Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores

In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.     

Molecular Diagnostic and Prognostic Subtyping of Gliomas in Tunisian Population

It has become increasingly evident that morphologically similar gliomas may have distinct clinical phenotypes arising from diverse genetic signatures. To date, glial tumours from the Tunisian population have not been investigated. To address this, we correlated the clinico-pathology with molecular data of 110 gliomas by a combination of HM450K array, MLPA and TMA-IHC. PTEN loss and EGFR amplification were distributed in different glioma histological groups. However, 1p19q co-deletion and KIAA1549:BRAF fusion were, respectively, restricted to Oligodendroglioma and Pilocytic Astrocytoma. CDKN2A loss and EGFR overexpression were more common within high-grade gliomas. Furthermore, survival statistical correlations led us to identify Glioblastoma (GB) prognosis subtypes. In fact, significant lower overall survival (OS) was detected within GB that overexpressed EGFR and Cox2. In addition, IDH1R132H mutation seemed to provide a markedly survival advantage. Interestingly, the association of IDHR132H mutation and EGFR normal status, as well as the association of differentiation markers, defined GB subtypes with good prognosis. By contrast, poor survival GB subtypes were defined by the combination of PTEN loss with PDGFRa expression and/or EGFR amplification. Additionally, GB presenting p53-negative staining associated with CDKN2A loss or p21 positivity represented a subtype with short survival. Thus, distinct molecular subtypes with individualised prognosis were identified. Interestingly, we found a unique histone mutation in a poor survival young adult GB case. This tumour exceptionally associated the H3F3A G34R mutation and MYCN amplification as well as 1p36 loss and 10q loss. Furthermore, by exhibiting a remarkable methylation profile, it emphasised the oncogenic power of G34R mutation connecting gliomagenesis and chromatin regulation.     

A multiresolution approach to orientation assignment in 3D electron microscopy of single particles

Three-dimensional (3D) electron microscopy (3DEM) aims at the determination of the spatial distribution of the Coulomb potential of macromolecular complexes. The 3D reconstruction of a macromolecule using single-particle techniques involves thousands of 2D projections. One of the key parameters required to perform such a 3D reconstruction is the orientation of each projection image as well as its in-plane orientation. This information is unknown experimentally and must be determined using image-processing techniques. We propose the use of wavelets to match the experimental projections with those obtained from a reference 3D model. The wavelet decomposition of the projection images provides a framework for a multiscale matching algorithm in which speed and robustness to noise are gained. Furthermore, this multiresolution approach is combined with a novel orientation selection strategy. Results obtained from computer simulations as well as experimental data encourage the use of this approach.     

Capacity for sustained terrestrial locomotion in an insect: Energetics,thermal dependence,and kinematics

Summary The capacity for sustained, terrestrial locomotion in the cockroach. Blaberus discoidalis, was determined in relation to running speed, metabolic cost, aerobic capacity, and ambient temperature (T _a=15, 23, and 34°C; acclimation temperature=24°C). Steady-state thoracic temperature (T _tss) increased linearly with speed at each T _a.The difference between T _tss and T _awas similar at each experimental temperature with a maximum increase of 7°C. Steady-state oxygen consumption (VO_2ss) increased linearly with speed at each T _aand had a low thermal dependence (Q₁₀=1.0-1.4). The minimum cost of locomotion (the slope of the VO_2ss versus speed function) was independent of T _a.Cockroaches attained a maximal oxygen consumption (VO_2max). increased with T _afrom 2.1 ml O₂·g^-1·h^-1 at 15°C to 4.9 ml O₂·g^-1·h^-1 at 23°C, but showed no further increase at 34°C, VO_2max increased 23-fold over resting VO₂ at 23°C, 10-fold at 34°C, and 15-fold at 15°C. Endurance correlated with the speed at which VO_2max was attained (MAS, maximal aerobic speed). Temperature affected the kinematics of locomotion. compared to cockroaches running at the same speed, but higher temperatures (23–34°C), low temperature (15°C) increased protraction time, reduced stride frequency, and reduced stability by increasing body pitching. The thermal independence of the minimum cost of locomotion (C_min), the low thermal dependence of VO_2ss (i.e., y-intercept of the VO_2ss versus speed function), and a typical Q₁₀ of 2.0 for VO_2max combined to increase MAS and endurance in B. discoidalis when T _awas increased from 15 to 23°C. Exerciserelated endothermy enabled running cockroaches to attain a greater VO_2max, metabolic scope, and endurance capacity at 23°C than would be possible if T _tss remained equal to T _a. The MAS of B. discoidalis was similar to that of other arthropods that use trachea, but was 2-fold greater than ectotherms, such as salamanders, frogs, and crabs of a comparable body mass.Abbreviations T _a ambient temperature - T _t thoracic temperature - T _tss steady state thoracic temperature during exercise - T _trest thoracic temperature during rest - VO₂ oxygen consumption - VO_2rest oxygen consumption during rest - VO_2ss steady-state oxygen consumption during exercise - VO_2max maximal oxygen consumption; MAS maximum aerobic speed - C _min minimum cost of locomotion - t _end endurance time     

Prevalence of antibodies to Trypanosoma cruzi in raccoons (Procyon lotor) from an urban area of northern Virginia

Raccoons (Procyon lotor) are reservoir hosts for Trypanosoma cruzi. A 3-yr-long serological survey was conducted to determine the prevalence of antibodies to this zoonotic parasite in raccoons collected from Fairfax County, Virginia, a suburban/urban area outside Washington, D.C. Serum samples from 464 raccoons were examined for T. cruzi antibodies at a 1:40 dilution with an indirect fluorescent antibody test (IFAT) and Brazil strain T. cruzi amastigotes and trypomastigotes as antigen. A positive IFAT test was found in 154 (33%) of the 464 samples. The yearly prevalence was 49 of 132 (37%) in 2000; 19 of 120 (16%) in 2001; and 86 of 212 (41%) in 2002. Our study indicates that raccoons in this area of Virginia are frequently exposed to T. cruzi.     

Replication-independent histone deposition by the HIR complex and Asf1

The orderly deposition of histones onto DNA is mediated by conserved assembly complexes, including chromatin assembly factor-1 (CAF-1) and the Hir proteins . CAF-1 and the Hir proteins operate in distinct but functionally overlapping histone deposition pathways in vivo . The Hir proteins and CAF-1 share a common partner, the highly conserved histone H3/H4 binding protein Asf1, which binds the middle subunit of CAF-1 as well as to Hir proteins . Asf1 binds to newly synthesized histones H3/H4 , and this complex stimulates histone deposition by CAF-1 . In yeast, Asf1 is required for the contribution of the Hir proteins to gene silencing . Here, we demonstrate that Hir1, Hir2, Hir3, and Hpc2 comprise the HIR complex, which copurifies with the histone deposition protein Asf1. Together, the HIR complex and Asf1 deposit histones onto DNA in a replication-independent manner. Histone deposition by the HIR complex and Asf1 is impaired by a mutation in Asf1 that inhibits HIR binding. These data indicate that the HIR complex and Asf1 proteins function together as a conserved eukaryotic pathway for histone replacement throughout the cell cycle.     

Protein biomarkers for subtyping breast cancer and implications for future research

Introduction: Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure.

Areas covered: This review provides a summary of immunohistochemistry, reverse phase protein array, mass spectrometry, and integrative studies that are revealing differences in biological functions within and between breast cancer subtypes. We conclude with a discussion of rigor and reproducibility for proteomic-based biomarker discovery.

Expert commentary: Innovations in proteomics, including implementation of assay guidelines and standards, are facilitating refinement of breast cancer subtypes. Proteomic and phosphoproteomic information distinguish biologically functional subtypes, are predictive of recurrence, and indicate likelihood of drug resistance. Actionable, activated signal transduction pathways can now be quantified and characterized. Proteomic biomarker validation in large, well-designed studies should become a public health priority to capitalize on the wealth of information gleaned from the proteome.     

Consent for participating in clinical trials ‐ Is it really informed?

The article explores the challenges of ensuring voluntary and informed consent which is obtained from potential research subjects in the north‐eastern part of Romania. This study is one of the first empirical papers of this nature in Romania. The study used a quantitative survey design using the adapted Quality of Informed Consent (QuIC) questionnaire. The target population consisted of 100 adult persons who voluntarily enrolled in clinical trials. The informed consent form must contain details regarding the potential risks and benefits, the aim of the clinical trial, study design, confidentiality, insurance and contact details in case of additional questions. Our study confirmed that although all required information was included in the ICF, few clinical trial participants truly understood it. We also found that the most important predictive factor for a good subjective and objective understanding of the clinical trial was the level of education. Our study suggests that researchers should consider putting more effort in order to help clinical trials participants achieve a better understanding of the informed consent. In this way they will ensure that participants’ decision‐making is meaningful and that their interests are protected.     

Investigating zoonotic infection barriers to ape Plasmodium parasites using faecal DNA analysis

African apes are endemically infected with numerous Plasmodium spp. including close relatives of human Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae. Although these ape parasites are not believed to pose a zoonotic threat, their ability to colonise humans has not been fully explored. In particular, it remains unknown whether ape parasites are able to initiate exo-erythrocytic replication in human hepatocytes following the bite of an infective mosquito. Since animal studies have shown that liver stage infection can result in the excretion of parasite nucleic acids into the bile, we screened faecal samples from 504 rural Cameroonians for Plasmodium DNA. Using pan-Laverania as well as P. malariae- and P. vivax-specific primer sets, we amplified human P. falciparum (n?=?14), P. malariae (n?=?1), and P. ovale wallikeri (n?=?1) mitochondrial sequences from faecal DNA of 15 individuals. However, despite using an intensified PCR screening approach we failed to detect ape Laverania, ape P. vivax or ape P. malariae parasites in these same subjects. One faecal sample from a hunter-gatherer contained a sequence closely related to the porcupine parasite Plasmodium atheruri. Since this same faecal sample also contained porcupine mitochondrial DNA, but a matching blood sample was Plasmodium-negative, it is likely that this hunter-gatherer consumed Plasmodium-infected bushmeat. Faecal Plasmodium detection was not secondary to intestinal bleeding and/or infection with gastrointestinal parasites, but indicative of blood parasitaemia. Quantitative PCR identified 26-fold more parasite DNA in the blood of faecal Plasmodium-positive than faecal Plasmodium-negative individuals (P?=?0.01). However, among blood-positive individuals only 10% - 20% had detectable Plasmodium sequences in their stool. Thus, faecal screening of rural Cameroonians failed to uncover abortive ape Plasmodium infections, but detected infection with human parasites, albeit with reduced sensitivity compared with blood analysis.