Effective global conservation strategies

Using data on the global distribution of mammal, bird and amphibian species, Grenyer et al. conclude that planning based on individual taxa does not provide efficient solutions for the conservation of other taxa. They also report that the performance of existing global conservation strategies-endemic bird areas, biodiversity hotspots and global 200 ecoregions-in representing those taxa is often no better (and in some cases worse) than random. I argue here that the methodology used by Grenyer et al. was not appropriate for purported globally comprehensive analyses. Focusing on analyses of rare species as an example, I demonstrate how the data actually reveal substantial cross-taxon surrogacy and good performance of existing global conservation strategies.     

A new parsimonious recurrent forecasting model in singular spectrum analysis

Singular spectrum analysis (SSA) is a powerful nonparametric method in the area of time series analysis that has shown its capability in different applications areas. SSA depends on two main choices: the window length L and the number of eigentriples used for grouping r. One of the most important issues when analyzing time series is the forecast of new observations. When using SSA for time series forecasting there are several alternative algorithms, the most widely used being the recurrent forecasting model, which assumes that a given observation can be written as a linear combination of the L?1 previous observations. However, when the window length L is large, the forecasting model is unlikely to be parsimonious. In this paper we propose a new parsimonious recurrent forecasting model that uses an optimal m(<L?1) coefficients in the linear combination of the recurrent SSA. Our results support the idea of using this new parsimonious recurrent forecasting model instead of the standard recurrent SSA forecasting model.     

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leukemia (CLL), the most frequent leukemia in adults in Western countries. We found 1,246 somatic mutations potentially affecting gene function and identified 78 genes with predicted functional alterations in more than one tumor sample. Among these genes, SF3B1, encoding a subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP), is somatically mutated in 9.7% of affected individuals. Further analysis in 279 individuals with CLL showed that SF3B1 mutations were associated with faster disease progression and poor overall survival. This work provides the first comprehensive catalog of somatic mutations in CLL with relevant clinical correlates and defines a large set of new genes that may drive the development of this common form of leukemia. The results reinforce the idea that targeting several well-known genetic pathways, including mRNA splicing, could be useful in the treatment of CLL and other malignancies.     

Reproductive behaviour of the glass frog Hyalinobatrachium cappellei (Anura: Centrolenidae) in the Southern Amazon

Frog species of the Centrolenidae family exhibit a high variation in reproductive behaviours. Herein we describe the reproductive, ecological, acoustic and behavioural features of Hyalinobatrachium cappellei in Southern Amazon. Two hypotheses were also evaluated: (1) are ecological characteristics of the reproductive site related to male size and quantity of eggs and clutches? And (2) do males with one or more existing clutches at reproductive sites accumulate more new clutches than those males initially without them? This study was conducted at two streams, with sampling at 1 km each in Southern Amazon. Species reproduction occurred during the wet season and was considered prolonged breeding. Although male vocalization occurred on both the upper and underside of leaves, clutches were most often deposited on the underside of leaves. Males emitted a courtship call upon female approach. The process of female approach until oviposition lasted approximately eight hours. After oviposition, females left the breeding site while males remained near the clutch, covering it with the belly in ventral brooding behaviour. Thus, egg attendance is reported for the first time for this species. No intraspecific or interspecific aggressive behaviour was recorded. There was no relationship between habitat characteristics of the reproductive sites and male size, number of eggs and clutches. However, after 10 days of monitoring, we found evidences that parental males had a higher number of clutches than those males initially without clutches. Similar to other glass frog species, the behavioural characteristics of H. cappellei make this species an excellent model to use in evaluating the cost-effectiveness of parental care and the importance of egg attendance for offspring survival. Therefore, these data contribute towards a better understanding of the complex phylogenetic and biogeographic relationships between centrolenid lineages.     

Approaches to identify and characterize microProteins and their potential uses in biotechnology

MicroProteins are small proteins that contain a single protein domain and are related to larger, often multi-domain proteins. At the molecular level, microProteins act by interfering with the formation of higher order protein complexes. In the past years, several microProteins have been identified in plants and animals that strongly influence biological processes. Due to their ability to act as dominant regulators in a targeted manner, microProteins have a high potential for biotechnological use. In this review, we present different ways in which microProteins are generated and we elaborate on techniques used to identify and characterize them. Finally, we give an outlook on possible applications in biotechnology.     

Insulin gene region-encoded susceptibility to type 1 diabetes is not restricted to HLA-DR4-positive individuals.

Type 1 or insulin-dependent diabetes mellitus (IDDM) is an autoimmune disease of the insulin-producing pancreatic beta-cells which is determined by both genetic and environmental factors. The major histocompatibility complex and the insulin gene region (INS) on human chromosomes 6p and 11p, respectively, contain susceptibility genes. Using a mostly French data set, evidence for linkage of INS to IDDM was recently obtained but only in male meioses (suggesting involvement of maternal imprinting) and only in HLA-DR4-positive diabetics. In contrast, we find evidence for linkage in both male and female meioses and that the effect of the susceptibility gene(s) in the INS region is not dependent on the presence of HLA-DR4.     

The peroxisomal protein import machinery – a case report of transient ubiquitination with a new flavor

The peroxisomal protein import machinery displays remarkable properties. Be it its capacity to accept already folded proteins as substrates, its complex architecture or its energetics, almost every aspect of this machinery seems unique. The list of unusual properties is still growing as shown by the recent finding that one of its central components, Pex5p, is transiently monoubiquitinated at a cysteine residue. However, the data gathered in recent years also suggest that the peroxisomal import machinery is not that exclusive and similarities with p97/Cdc48-mediated processes and with multisubunit RING-E3 ligases are starting to emerge. Here, we discuss these data trying to distill the principles by which this complex machinery operates. Received 16 July 2008; received after revision 25 August 2008; accepted 29 August 2008     

Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24

Prostate cancer is the most prevalent noncutaneous cancer in males in developed regions, with African American men having among the highest worldwide incidence and mortality rates. Here we report a second genetic variant in the 8q24 region that, in conjunction with another variant we recently discovered, accounts for about 11%-13% of prostate cancer cases in individuals of European descent and 31% of cases in African Americans. We made the current discovery through a genome-wide association scan of 1,453 affected Icelandic individuals and 3,064 controls using the Illumina HumanHap300 BeadChip followed by four replication studies. A key step in the discovery was the construction of a 14-SNP haplotype that efficiently tags a relatively uncommon (2%-4%) susceptibility variant in individuals of European descent that happens to be very common (approximately 42%) in African Americans. The newly identified variant shows a stronger association with affected individuals who have an earlier age at diagnosis.