Towards a more rapid diagnosis of rapidly progressive glomerulonephritis.

An attempt was made to provide simple practical guidelines to alert general practitioners to the diagnosis of rapidly progressive glomerulonephritis and lead to early referral to hospital. The duration of illness before referral to this hospital and its effect on outcome in patients with crescentic nephritis were assessed retrospectively from the case notes of 24 patients referred over two years. Four patients had Goodpasture''s syndrome, 11 Wegener''s granulomatosis, seven microscopic polyarteritis, and two idiopathic progressive glomerulonephritis. The duration of symptoms before referral to the local hospital was similar in the four groups of patients and varied from one week to 28 months (mean 10 months). The duration of stay in the local hospital was two, nine, 11, and 180 days in the patients with Goodpasture''s syndrome and a mean of four days (range one to eight) in those with Wegener''s granulomatosis and 10 days (one to 18 days) in those with microscopic polyarteritis. In the local hospital the diagnosis was based on the results of renal biopsy and detection of antibodies to glomerular basement membrane in two patients with Goodpasture''s syndrome and on the results of renal biopsy in seven of the other patients aided by the detection of antibodies to the cytoplasm of neutrophils (ANCA) in 10. Three of the 24 patients died and four required maintenance haemodialysis. Patients who present to their general practitioners with persistent non-specific symptoms should have a urine dipstick test and then blood tests and emergency referral to hospital if necessary. Hospital physicians should be aware of the speed and accuracy with which current assays can confirm a diagnosis of rapidly progressive glomerulonephritis.     

Impact of simian immunodeficiency virus infection on chimpanzee population dynamics

Like human immunodeficiency virus type 1 (HIV-1), simian immunodeficiency virus of chimpanzees (SIVcpz) can cause CD4+ T cell loss and premature death. Here, we used molecular surveillance tools and mathematical modeling to estimate the impact of SIVcpz infection on chimpanzee population dynamics. Habituated (Mitumba and Kasekela) and non-habituated (Kalande) chimpanzees were studied in Gombe National Park, Tanzania. Ape population sizes were determined from demographic records (Mitumba and Kasekela) or individual sightings and genotyping (Kalande), while SIVcpz prevalence rates were monitored using non-invasive methods. Between 2002-2009, the Mitumba and Kasekela communities experienced mean annual growth rates of 1.9% and 2.4%, respectively, while Kalande chimpanzees suffered a significant decline, with a mean growth rate of -6.5% to -7.4%, depending on population estimates. A rapid decline in Kalande was first noted in the 1990s and originally attributed to poaching and reduced food sources. However, between 2002-2009, we found a mean SIVcpz prevalence in Kalande of 46.1%, which was almost four times higher than the prevalence in Mitumba (12.7%) and Kasekela (12.1%). To explore whether SIVcpz contributed to the Kalande decline, we used empirically determined SIVcpz transmission probabilities as well as chimpanzee mortality, mating and migration data to model the effect of viral pathogenicity on chimpanzee population growth. Deterministic calculations indicated that a prevalence of greater than 3.4% would result in negative growth and eventual population extinction, even using conservative mortality estimates. However, stochastic models revealed that in representative populations, SIVcpz, and not its host species, frequently went extinct. High SIVcpz transmission probability and excess mortality reduced population persistence, while intercommunity migration often rescued infected communities, even when immigrating females had a chance of being SIVcpz infected. Together, these results suggest that the decline of the Kalande community was caused, at least in part, by high levels of SIVcpz infection. However, population extinction is not an inevitable consequence of SIVcpz infection, but depends on additional variables, such as migration, that promote survival. These findings are consistent with the uneven distribution of SIVcpz throughout central Africa and explain how chimpanzees in Gombe and elsewhere can be at equipoise with this pathogen.     

Foraging strategies as a function of season and rank among wild female chimpanzees (Pan troglodytes)

Among mammals, female reproduction is generally thought to befood limited, and dominance should theoretically afford high-rankingfemales with access to better food resources. Although the importanceof dominance rank among female chimpanzees (Pan troglodytes)has been debated in the past, mounting evidence suggests thatrank is very important among females (P. t. schweinfurthii)at Gombe National Park, Tanzania. In this study, we investigatedthe influence of season and dominance rank on female foragingstrategies. We found that high-ranking females spent less timeforaging and tended to have a narrower diet breadth and higherdiet quality than subordinate females. In this way, subordinatefemale foraging strategies were consistent with how femalesin general adapted to periods of food scarcity. The resultsof this study therefore suggest that low-ranking females mayface persistent "food scarcity" as a result of interferencefood competition. We also provide evidence that subordinatesmay forage less efficiently because they occupy lower qualityhabitats or avoid associating with dominant females in sharedareas.     

Spatial and temporal variation in fish assemblage structure in the Mary River,south-eastern Queensland: the influence of habitat structure

Synopsis Fish assemblages at eleven sites within the Mary River were sampled over a 15 month period by back-pack electrofishing. The study took place during a period of abnormally low flows but included two high flow events one of which approached record levels. Spatial and temporal variation in fish assemblage structure was pronounced. Spatial variation was related to position within the catchment and correlated with habitat attributes related to substrate composition and water depth. The absence of a strong effect due to water velocity was probably due to overall low water flows throughout the study period. Temporal variation at some sites, particularly headwater sites, was correlated with changes in the amount and type of cover available to fishes. Cover was significantly correlated with the mean species richness of each site. Flooding had very little effect on both fish assemblage structure and the physical structure of the habitat but resulted in substantial reduction in the amount and type of cover available to fishes. The flow regime of the Mary River was highly variable and consequently both the timing and duration of high and low flows was unpredictable.     

The effect of temperature and solution pH on the nucleation of tetragonal lysozyme crystals.

Part of the challenge of macromolecular crystal growth for structure determination is obtaining crystals with a volume suitable for x-ray analysis. In this respect an understanding of the effect of solution conditions on macromolecule nucleation rates is advantageous. This study investigated the effects of supersaturation, temperature, and pH on the nucleation rate of tetragonal lysozyme crystals. Batch crystallization plates were prepared at given solution concentrations and incubated at set temperatures over 1 week. The number of crystals per well with their size and axial ratios were recorded and correlated with solution conditions. Crystal numbers were found to increase with increasing supersaturation and temperature. The most significant variable, however, was pH; crystal numbers changed by two orders of magnitude over the pH range 4.0-5.2. Crystal size also varied with solution conditions, with the largest crystals obtained at pH 5.2. Having optimized the crystallization conditions, we prepared a batch of crystals under the same initial conditions, and 50 of these crystals were analyzed by x-ray diffraction techniques. The results indicate that even under the same crystallization conditions, a marked variation in crystal properties exists.     

From nest to nest--influence of ecology and reproduction on the active period of adult Gombe chimpanzees

The time spent between sleeping periods, which is called the active period, has to accommodate all essential activities, including feeding, resting, social behavior, and reproduction. To minimize costs in terms of, e.g., predation risk, suboptimal foraging, or sleep deficiency, the active period of diurnal animals should be less than or equal to the daylight period. Thus, the active period of an animal should be shaped by local environmental conditions as well as by metabolic and reproductive demands. Chimpanzees, which exhibit reduced predator pressure and a flexible fission-fusion society, were chosen as a model to explore these links. We investigated the influence of sex, female reproductive status, dominance rank, and season on the duration of the active period of adult chimpanzees at Gombe National Park, Tanzania (1975-1992). Sexually nonreceptive females had shorter active periods compared to males, while receptive females had even longer active periods than males. Dominance rank did not influence the duration of the active period of nonreceptive females, but high- and middle-ranking males had shorter active periods compared to low-ranking males. Nonreceptive females exhibited longer active periods during the dry season than in the wet season. No seasonal effect was discovered for males, perhaps because they already had long active periods in the wet season. Nonreceptive females seem to be able to accommodate all essential activities in the daylight period available, probably because they live less socially than males. Thus, the active period does not reflect differences in female competitive abilities, but does reflect such differences in males. The duration of the active period appears to be a simple, reliable tool for exploring basic responses and constraints in animal societies.     

Life in the fast lane for protein crystallization and X-ray crystallography

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain “low-hanging fruit” protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).     

Urine as a high‐quality source of host genomic DNA from wild populations

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole‐genome, exome) in generating genome‐scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole‐genome capture at generating usable data from low‐quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.