The influence of low-frequency variability on tree-rings based climate reconstruction: a case study from central Italy (Roman coast)

Tree rings are among the best sources of proxy data for reconstructing past climatic records. In this study we explore for the first time what type of climatic signals can be reconstructed from stone pine (Pinus pinea L.) based on tree-rings from central Italy (Roman coast). Samples from 112 stone pine trees from stands with different age classes were collected at two locations, Castel Fusano and Castelporziano. In determining the particular target variable for climate reconstruction we explored a wide range of climatic signals (from monthly to multiple year scale) for correlations with tree ring chronologies produced using a variety of detrending methods. We reconstructed short term (autumn-early winter) and long term (3 years precipitation) signals during the 150 years of available data using the “classical” detrending method but also methods preserving their low frequency variability (ABD and RCS) within the chronologies. By setting the best multiple year precipitation drivers at an annual scale and applying a simple percentile threshold approach, we identified the wettest and driest climatic events. The best accuracy in identifying the climatic thresholds was obtained with the ABD method, which also showed the best cross spectral correlation with a long precipitation record. Our reconstruction underpins that since ca. 1850 the Roman coast has experienced its driest conditions in terms of 2-3 year rainfall sums during the last 50 years of the 20th Century. This finding may be used in the context of identifying the long-term natural variability of the region in relation to climate change as it is expected to affect the Mediterranean

Molecular dynamics recipes for genome research

Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect

RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts

The physiology and behavior of living organisms are featured by time-related variations driven by molecular clockworks that arose during evolution stochastically and heterogeneously. Over the years, several high-throughput experiments were performed to evaluate time-dependent gene expression in different cell types across several species and experimental conditions. Here, these were retrieved, manually curated, and analyzed by two software packages, BioCycle and MetaCycle, to infer circadian or ultradian transcripts across different species. These transcripts were stored in RhythmicDB and made publically available

A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics

Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components

Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer

Alterations in the balance of mRNA and microRNA (miRNA) expression profiles contribute to the onset and development of colorectal cancer. The regulatory functions of individual miRNA-gene pairs are widely acknowledged, but group effects are largely unexplored. We performed an integrative analysis of mRNA–miRNA and miRNA–miRNA interactions using high-throughput mRNA and miRNA expression profiles obtained from matched specimens of human colorectal cancer tissue and adjacent non- tumorous mucosa. This investigation resulted in a hypernetwork-based model, whose functional back- bone was fulfilled by tight micro-societies of miR- NAs. These proved to modulate several genes that are known to control a set of significantly enriched cancer-enhancer and cancer-protection biological processes, and that an array of upstream regulatory analyses demonstrated to be dependent on miR-145, a cell cycle and MAPK signalling cascade master regulator. In conclusion, we reveal miRNA-gene clusters and gene families with close functional relationships and highlight the role of miR-145 as potent upstream regulator of a complex RNA–RNA crosstalk, which mechanistically modulates several signalling path- ways and regulatory circuits that when deranged are relevant to the changes occurring in colorectal carcinogenesis

Characterization of Italian isolates of Inonotus rickii

Thirty-seven isolates of Inonotus rickii, a pathogenic fungus causing white rot and cankers, were collected from diseased boxelder trees lining boulevards in Rome and from other hosts in Rome and Sicily. During the survey, it was observed that this fungus occasionally produced basidiomes, but more frequently it had anamorphic structures that released a brown powdery mass of chlamydospores, presumably acting as asexual propagules. All isolates were characterized using random amplified microsatellite analysis and somatic incompatibility tests in order to investigate the diversity of genotypes within and between the different disease centers surveyed in Italy. The results suggest that both sexual and asexual reproduction play an important role in the spread of this disease, with important epidemiological implications. 

DWI-MR and PET-CT Functional Imaging for Boost Tumor Volume Delineation in Neoadjuvant Rectal Cancer Treatment

BACKGROUND/AIM T2 weighted magnetic resonance (MR) imaging is the gold standard for locally advanced rectal cancer (LARC) staging. The potential benefit of functional imaging, as diffusion-weighted MR (DWI) and positron emission tomography-computed tomography (PET-CT), could be considered for treatment intensification strategies. Dose intensification resulted in better pathological complete response (pCR) rates. This study evaluated the inter-observer agreement between two radiation oncologists, and the difference in gross tumor volume (GTV) delineation in simulation-CT, T2-MR, DWI-MR, and PET-CT in patients with LARC. PATIENTS AND METHODS Two radiation oncologists prospectively delineated GTVs of 24 patients on simul-CT (CT$_{GTV}$), T2-weighted MR (T2$_{GTV}$), echo planar b1000 DWI (DWI$_{GTV}$) and PET-CT (PET$_{GTV}$). Observers' agreement was assessed using Dice index. Kruskal-Wallis test assessed differences between methods. RESULTS Mean CT$_{GTV}$, T2$_{GTV}$, DWI$_{GTV}$, and PET$_{GTV}$ were 41.3±26.9 cc, 25.9±15.2 cc, 21±14.8 cc, and 37.7±27.7 cc for the first observer, and 42.2±27.9 cc, 27.6±16.9 cc, 19.9±14.9cc, and 34.8±24.3 cc for the second observer, respectively. Mean Dice index was 0.85 for CT$_{GTV}$, 0.84 for T2$_{GTV}$, 0.82 for DWI$_{GTV}$, and 0.89 for PET$_{GTV}$, representative of almost perfect agreement. Kruskal-Wallis test showed a statistically significant difference between methods (p=0.009). Dunn test showed there were differences between DWI$_{GTV}$ vs. PET$_{GTV}$ (p=0.040) and DWI$_{GTV}$ vs. CT$_{GTV}$ (p=0.008). CONCLUSION DWI resulted in smaller volume delineation compared to CT, T2-MR, and PET-CT functional images. Almost perfect agreements were reported for each imaging modality between two observers. DWI-MR seems to remain the optimal strategy for boost volume delineation for dose escalation in patients with LARC

Mirna Expression Profiles Identify Drivers in Colorectal and Pancreatic Cancers

Altered expression of microRNAs (miRNAs) hallmarks many cancer types. The study of the associations of miRNA expression profile and cancer phenotype could help identify the links between deregulation of miRNA expression and oncogenic pathways.Expression profiling of 866 human miRNAs in 19 colorectal and 17 pancreatic cancers and in matched adjacent normal tissues was investigated. Classical paired t-test and random forest analyses were applied to identify miRNAs associated with tissue-specific tumors. Network analysis based on a computational approach to mine associations between cancer types and miRNAs was performed. in pancreatic cancers.MiRNA expression profiles may identify cancer-specific signatures and potentially useful biomarkers for the diagnosis of tissue specific cancers. miRNA-network analysis help identify altered miRNA regulatory networks that could play a role in tumor pathogenesis