Growing up on a farm protects children from asthma. In this study, the investigators show that the diversity of microbial exposure of farm children as compared with children in the reference group ...can explain the observed protective effect.
Environmental exposure to microorganisms has repeatedly been found to be inversely related to the manifestation of atopic diseases such as asthma and hay fever. This observation has been made in various contexts, including the studies conducted in the Republic of Karelia (Russia) and North Karelia (Finland), in which two populations in geographically adjacent areas live under different environmental conditions. In the population with higher bacterial exposures, the prevalence of asthma and atopy was substantially lower.
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Another example supporting this notion is the lower prevalence of asthma and atopy among children raised on a farm.
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Many studies using microbial products, such . . .
IDH1 encodes isocitrate dehydrogenase 1, which participates in the citric acid cycle and was recently reported to be mutated in 12% of glioblastomas. We assessed IDH1 mutations in 321 gliomas of ...various histological types and biological behaviors. A total of 130 IDH1 mutations was detected, and all were located at amino acid residue 132. Of these, 91% were G→A mutations (Arg→His). IDH1 mutations were frequent in low-grade diffuse astrocytomas (88%) and in secondary glioblastomas that developed through progression from low-grade diffuse or anaplastic astrocytoma (82%). Similarly, high frequencies of IDH1 mutations were found in oligodendrogliomas (79%) and oligoastrocytomas (94%). Analyses of multiple biopsies from the same patient (51 cases) showed that there were no cases in which an IDH1 mutation occurred after the acquisition of either a TP53 mutation or loss of 1p/19q, suggesting that IDH1 mutations are very early events in gliomagenesis and may affect a common glial precursor cell population. IDH1 mutations were co-present with TP53 mutations in 63% of low-grade diffuse astrocytomas and with loss of heterozygosity 1p/19q in 64% of oligodendrogliomas; they were rare in pilocytic astrocytomas (10%) and primary glioblastomas (5%) and absent in ependymomas. The frequent presence of IDH1 mutations in secondary glioblastomas and their near-complete absence in primary glioblastomas reinforce the concept that despite their histological similarities, these subtypes are genetically and clinically distinct entities.
Microbial electrochemical systems (MESs) are an attracting technology for the disposal of wastewater treatment and simultaneous energy production. In MESs, at the anode microorganisms through the ...catalytic activity generates electrons that can be converted into electricity or other valuable chemical compounds. Microorganisms those having ability to donate and accept electrons to and from anode and cathode electrodes, respectively are recognized as ‘exoelectrogens’. In the MESs, it renders an important function for its performance. In the present mini-review, we have discussed the role of microbiome including pure culture, enriched culture and mixed culture in different BESs application. The effects of operational and biological factors on microbiome development have been discussed. Further discussion about the molecular techniques for the evaluation of microbial community analysis is addressed. In addition different electrochemical techniques for extracellular electron transfer (EET) mechanism of electroactive biofilms have been discussed. This review highlights the importance of microbiome in the development of MESs, effective operational factors for exo-electrogens activities as well their key challenges and future technological aspects are also briefly discussed.
•Key microbiomes involved in MECs were summarized and discussed.•The effects of operational factors on microbiome development have been discussed.•Monitoring of microbial communities and their importance were reviewed.•Bottlenecks associated with scale up of MEC technology are discussed.
Background
Single sample predictors (SSPs) and Subtype classification models (SCMs) are gene expression-based classifiers used to identify the four primary molecular subtypes of breast cancer ...(basal-like, HER2-enriched, luminal A, and luminal B). SSPs use hierarchical clustering, followed by nearest centroid classification, based on large sets of tumor-intrinsic genes. SCMs use a mixture of Gaussian distributions based on sets of genes with expression specifically correlated with three key breast cancer genes (estrogen receptor ER, HER2, and aurora kinase A AURKA). The aim of this study was to compare the robustness, classification concordance, and prognostic value of these classifiers with those of a simplified three-gene SCM in a large compendium of microarray datasets.
Methods
Thirty-six publicly available breast cancer datasets (n = 5715) were subjected to molecular subtyping using five published classifiers (three SSPs and two SCMs) and SCMGENE, the new three-gene (ER, HER2, and AURKA) SCM. We used the prediction strength statistic to estimate robustness of the classification models, defined as the capacity of a classifier to assign the same tumors to the same subtypes independently of the dataset used to fit it. We used Cohen κ and Cramer V coefficients to assess concordance between the subtype classifiers and association with clinical variables, respectively. We used Kaplan-Meier survival curves and cross-validated partial likelihood to compare prognostic value of the resulting classifications. All statistical tests were two-sided.
Results
SCMs were statistically significantly more robust than SSPs, with SCMGENE being the most robust because of its simplicity. SCMGENE was statistically significantly concordant with published SCMs (κ = 0.65-0.70) and SSPs (κ = 0.34-0.59), statistically significantly associated with ER (V = 0.64), HER2 (V = 0.52) status, and histological grade (V = 0.55), and yielded similar strong prognostic value.
Conclusion
Our results suggest that adequate classification of the major and clinically relevant molecular subtypes of breast cancer can be robustly achieved with quantitative measurements of three key genes.
Recurrent somatic mutations in MED12 exon 2 have recently been reported in uterine leiomyomas. The recurrent nature of the mutations strongly suggests that the mutations may play important roles in ...the pathogenesis of uterine leiomyomas. The aim of our study was to see whether MED12 exon 2 mutations occur in other human tumors besides uterine leiomyomas. We also attempted to confirm occurrence of the MED12 mutations in uterine leiomyomas of Korean patients. For this, we analyzed 1,862 tumor tissues, including a variety of carcinomas, leukemias and stromal tumors by single‐strand conformation polymorphism analysis. We found MED12 mutations in 35 uterine leiomyomas (35/67; 52.2%) and one colon carcinoma (0.3%), but none in other tumors. The MED12 mutations consisted of missense (77%) and inframe insertion‐deletion (23%) mutations, the pattern of which was similar to the earlier report. Our data indicate that MED12 exon 2 mutations may be tissue‐specific to uterine leiomyoma and rare in other tumors. Our study suggests that the MED12 mutations play unique roles in the pathogenesis of uterine leiomyomas and mutated MED12 could be therapeutically targeted in uterine leiomyomas.
The median survival of glioblastoma patients is ∼12 months. However, 3–5% of the patients survives for more than 3 years and are referred to as long-term survivors. The clinical and molecular factors ...that contribute to long-term survival are still unknown. To identify specific parameters that might be associated with this phenomenon, we performed a detailed clinical and molecular analysis of 55 primary glioblastoma long-term survivors recruited at the six clinical centres of the German Glioma Network and one associated centre. An evaluation form was developed and used to document demographic, clinical and treatment-associated parameters. In addition, environmental risk factors, associated diseases and occupational risks were assessed. These patients were characterized by young age at diagnosis and a good initial Karnofsky performance score (KPS). None of the evaluated socioeconomic, environmental and occupational factors were associated with long-term survival. Molecular analyses revealed MGMT hypermethylation in 28 of 36 tumours (74%) investigated. TP53 mutations were found in 9 of 31 tumours (29%) and EGFR amplification in 10 of 38 tumours (26%). Only 2 of 32 tumours (6%) carried combined 1p and 19q deletions. Comparison of these data with results from an independent series of 141 consecutive unselected glioblastoma patients registered in the German Glioma Network revealed significantly more frequent MGMT hypermethylation in the long-term survivor group. Taken together, our findings underline the association of glioblastoma long-term survival with prognostically favourable clinical factors, in particular young age and good initial performance score, as well as MGMT promoter hypermethylation.
TP53 mutations have been described in chronic lymphocytic leukemia (CLL) and have been associated with poor prognosis in retrospective studies. We aimed to address the frequency and prognostic value ...of TP53 abnormalities in patients with CLL in the context of a prospective randomized trial.
We analyzed 529 CLL samples from the LRF CLL4 (Leukaemia Research Foundation Chronic Lymphocytic Leukemia 4) trial (chlorambucil v fludarabine with or without cyclophosphamide) at the time of random assignment for mutations in the TP53 gene. TP53 mutation status was correlated with response and survival data.
Mutations of TP53 were found in 40 patients (7.6%), including 25 (76%) of 33 with 17p deletion and 13 (3%) of 487 without that deletion. There was no significant correlation between TP53 mutations and age, stage, IGHV gene mutations, CD38 and ZAP-70 expression, or any other chromosomal abnormality other than 17p deletion, in which concordance was high (96%). TP53 mutations were significantly associated with poorer overall response rates (27% v 83%; P < .001) and shorter progression-free survival (PFS) and overall survival (OS; 5-year PFS: 5% v 17%; 5-year OS: 20% v 59%; P < .001 for both). Multivariate analysis that included baseline clinical variables, treatment, and known adverse genetic factors confirmed that TP53 mutations have added prognostic value.
TP53 mutations are associated with impaired response and shorter survival in patients with CLL. Analysis of TP53 mutations should be performed in patients with CLL who have progressive disease before starting first-line treatment, and those with mutations should be selected for novel experimental therapies.
The availability and application of culture-independent tools that enable a detailed investigation of the microbiota and microbial biodiversity of food systems has had a major impact on food ...microbiology. This review focuses on the application of DNA-based technologies, such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient gel electrophoresis (TTGE), single stranded conformation polymorphisms (SSCP), the polymerase chain reaction (PCR) and others, to investigate the diversity, dynamics and identity of microbes in dairy products from raw milk. Here, we will highlight the benefits associated with culture-independent methods which include enhanced sensitivity, rapidity and the detection of microorganisms not previously associated with such products.
► Demonstrates the benefits of employing molecular biology for dairy microbiology investigations. ► Summarises a vast quantity of papers which have unveiled the rich microbial diversity of raw milk and raw milk cheeses. ► Reveals the benefit of culture independent approaches when investigating the microbial quality/safety of these products.
A subset of lung cancers harbors a small inversion within chromosome 2p, giving rise to a transforming fusion gene, EML4-ALK (echinoderm microtubule-associated protein-like 4 gene and the anaplastic ...lymphoma kinase gene), which encodes an activated tyrosine kinase. We have earlier examined the presence of EML4-ALK by multiplex reverse transcription-polymerase chain reaction in 363 specimens of lung cancer, identifying 11 adenocarcinoma cases featuring the fusion gene. In this study, we clinicopathologically examined the characteristics of the EML4-ALK-positive cases, including the mutation status of EGFR, KRAS, and TP53, and whether they were of thyroid transcription factor-1 (TTF-1) cell lineage or not. Of 11 patients, 4 (36%) with EML4-ALK-positive lung adenocarcinomas who were below 50 years of age were affected by these diseases, as compared with 12 of 242 patients (5.0%) with EML4-ALK-negative lung adenocarcinomas (P=0.00038). EML4-ALK-positive lung adenocarcinomas were characterized by less-differentiated grade (P=0.0082) and acinar-predominant structure (P<0.0001) in histology. Furthermore, the presence of EML4-ALK appears to be mutually exclusive for EGFR and KRAS mutations (P=0.00018), whereas coexisting with TP53 mutations at a low frequency (1/11=9.1%), and correlating with non- or light smoking (P=0.040), in line with the TTF-1 immunoreactivity. Thus, EML4-ALK-positive tumors may form a distinct entity among lung adenocarcinomas, characterized by young onset, acinar histology, no or rare mutations in EGFR, KRAS, and TP53, and a TTF-1 cell lineage, all in agreement with the prevalence in non- or light smokers.
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