the global generality of pyric herbivory in fire-prone grassy biomes.

     

ThechlL (frxC) gene: Phylogenetic distribution in vascular plants and DNA sequence fromPolystichum acrostichoides (Pteridophyta) andSynechococcus sp. 7002 (Cyanobacteria)

We examinedchlL (frxC) gene evolution using several approaches. Sequences from the chloroplast genome of the fernPolystichum acrostichoides and from the cyanobacteriumSynechococcus sp. 7002 were determined and found to be highly conserved. A complete physical map of the fern chloroplast genome and partial maps of other vascular plant taxa show thatchlL is located primarily in the small single copy region as inMarchantia polymorpha. A survey of a wide variety of non-angiospermous vascular plant DNAs shows thatchlL is widely distributed but has been lost in the pteridophytePsilotum and (presumably independently) within the Gnetalean gymnosperms.The namefrxC was originally used to denote a gene encoding a product with probable Fe : S cluster binding activity. This activity was postulated due to the amino acid sequence similarity between this product and the Fe : S-binding nitrogenase iron proteinnifH. Fe : S-binding is a property shared by ferredoxins, which are denoted by the prefix frx. However, this gene does not encode a ferredoxin. It is much larger than any known ferredoxin, it binds its Fe : S cluster between two halves of a homodimer (Fujita & al. 1989,Burke & al. 1993 a, c) instead of within a single subunit, and it lacks the pattern of clustered cysteines present in all ferredoxins (Meyer 1988). Therefore, we use the namechlL to recognize the sequence and functional similarities to the bacterial PChlide reductase subunit,bchL. Similar usage has been adopted for this (Suzuki & Bauer 1992) and other (Choquet & al. 1992,Burke & al. 1993b) PChlide reductase subunits.