Immune recognition. A new receptor for beta-glucans.

The carbohydrate polymers known as beta-1,3-d-glucans exert potent effects on the immune system - stimulating antitumour and antimicrobial activity, for example - by binding to receptors on macrophages and other white blood cells and activating them. Although beta-glucans are known to bind to receptors, such as complement receptor 3 (ref. 1), there is evidence that another beta-glucan receptor is present on macrophages. Here we identify this unknown receptor as dectin-1 (ref. 2), a finding that provides new insights into the innate immune recognition of beta-glucans.     

MCS: A Method for Finding the Number of Clusters

This paper proposes a maximum clustering similarity (MCS) method for determining the number of clusters in a data set by studying the behavior of similarity indices comparing two (of several) clustering methods. The similarity between the two clusterings is calculated at the same number of clusters, using the indices of Rand (R), Fowlkes and Mallows (FM), and Kulczynski (K) each corrected for chance agreement. The number of clusters at which the index attains its maximum is a candidate for the optimal number of clusters. The proposed method is applied to simulated bivariate normal data, and further extended for use in circular data. Its performance is compared to the criteria discussed in Tibshirani, Walther, and Hastie (2001). The proposed method is not based on any distributional or data assumption which makes it widely applicable to any type of data that can be clustered using at least two clustering algorithms.     

Nest architecture in polydomous grass-cutting ants (Acromyrmex balzani)

Acromyrmex balzani is a grass-cutting ant species frequently found in Cerrado areas. However, little is known about the architecture of the polydomous nests of this ant. Fifteen A. balzani nests located in a cerrado region in Botucatu, São Paulo, Brazil, were studied. The polydomous nests were studied in three ways. First, we investigated the architecture in nests moulded with cement and without moulding. Second, we performed an aggressiveness test among workers in different subnests and nests. Third, we excavated the nest and collected the colony to measure the population, verifying the existence or not of a queen in all nests. A cement mould was made of seven nests to permit better visualization of internal structures such as chambers and tunnels. Eight nests were excavated without moulding and white neutral talc was used to highlight the parts of the nests. After excavation, the depth and dimensions (length, width and height) of the chambers were measured. The results showed that the nests had a single entrance hole whose structure consisted of straw and other plant residues in winter. Mounds of loose soil, if present, were found 6–48 cm from the hole. The number of chambers containing fungus ranged from one to five, with the first being found a few centimetres beneath the ground surface (4 cm) and the last up to a maximum depth of 160 cm. The length of the tunnels ranged from 12 to 28 cm. These tunnels were built in a vertical or inclined position, leading to the chambers. No waste chambers were found, with the waste being deposited externally. Additionally, the polydomous nests contained one to eight subnests. In the aggressiveness test, when concolonial workers were confronted, no aggressiveness was observed. In contrast, when allocolonial workers were confronted, there was a high incidence of aggression among them. Excavation of polydomous nests showed only one queen for each polydomous nest, i.e. subnests with a single queen. Our study contributes to a better understanding of the so far unknown nest architecture of the polydomous grass-cutting ant A. balzani.     

Common loss-of-function variants of the epidermal barrier protein filaggrin are a major predisposing factor for atopic dermatitis

Atopic disease, including atopic dermatitis (eczema), allergy and asthma, has increased in frequency in recent decades and now affects approximately 20% of the population in the developed world. Twin and family studies have shown that predisposition to atopic disease is highly heritable. Although most genetic studies have focused on immunological mechanisms, a primary epithelial barrier defect has been anticipated. Filaggrin is a key protein that facilitates terminal differentiation of the epidermis and formation of the skin barrier. Here we show that two independent loss-of-function genetic variants (R510X and 2282del4) in the gene encoding filaggrin (FLG) are very strong predisposing factors for atopic dermatitis. These variants are carried by approximately 9% of people of European origin. These variants also show highly significant association with asthma occurring in the context of atopic dermatitis. This work establishes a key role for impaired skin barrier function in the development of atopic disease.     

ANG mutations segregate with familial and 'sporadic' amyotrophic lateral sclerosis

We recently identified angiogenin (ANG) as a candidate susceptibility gene for amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder characterized by adult-onset loss of motor neurons. We now report the finding of seven missense mutations in 15 individuals, of whom four had familial ALS and 11 apparently 'sporadic' ALS. Our findings provide further evidence that variations in hypoxia-inducible genes have an important role in motor neuron degeneration.     

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets

We present the first analysis of the human proteome with regard to interactions between proteins. We also compare the human interactome with the available interaction datasets from yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans) and fly (Drosophila melanogaster). Of >70,000 binary interactions, only 42 were common to human, worm and fly, and only 16 were common to all four datasets. An additional 36 interactions were common to fly and worm but were not observed in humans, although a coimmunoprecipitation assay showed that 9 of the interactions do occur in humans. A re-examination of the connectivity of essential genes in yeast and humans indicated that the available data do not support the presumption that the number of interaction partners can accurately predict whether a gene is essential. Finally, we found that proteins encoded by genes mutated in inherited genetic disorders are likely to interact with proteins known to cause similar disorders, suggesting the existence of disease subnetworks. The human interaction map constructed from our analysis should facilitate an integrative systems biology approach to elucidating the cellular networks that contribute to health and disease states.     

The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana

Light has an important role in modulating seedling growth and flowering time. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a latitudinal cline dependent on FRIGIDA, a locus that together with FLOWERING LOCUS C explains a large portion of the variation in A. thaliana flowering time. In a genome-wide scan for association of 65 loci with latitude, there was an excess of significant P values, indicative of population structure. Nevertheless, PHYC was the most strongly associated locus across 163 strains, suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work, together with previous findings, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response.     

A common variant associated with prostate cancer in European and African populations

With the increasing incidence of prostate cancer, identifying common genetic variants that confer risk of the disease is important. Here we report such a variant on chromosome 8q24, a region initially identified through a study of Icelandic families. Allele -8 of the microsatellite DG8S737 was associated with prostate cancer in three case-control series of European ancestry from Iceland, Sweden and the US. The estimated odds ratio (OR) of the allele is 1.62 (P = 2.7 x 10(-11)). About 19% of affected men and 13% of the general population carry at least one copy, yielding a population attributable risk (PAR) of approximately 8%. The association was also replicated in an African American case-control group with a similar OR, in which 41% of affected individuals and 30% of the population are carriers. This leads to a greater estimated PAR (16%) that may contribute to higher incidence of prostate cancer in African American men than in men of European ancestry.