Identifying subgroup markers in heterogeneous populations

Traditional methods that aim to identify biomarkers that distinguish between two groups, like Significance Analysis of Microarrays or the t-test, perform optimally when such biomarkers show homogeneous behavior within each group and differential behavior between the groups. However, in many applications, this is not the case. Instead, a subgroup of samples in one group shows differential behavior with respect to all other samples. To successfully detect markers showing such imbalanced patterns of differential signal, a different approach is required. We propose a novel method, specifically designed for the Detection of Imbalanced Differential Signal (DIDS). We use an artificial dataset and a human breast cancer dataset to measure its performance and compare it with three traditional methods and four approaches that take imbalanced signal into account. Supported by extensive experimental results, we show that DIDS outperforms all other approaches in terms of power and positive predictive value. In a mouse breast cancer dataset, DIDS is the only approach that detects a functionally validated marker of chemotherapy resistance. DIDS can be applied to any continuous value data, including gene expression data, and in any context where imbalanced differential signal is manifested.     

Spatio-temporal history of the disjunct family Tecophilaeaceae: a tale involving the colonization of three Mediterranean-type ecosystems

Background and Aims

Tecophilaeaceae (27 species distributed in eight genera) have a disjunct distribution in California, Chile and southern and tropical mainland Africa. Moreover, although the family mainly occurs in arid ecosystems, it has colonized three Mediterranean-type ecosystems. In this study, the spatio-temporal history of the family is examined using DNA sequence data from six plastid regions.

Methods

Modern methods in divergence time estimation (BEAST), diversification (LTT and GeoSSE) and biogeography (LAGRANGE) are applied to infer the evolutionary history of Tecophilaeaceae. To take into account dating and phylogenetic uncertainty, the biogeographical inferences were run over a set of dated Bayesian trees and the analyses were constrained according to palaeogeographical evidence.

Key Results

The analyses showed that the current distribution and diversification of the family were influenced primarily by the break up of Gondwana, separating the family into two main clades, and the establishment of a Mediterranean climate in Chile, coinciding with the radiation of Conanthera. Finally, unlike many other groups, no shifts in diversification rates were observed associated with the dispersals in the Cape region of South Africa.

Conclusions

Although modest in size, Tecophilaeaceae have a complex spatio-temporal history. The family is now most diverse in arid ecosystems in southern Africa, but is expected to have originated in sub-tropical Africa. It has subsequently colonized Mediterranean-type ecosystems in both the Northern and Southern Hemispheres, but well before the onset of the Mediterranean climate in these regions. Only one lineage, genus Conanthera, has apparently diversified to any extent under the impetus of a Mediterranean climate.     

Fungizide: Risiken der resistenzentwicklung und suche nach neuen targets

Trotz intensiver Bemühungen im Bereich des Pflanzenschutzes sind weltweit erhebliche Verluste im Bereich pflanzlicher Erntegüter zu verzeichnen. Rund ein Drittel der Verluste werden mikrobiellen Schaderregern, also Pilzen, Bakterien und Viren, zugeschrieben. Besonders schwierig ist der Tatsache zu begegnen, dass Pilze gegenüber spezifisch wirkenden Fungiziden Insensitivitäten bzw. Resistenzen entwickeln. Aus diesem Grunde muss über geeignete Strategien beim Fungizideinsatz, beim ‘Disease management’ und bei der Suche nach neuen, hochwirksamen Fungiziden nachgedacht werden. Der Erfolg bei der Suche nach neuen Fungiziden wird stark davon abhängen, ob neue Zielmoleküle für potentielle Fungizide entdeckt werden können. Dabei können moderne molekulargenetische Techniken von großem Nutzen sein.     

A new Pliocene mollusk fauna from Mejillones, northern Chile

A new Pliocene (3.4 Ma) mollusk fauna from Mejillones Peninsula, northern Chile is described and compared with the Pliocene La Cueva fauna of little constrained age from central Chile and some species from the Huenteguapi Sandstone overlying the Ranquil Formation on Arauco Peninsula, south central Chile. Preliminary correlation is based on faunal similarities. A total of 45 taxa were identified, of which Cyclocardia kieli sp. nov. is new to science. New combinations are Macron escalonia (Vermeij and DeVries, 1997), Austrofusus steinmanni (Möricke, 1896) and Leukoma antiqua (King, 1832). For several species, the oldest occurrences and range extensions are reported. Co-occurrence of warm water taxa, previously assigned to MIS 11, and typical Pliocene taxa on Mejillones cannot be confirmed. Pliocene and Pleistocene mollusk faunas from Mejillones are listed for comparison.     

Role of the Phosphatidylserine Receptor TIM-1 in Enveloped-Virus Entry

The cell surface receptor T cell immunoglobulin mucin domain 1 (TIM-1) dramatically enhances filovirus infection of epithelial cells. Here, we showed that key phosphatidylserine (PtdSer) binding residues of the TIM-1 IgV domain are critical for Ebola virus (EBOV) entry through direct interaction with PtdSer on the viral envelope. PtdSer liposomes but not phosphatidylcholine liposomes competed with TIM-1 for EBOV pseudovirion binding and transduction. Further, annexin V (AnxV) substituted for the TIM-1 IgV domain, supporting a PtdSer-dependent mechanism. Our findings suggest that TIM-1-dependent uptake of EBOV occurs by apoptotic mimicry. Additionally, TIM-1 enhanced infection of a wide range of enveloped viruses, including alphaviruses and a baculovirus. As further evidence of the critical role of enveloped-virion-associated PtdSer in TIM-1-mediated uptake, TIM-1 enhanced internalization of pseudovirions and virus-like proteins (VLPs) lacking a glycoprotein, providing evidence that TIM-1 and PtdSer-binding receptors can mediate virus uptake independent of a glycoprotein. These results provide evidence for a broad role of TIM-1 as a PtdSer-binding receptor that mediates enveloped-virus uptake. Utilization of PtdSer-binding receptors may explain the wide tropism of many of these viruses and provide new avenues for controlling their virulence.     

Ion-specific Effects on Prion Nucleation and Strain Formation

Ordered, fibrous, self-seeding aggregates of misfolded proteins known as amyloids are associated with important diseases in mammals and control phenotypic traits in fungi. A given protein may adopt multiple amyloid conformations, known as variants or strains, each of which leads to a distinct disease pattern or phenotype. Here, we study the effect of Hofmeister ions on amyloid nucleation and strain generation by the prion domain-containing fragment (Sup35NM) of a yeast protein Sup35p. Strongly hydrated anions (kosmotropes) initiate nucleation quickly and cause rapid fiber elongation, whereas poorly hydrated anions (chaotropes) delay nucleation and mildly affect the elongation rate. For the first time, we demonstrate that kosmotropes favor formation of amyloid strains that are characterized by lower thermostability and higher frangibility in vitro and stronger phenotypic and proliferation patterns effectively in vivo as compared with amyloids formed in chaotropes. These phenomena point to inherent differences in the biochemistry of Hofmeister ions. Our work shows that the ionic composition of a solution not only influences the kinetics of amyloid nucleation but also determines the amyloid strain that is preferentially formed.