A Statistical Approach to Identify Ancient Template DNA

One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authentication of sequences obtained from ancient human remains is thought by many to be rather challenging. We propose a novel approach, based on the c statistic, that can be employed to help identify the sequence motif of an endogenous template, based on a sample of sequences that reflect the nucleotide composition of individual template molecules obtained from ancient tissues (such as cloned products from a PCR amplification). The c statistic exploits as information the most common form of postmortem damage observed among clone sequences in ancient DNA studies, namely, lesion-induced substitutions caused by cytosine deamination events. Analyses of simulated sets of templates with miscoding lesions and real sets of clone sequences from the literature indicate that the c-based approach is highly effective in identifying endogenous sequence motifs, even when they are not present among the sampled clones. The proposed approach is likely to be of general use to researchers working with DNA from ancient tissues, particularly from human remains, where authentication of results has been most challenging. [Reviewing Editor: Dr. Magnus Nordborg]     

Getting ready for the marriage market? The association between divorce risks and investments in attractive body mass among married Europeans

This article explores to what extent married middle-aged individuals in Europe are governed by the risk of experiencing divorce, when shaping their physical appearance. The main result is that divorce risks, proxied by national divorce rates, are negatively connected to body mass index (BMI) among married individuals but unrelated to BMI among singles. Hence, it seems that married people in societies where divorce risks are high are more inclined to invest in their outer appearance. One interpretation is that high divorce rates make married people prepare for a potential divorce and future return to the marriage market.     

Diet-dependent depletion of queuosine in tRNAs in Caenorhabditis elegans does not lead to a developmental block

Queuosine (Q), a hypermodified nucleoside, occurs at the wobble position of transfer RNAs (tRNAs) with GUN anticodons. In eubacteria, absence of Q affects messenger RNA (mRNA) translation and reduces the virulence of certain pathogenic strains. In animal cells, changes in the abundance of Q have been shown to correlate with diverse phenomena including stress tolerance, cell proliferation and tumour growth but the function of Q in animals is poorly understood. Animals are thought to obtain Q (or its analogues) as a micronutrient from dietary sources such as gut microflora. However, the difficulty of maintaining animals under bacteria-free conditions on Q-deficient diets has severely hampered the study of Q metabolism and function in animals. In this study, we show that as in higher animals, tRNAs in the nematode Caenorhabditis elegans are modified by Q and its sugar derivatives. When the worms were fed on Q-deficient Escherichia coli, Q modification was absent from the worm tRNAs suggesting that C. elegans lacks a de novo pathway of Q biosynthesis. The inherent advantages of C. elegans as a model organism, and the simplicity of conferring a Q-deficient phenotype on it make it an ideal system to investigate the function of Q modification in tRNA.     

Effects of interferon gamma on native human acute myelogenous leukaemia cells

T cell targeting immunotherapy is now considered a possible strategy in acute myelogenous leukaemia (AML), and IFNγ release may then contribute to the antileukaemic effects. We investigated the effects of IFNγ on native human AML cells. Normal T cells could be activated to release IFNγ in the presence of AML cells. Furthermore, high levels of CD119 (IFNγ receptor α chain) expression were observed for all 39 patients examined. Receptor expression was decreased after exposure to exogenous IFNγ, and receptor ligation caused Stat1 phosphorylation but no phosphorylation of the alternative messengers Erk1/2. The effect of exogenous IFNγ on AML blast proliferation was dependent on the local cytokine network and IFNγ (1) inhibited proliferation in the presence of exogenous IL1β, GM-CSF, G-CSF and SCF; (2) had divergent effects in the presence of IL3 and Flt3 (65 patients examined); (3) inhibited proliferation in the presence of endothelial cells but had divergent effects in the presence of fibroblasts, osteoblasts and normal stromal cells (65 patients examined). IFNγ increased stress-induced (spontaneous) in vitro apoptosis as well as cytarabine-induced apoptosis only for a subset of patients. Furthermore, IFNγ decreased the release of proangiogenic CXCL8 and increased the release of antiangiogenic CXCL9–11. We conclude that IFNγ can be released in the presence of native human AML cells and affect AML cell proliferation, regulation of apoptosis and the balance between pro- and antiangiogenic chemokine release.     

A periodic analysis of longitudinal binary responses: a case study of clinical mastitis in Norwegian Red cows

A Bayesian procedure for analyzing longitudinal binary responses using a periodic cosine function was developed. It was assumed that, after adjustment for "seasonal" effects, the oscillation of the underlying latent variables for longitudinal binary responses was a stationary series. Based on this assumption, a single dimension sinusoidal analysis of longitudinal binary responses using the Gibbs sampling and Metropolis algorithms was implemented in a study of clinical mastitis records of Norwegian Red cows taken over five lactations.     

Emodin negatively affects the phosphoinositide 3-kinase/AKT signalling pathway: a study on its mechanism of action

The development of selective cell-permeable inhibitors of protein kinases whose aberrant activation contributes to cell transformation is a promising approach in cancer treatment. Emodin is a natural anthraquinone derivative that exhibits anti-proliferative effects in various cancer cell lines by efficient induction of apoptosis. The phosphoinositide 3-kinase (PI3K)/AKT pathway has been shown to be central in the promotion of cell survival since the alteration of this signalling cascade is a frequent event in human malignancies. Previous published results indicated that treatment of cells with inhibitors of protein kinase CK2, such as emodin, induces apoptosis and that the anti-apoptotic effect of CK2 is partially mediated by target phosphorylation and up-regulation of AKT by CK2. In the present study, a screening with selected CK2 inhibitors induced a variable response with respect to AKT down-regulation, emodin being the most effective, suggesting that other mechanisms other than the inhibition of CK2 were responsible for the emodin-mediated modulation of AKT. We found that emodin does not directly affect AKT kinase. Furthermore, we show that the down-regulation of AKT is due to the emodin-mediated target inhibition of components of the PI3K pathway, which directly or indirectly affect AKT activity, i.e. the mammalian target of rapamycin and the phosphatase and tensin homolog deleted on chromosome 10, but not the phosphoinositide-dependent kinase 1. Taken together, our results highlight a new mechanism by which emodin exerts anti-cancer activity and suggest the further investigation of plant polyphenols, such as emodin, as therapeutic and preventive agents for cancer therapy.     

Ultrastructure and development of the rhabdomeric eyes in Lineus viridis (Heteronemertea, Nemertea)

Nemerteans are undoubtedly members of the Spiralia, although their phylogenetic relationships are still a matter of debate. The apparently acoelomate organization suggests a relationship with the platyhelminths, whereas the blood-vascular system has been interpreted as an equivalent to coelomic cavities of annelids, indicating a close relation between annelids and nemerteans. Like other spiralians, most nemertean species are known to have one or several pairs of rhabdomeric and subepidermally situated eyes when adult. The development of these eyes as well as the mode in which the eyes are multiplied is as yet unknown. This is the first attempt to investigate eye formation in a nemertean. In the heteronemertean Lineus viridis (Müller, 1774) the everse rhabdomeric eyes are located deeply underneath the epidermis and consist of a few pigment cells that form a cup-like structure with interdigitating processes that contain numerous pigment granules. In hatchlings, the optical cavity contains processes of 12 sensory cells, each bearing a single cilium and various microvilli. The perikarya of these cells are located distally from the pigment cup. During further development the number of cells increases. Eye development starts with a small anlage situated underneath the epidermis, irrespective of whether this is the first eye or any additional one. The anlage consists of five unpigmented cells and three dendritic processes, each bearing apical microvilli and a single cilium. There is no evidence for an epidermal origin of the eyes. In L. viridis eye formation resembles that described in platyhelminths in which eyes also develop as cerebral derivatives. Although this result has the potential to influence the discussion on the position of Nemertea, the data have to be interpreted with care, since development of L. viridis is derived within the Nemertea.     

Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres

Background  

Mammalian centromere formation is dependent on chromatin that contains centromere protein (CENP)-A, which is the centromere-specific histone H3 variant. Human neocentromeres have acquired CENP-A chromatin epigenetically in ectopic chromosomal locations on low-copy complex DNA. Neocentromeres permit detailed investigation of centromeric chromatin organization that is not possible in the highly repetitive alpha satellite DNA present at endogenous centromeres.     

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies

Ontological analysis facilitates the interpretation of microarray data. Here we describe new ontological analysis methods which, unlike existing approaches, are threshold-free and statistically powerful. We perform extensive evaluations and introduce a new concept, detection spectra, to characterize methods. We show that different ontological analysis methods exhibit distinct detection spectra, and that it is critical to account for this diversity. Our results argue strongly against the continued use of existing methods, and provide directions towards an enhanced approach.