Estimating bacterial diversity from clone libraries with flat rank abundance distributions

There are a number of parametric and non-parametric methods for estimating diversity. However all such methods employ either the proportional abundance of the most abundant taxon in a sample or require that a specific taxon is sampled more than once. Consequently, the available methods for estimating diversity cannot be applied to samples consisting entirely of singletons, which might be characteristic of some hyperdiverse communities. Here we present a non-parametric method that estimates the probability that a given number of unique taxa would be sampled from a community with a particular diversity. We have applied this approach to a well known data set of 100 unique clones from a sample of Amazonian soil (Borneman and Triplett (1997) Appl Environ Microbiol 63: 2647-2653) and determine the probability that this observation would be made from an environment of a given diversity. On this basis we can state this observation would be very unlikely (P = 0.006) if the soil diversity was less than 10(3), and quite unlikely (P = 0.6) if the diversity was less than 10(4), and probable (P = 0.95) if the diversity was about 10(5). There are essentially no contestable assumptions in our method. Thus we are able to offer almost unequivocal evidence that the bacterial diversity, of at least soils, is very large and a method that may be used to interpret samples consisting entirely of singletons from other hyperdiverse communities.     

Density and population structure of owl monkeys (Aotus azarai) in the Argentinean Chaco

Owl monkeys are small monogamous primates ranging over a wide area extending from Panama to the Chaco region of northern Argentina. The Chaco, an alluvial plain covering over one million km2 of Argentina, Bolivia, Brazil, and Paraguay, consists of a mosaic of grasslands, savannas, xeric thorn forests, and gallery forests. The region shows significant seasonal variation in climate, rainfall, and food availability. The goal of this study was to determine the density, size, and structure of a population of Aotus azarai in the seasonal gallery forests of the eastern Argentinean Chaco. Reported population density, as well as group size and composition are based on data collected from 11 groups contacted on approximately 900 occasions, and observed for over 2,000 hours during a three-year period. Group and individual densities were 16 groups/km2 and 64 individuals/km2, respectively. Approximately half of the groups (n = 5) were small groups which had three individuals most of the time and never more than four, whereas the remaining groups were large groups composed of four or five individuals, and sometimes even six or seven individuals. This is the first study of A. azarai based on monitoring of a relatively large number of distinct groups. Our data suggest that owl monkeys in the seasonal subtropical forests of Formosa live at a density as high as those reported for owl monkey populations observed in tropical forests. The data also show that the social groups in the owl monkey population are of comparable size and composition to those characteristic of populations in the tropics.     

Altruism,tit for tat and ‘outlaw’ genes

Summary In a prior study we combined game theory and inclusive fitness models to examine whether the guarded altruism that can evolve among non-relatives (tit for tat, TFT) might also evolve among close relatives, supplanting unconditional altruism. In most cases, TFT replaced unconditional altruism in family-structured models. Even when TFT is selected at a single locus, however, by withholding altruism from non-reciprocating relatives it may qualify as an outlaw from the standpoint of modifier genes at other loci. Here we examine this possibility with a series of haploid, two-locus models in which a modifier gene transforms TFT into unconditional altruism. The modifier allele spreads to fixation whenever Hamilton's Rule is satisfied, resulting in an unconditional altruist replacing the TFT strategy. As such, TFT may be regarded as an outlaw vulnerable to suppression by alleles at other loci.     

N-(5-chloro-2-(hydroxymethyl)-N-alkyl-arylsulfonamides as gamma-secretase inhibitors

A series of N-alkylbenzenesulfonamides were developed from a high throughput screening hit. Classic and parallel synthesis strategies were employed to produce compounds with good in vitro and in vivo gamma-secretase activity.     

Shyness and boldness in humans and other animals

The shy-bold continuum is a fundamental axis of behavioral variation in humans and at least some other species, but its taxonomic distribution and evolutionary implications are unknown. Models of optimal risk, density- or frequency-dependent selection, and phenotypic plasticity can provide a theoretical framework for understanding shyness and boldness as a product of natural selection. We sketch this framework and review the few empirical studies of shyness and boldness in natural populations. The study of shyness and boldness adds an interesting new dimension to behavioral ecology by focusing on the nature of continuous behavioral variation that exists within the familiar categories of age, sex and size.     

International Differences in Treatment and Clinical Outcomes for High Grade Glioma

Background

High grade gliomas are the most common type of malignant brain tumor, and despite their rarity, cause significant morbidity and mortality. This study aimed to compare the treatment patterns of high grade glioma to examine survival patterns in patients who receive specific treatments between cohorts in Ohio and Taiwan.

Method

Patients aged 18 years and older at age of diagnosis with World Health Organization (WHO) grade III or IV astrocytoma from 2007-2012 were selected from the Ohio Brain Tumor Study and the Taiwan Cancer Registry. The treatment information was derived from medical chart reviews in Ohio and National Health Insurance Research Data in Taiwan. Treatment examined included surgical procedure (brain biopsy and/or resection), radiotherapy (radiation and/or radiosurgery), and alkylating chemotherapy. Kaplan-Meier and parametric survival models were used to examine the effect of treatment on survival, adjusted for age, sex, and comorbidities.

Results

294 patients in Ohio and 1,097 patients in Taiwan met the inclusion criteria. 70.3% patients in Ohio and 51.4% in Taiwan received surgical resection, followed by concurrent chemoradiation. Patients who received this treatment had the highest survival rate, with a 1-year survival rate of 72.8% in Ohio and 73.4% in Taiwan. Patients who did not receive surgical resection, followed by concurrent chemoradiation had an increased risk of death (hazard ratio of 5.03 [95% confidence interval (CI): 3.61-7.02] in Ohio and 1.49 [95% CI: 1.31-1.71] in Taiwan) after adjustment for age, sex, and comorbidities.

Conclusion

Surgical resection followed by concurrent chemoradiation was associated with higher survival rate of patients with high grade glioma in both Ohio and Taiwan; however, one-third of patients in Ohio and half in Taiwan did not receive this treatment.     

Probabilistic Models to Describe the Dynamics of Migrating Microbial Communities

In all but the most sterile environments bacteria will reside in fluid being transported through conduits and some of these will attach and grow as biofilms on the conduit walls. The concentration and diversity of bacteria in the fluid at the point of delivery will be a mix of those when it entered the conduit and those that have become entrained into the flow due to seeding from biofilms. Examples include fluids through conduits such as drinking water pipe networks, endotracheal tubes, catheters and ventilation systems. Here we present two probabilistic models to describe changes in the composition of bulk fluid microbial communities as they are transported through a conduit whilst exposed to biofilm communities. The first (discrete) model simulates absolute numbers of individual cells, whereas the other (continuous) model simulates the relative abundance of taxa in the bulk fluid. The discrete model is founded on a birth-death process whereby the community changes one individual at a time and the numbers of cells in the system can vary. The continuous model is a stochastic differential equation derived from the discrete model and can also accommodate changes in the carrying capacity of the bulk fluid. These models provide a novel Lagrangian framework to investigate and predict the dynamics of migrating microbial communities. In this paper we compare the two models, discuss their merits, possible applications and present simulation results in the context of drinking water distribution systems. Our results provide novel insight into the effects of stochastic dynamics on the composition of non-stationary microbial communities that are exposed to biofilms and provides a new avenue for modelling microbial dynamics in systems where fluids are being transported.