Peatland microbial communities as indicators of the extreme atmospheric dust deposition

We investigated a peat profile from the Izery Mountains, located within the so-called Black Triangle, the border area of Poland, Czech Republic, and Germany. This peatland suffered from an extreme atmospheric pollution during the last 50 years, which created an exceptional natural experiment to examine the impact of pollution on peatland microbes. Testate amoebae (TA), Centropyxis aerophila and Phryganella acropodia, were distinguished as a proxy of atmospheric pollution caused by extensive brown coal combustion. We recorded a decline of mixotrophic TA and development of agglutinated taxa as a response for the extreme concentration of Al (30 g kg−1) and Cu (96 mg kg−1) as well as the extreme amount of fly ash particles determined by scanning electron microscopy (SEM) analysis, which were used by TA for shell construction. Titanium (5.9 %), aluminum (4.7 %), and chromium (4.2 %) significantly explained the highest percentage of the variance in TA data. Elements such as Al, Ti, Cr, Ni, and Cu were highly correlated (r>0.7, p<0.01) with pseudostome position/body size ratio and pseudostome position. Changes in the community structure, functional diversity, and mechanisms of shell construction were recognized as the indicators of dust pollution. We strengthen the importance of the TA as the bioindicators of the recent atmospheric pollution

Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma

The current model for breast cancer progression proposes independent “low‐grade (LG) like” and “high‐grade (HG) like” pathways but lacks a known precursor to HG cancer. We applied low coverage whole genome sequencing to atypical ductal hyperplasia (ADH) with and without carcinoma to shed light on breast cancer progression. 14/20 isolated ADH cases harboured at least one copy number alteration (CNA), but had fewer aberrations than LG or HG ductal carcinoma in situ (DCIS). ADH carried more HG‐like CNA than LG DCIS (eg. 8q gain). Correspondingly, 64% (7/11) of ADH cases with synchronous HG carcinoma were clonally related, similar to LG carcinoma (67%, 6/9). This study represents a significant shift in our understanding of breast cancer progression, with ADH as a common precursor lesion to the independent “low‐grade like” and “high‐grade like” pathways. These data suggest that ADH can be a precursor of HG breast cancer and that LG and HG carcinomas can evolve from a similar ancestor lesion. We propose that although LG DCIS may be committed to a LG molecular pathway, ADH may remain multipotent, progressing to either LG or HG carcinoma. This multipotent nature suggests that some ADH could be more clinically significant than LG DCIS, requiring biomarkers for personalising management

A classification model for distinguishing copy number variants from cancer-related alterations

<p>Abstract</p> <p>Background</p> <p>Both somatic copy number alterations (CNAs) and germline copy number variants (CNVs) that are prevalent in healthy individuals can appear as recurrent changes in comparative genomic hybridization (CGH) analyses of tumors. In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively.</p> <p>Results</p> <p>We develop a prediction model that distinguishes CNVs from CNAs based on the information contained in the DGV and several other variables, including segment's length, height, closeness to a telomere or centromere and occurrence in other patients. The models are fitted on data from glioblastoma and their corresponding normal samples that were collected as part of The Cancer Genome Atlas project and hybridized to Agilent 244 K arrays.</p> <p>Conclusions</p> <p>Using the DGV alone CNVs in the test set can be correctly identified with about 85% accuracy if the outliers are removed before segmentation and with 72% accuracy if the outliers are included, and additional variables improve the prediction by about 2-3% and 12%, respectively. Final models applied to data from ovarian tumors have about 90% accuracy with all the variables and 86% accuracy with the DGV alone.</p

Peatland Microbial Communities as Indicators of the Extreme Atmospheric Dust Deposition

We investigated a peat profile from the Izery Mountains, located within the so-called Black Triangle, the border area of Poland, Czech Republic, and Germany. This peatland suffered from an extreme atmospheric pollution during the last 50 years, which created an exceptional natural experiment to examine the impact of pollution on peatland microbes. Testate amoebae (TA), Centropyxis aerophila and Phryganella acropodia, were distinguished as a proxy of atmospheric pollution caused by extensive brown coal combustion. We recorded a decline of mixotrophic TA and development of agglutinated taxa as a response for the extreme concentration of Al (30 g kg−1) and Cu (96 mg kg−1) as well as the extreme amount of fly ash particles determined by scanning electron microscopy (SEM) analysis, which were used by TA for shell construction. Titanium (5.9 %), aluminum (4.7 %), and chromium (4.2 %) significantly explained the highest percentage of the variance in TA data. Elements such as Al, Ti, Cr, Ni, and Cu were highly correlated (r>0.7, p<0.01) with pseudostome position/body size ratio and pseudostome position. Changes in the community structure, functional diversity, and mechanisms of shell construction were recognized as the indicators of dust pollution. We strengthen the importance of the TA as the bioindicators of the recent atmospheric pollution

Skład pierwiastkowy popiołów lotnych: studium przypadku z wykorzystaniem metod nuklearnych i analitycznych

Epithermal neutron activation analysis along with ICP-OES, LA ICP-MS, and XRF were used to determine the elemental composition of coal fly ash from the Malta coal power station in the Mpumalanga province of South Africa. A total of 54 major, trace and rare earth elements were obtained by the four analytical techniques. The results were compared and the discrepancies discussed to show the merits and drawbacks of each of the techniques. It was shown that the elemental content of this particular coal fly ash are of the same order as the NIST standard reference material Coal Fly Ash 1633b.W celu określenia składu pierwiastkowego popiołów lotnych z elektrowni węglowej Malta w prowincji Mpumalanga w Republice Południowej Afryki wykorzystano epitermalną, neutronową analizę aktywacyjną oraz ICP-OES, LA ICP-MS i XRF. Za pomocą czterech techniki analitycznych oznaczono stężenia 54 głównych i śladowych pierwiastków oraz pierwiastków ziem rzadkich. Wyniki porównano, a także opisano różnice pokazujące zalety oraz wady każdej z wykorzystanych metod. Wykazano, że skład pierwiastkowy popiołu lotnego jest porównywalny ze składem standardowego materiału odniesienia NIST Węgiel Popiół Lotny 1633b

Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics

Context. Targeted needle biopsies are increasingly performed for the genetic characterization of cancer. While the nucleic acid content of core needle biopsies after standard pathology processing (i.e., formalin fixation and paraffin embedding (FFPE)) has been previously reported, little is known about the potential yield for molecular analysis at the time of biopsy sample acquisition. Objectives. Our objective was to improve the understanding of DNA and RNA yields from commonly used core needle biopsy techniques prior to sample processing. Methods. We performed 552 ex vivo 18 and 20G core biopsies in the lungs, liver, and kidneys. DNA and RNA were extracted from fresh-frozen core samples and quantified for statistical comparisons based on needle gauge, biopsy site, and tissue type. Results. Median tumor DNA yields from all 18G and 20G samples were 5880 ng and 2710 ng, respectively. Median tumor RNA yields from all 18G and 20G samples were 1100 ng and 230 ng, respectively. A wide range of DNA and RNA quantities (1060–13,390 ng and 370–6280 ng, respectively) were acquired. Median DNA and RNA yields from 18G needles were significantly greater than those from 20G needles across all organs (p<0.001). Conclusions. Core needle biopsy techniques for cancer diagnostics yield a broad range of DNA and RNA for molecular pathology, though quantities are greater than what has been reported for FFPE processed material. Since non-formalin-fixed DNA is advantageous for molecular studies, workflows that optimize core needle biopsy yield for molecular characterization should be explored