A three-stage kinetic model of amyloid fibrillation

Amyloid fibrillation has been intensively studied because of its association with various neurological disorders. While extensive time-dependent fibrillation experimental data are available and appear similar, few mechanistic models have been developed to unify those results. The aim of this work was to interpret these experimental results via a rigorous mathematical model that incorporates the physical chemistry of nucleation and fibril growth dynamics. A three-stage mechanism consisting of protein misfolding, nucleation, and fibril elongation is proposed and supported by the features of homogeneous fibrillation responses. Estimated by nonlinear least-squares algorithms, the rate constants for nucleation were approximately 10,000,000 times smaller than those for fibril growth. These results, coupled with the positive feedback characteristics of the elongation process, account for the typical sigmoidal behavior during fibrillation. In addition, experiments with different proteins, various initial concentrations, seeding versus nonseeding, and several agitation rates were analyzed with respect to fibrillation using our new model. The wide applicability of the model confirms that fibrillation kinetics may be fairly similar among amyloid proteins and for different environmental factors. Recommendations on further experiments and on the possible use of molecular simulations to determine the desired properties of potential fibrillation inhibitors are offered.     

New Genera and Species of ‘Giant’ Ostracods (Crustacea: Cyprididae) from Australia

Two new genera of giant ostracods Lacrimicypris n. gen. and Repandocypris n. gen. from Australia are described and eight new species:L. kumbar n. sp., R. austinensis n. sp., R. gleneagles n. sp., Mytilocypris coolcalalaya n. sp., Australocypris bennetti n. sp., A. beaumonti n. sp., A. mongerensis n. sp. and Caboncypris kondininensis n. sp. The number of known Australian genera and species of giant ostracods are now 6 and 21, respectively. Keys to genera and species are provided: all species can be distinguished using the hemipenis and male first leg. The usefulness of the bursa copulatrix as a species-level taxonomic character is highlighted. Most of the species described in this paper occur in salt lakes and existing ecological information on Western Australian species, as well as the distributions of all species, are summarized. Western Australia has a particularly rich halobiont fauna but current explanations relating richness of the halobiont fauna to the widespread occurrence of salt lakes appear incomplete. Australocypris bennetti is unusual in that it is frequently found at pH < 4. Its morphology differs slightly in acidic and alkaline waters.     

Occurrence of aquatic invertebrates of the wheatbelt region of Western Australia in relation to salinity

The wheatbelt region of Western Australia has been extensively cleared of indigenous vegetation for agriculture and is now severely affected by dryland salinity. Wetlands that were once freshwater are now saline and others are under threat, as are the animals and plants that inhabit them. Rising groundwater is also affecting the many naturally saline playas. To provide a framework for setting conservation priorities in this region a biological survey was undertaken, including sampling of aquatic invertebrates at 230 wetlands. In this paper, we have used data from the survey to summarise occurrence of species in relation to salinity. Total species richness at a wetland showed no response to salinity below 4.1 g l⁻¹ and then declined dramatically as salinity increased. When halophilic species were excluded from consideration, species richness was found to decline from 2.6 g l⁻¹. These patterns are compared to previous studies of richness-salinity relationships. There is some evidence that the freshwater invertebrate fauna of the wheatbelt may be comparatively salt tolerant, with 46% of freshwater species collected at salinities above 3 g l⁻¹ and 17% above 10 g l⁻¹, though these proportions differed between various invertebrate groups. While this tolerance will provide a buffer against the effects of mild salinisation, many species are at risk of regional extinction as salinisation becomes more widespread.     

Small, Membrane-bound, Alternatively Spliced Forms of Ankyrin 1 Associated with the Sarcoplasmic Reticulum of Mammalian Skeletal Muscle

We have recently found that the erythroid ankyrin gene, Ank1, expresses isoforms in mouse skeletal muscle, several of which share COOH-terminal sequence with previously known Ank1 isoforms but have a novel, highly hydrophobic 72–amino acid segment at their NH₂ termini. Here, through the use of domainspecific peptide antibodies, we report the presence of the small ankyrins in rat and rabbit skeletal muscle and demonstrate their selective association with the sarcoplasmic reticulum. In frozen sections of rat skeletal muscle, antibodies to the spectrin-binding domain (anti-p65) react only with a 210-kD Ank1 and label the sarcolemma and nuclei, while antibodies to the COOH terminus of the small ankyrin (anti-p6) react with peptides of 20 to 26 kD on immunoblots and decorate the myoplasm in a reticular pattern. Mice homozygous for the normoblastosis mutation (gene symbol nb) are deficient in the 210-kD ankyrin but contain normal levels of the small ankyrins in the myoplasm. In nb/nb skeletal muscle, anti-p65 label is absent from the sarcolemma, whereas anti-p6 label shows the same distribution as in control skeletal muscle. In normal skeletal muscle of the rat, anti-p6 decorates Z lines, as defined by antidesmin distribution, and is also present at M lines where it surrounds the thick myosin filaments. Immunoblots of the proteins isolated with rabbit sarcoplasmic reticulum indicate that the small ankyrins are highly enriched in this fraction. When expressed in transfected HEK 293 cells, the small ankyrins are distributed in a reticular pattern resembling the ER if the NH₂-terminal hydrophobic domain is present, but they are uniformly distributed in the cytosol if this domain is absent. These results suggest that the small ankyrins are integral membrane proteins of the sarcoplasmic reticulum. We propose that, unlike the 210-kD form of Ank1, previously localized to the sarcolemma and believed to be a part of the supporting cytoskeleton, the small Ank1 isoforms may stabilize the sarcoplasmic reticulum by linking it to the contractile apparatus.     

Identifying Corridors among Large Protected Areas in the United States

Conservation scientists emphasize the importance of maintaining a connected network of protected areas to prevent ecosystems and populations from becoming isolated, reduce the risk of extinction, and ultimately sustain biodiversity. Keeping protected areas connected in a network is increasingly recognized as a conservation priority in the current era of rapid climate change. Models that identify suitable linkages between core areas have been used to prioritize potentially important corridors for maintaining functional connectivity. Here, we identify the most “natural” (i.e., least human-modified) corridors between large protected areas in the contiguous Unites States. We aggregated results from multiple connectivity models to develop a composite map of corridors reflecting agreement of models run under different assumptions about how human modification of land may influence connectivity. To identify which land units are most important for sustaining structural connectivity, we used the composite map of corridors to evaluate connectivity priorities in two ways: (1) among land units outside of our pool of large core protected areas and (2) among units administratively protected as Inventoried Roadless (IRAs) or Wilderness Study Areas (WSAs). Corridor values varied substantially among classes of “unprotected” non-core land units, and land units of high connectivity value and priority represent diverse ownerships and existing levels of protections. We provide a ranking of IRAs and WSAs that should be prioritized for additional protection to maintain minimal human modification. Our results provide a coarse-scale assessment of connectivity priorities for maintaining a connected network of protected areas.     

Quantifying reliability and data deficiency in global vertebrate population trends using the Living Planet Index

Global biodiversity is facing a crisis, which must be solved through effective policies and on-the-ground conservation. But governments, NGOs, and scientists need reliable indicators to guide research, conservation actions, and policy decisions. Developing reliable indicators is challenging because the data underlying those tools is incomplete and biased. For example, the Living Planet Index tracks the changing status of global vertebrate biodiversity, but taxonomic, geographic and temporal gaps and biases are present in the aggregated data used to calculate trends. However, without a basis for real-world comparison, there is no way to directly assess an indicator's accuracy or reliability. Instead, a modelling approach can be used. We developed a model of trend reliability, using simulated datasets as stand-ins for the “real world”, degraded samples as stand-ins for indicator datasets (e.g., the Living Planet Database), and a distance measure to quantify reliability by comparing partially sampled to fully sampled trends. The model revealed that the proportion of species represented in the database is not always indicative of trend reliability. Important factors are the number and length of time series, as well as their mean growth rates and variance in their growth rates, both within and between time series. We found that many trends in the Living Planet Index need more data to be considered reliable, particularly trends across the global south. In general, bird trends are the most reliable, while reptile and amphibian trends are most in need of additional data. We simulated three different solutions for reducing data deficiency, and found that collating existing data (where available) is the most efficient way to improve trend reliability, whereas revisiting previously studied populations is a quick and efficient way to improve trend reliability until new long-term studies can be completed and made available.     

Testicular Biopsy in Evaluation of Male Infertility

Testicular biopsy findings in 100 infertile men were correlated with the clinical findings. Mild or moderately severe tubular lesions were seen in 57 cases and severe changes in 43. Clinical examination and semen analysis were no guide to the severity of the testicular lesion. Though patients with normal sized testes more commonly had mild tubular lesions, many were severe. Patients with small testes more often had severe lesions but some had only mild tubular changes. Biopsy findings in both aspermic and oligospermic patients ranged from normal to a complete loss of germinal tissue.Testicular biopsy is advocated in infertile men for the complete assessment of the case and for identifying those which are potentially treatable. Patients with a severe lesion can be spared further investigations. The choice and results of treatment are discussed, particularly the surgical treatment of varicocele or obstruction. Only patients with a mild or moderate testicular tubular lesion should participate in future trials with drugs for male infertility.     

Examination of a region showing linkage map discrepancies across sheep breeds

The availability of accurate linkage maps is an important step for the localization of genetic variants of interest. However, most studies in livestock assume the published map is applicable in their population despite the large differences between the breeds of a species. A region of sheep Chromosome 1 was previously identified as providing evidence for a marker order inconsistent with the published linkage map. In this study the identified region was investigated in more detail. Four microsatellite markers covering the central 5 cM of the inconsistent region and two flanking markers were genotyped in three sheep breeds, a commercial population (Charollais), an experimental population (Scottish Blackface), and a feral population (Soay). With the inclusion of the published linkage map, this provided evidence for three different marker orders across four sheep populations. Evidence for selection in this region was investigated using both a single-point allelic competition model and a multipoint allele-sharing statistic. Only the Charollais population provided evidence for selection, with significant transmission bias observed at marker BM7145. The implications of variation in linkage maps on the design and analysis of fine-mapping studies are discussed.