Value, but high costs in post-deposition data Curation

© The Author(s) 2016. Published by Oxford University Press. Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Value, but high costs in post-deposition data curation

Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Metastasis to the breast from an adenocarcinoma of the lung with extensive micropapillary component: a case report and review of the literature

Breast metastasis from extra-mammary malignancy is rare. Based on the literature an incidence of 0.4-1.3% is reported. The primary malignancies most commonly metastasizing to the breast are leukemia-lymphoma, and malignant melanoma. We present a case of metastasis to the breast from a pulmonary adenocarcinoma, with extensive micropapillary component, diagnosed concomitantly with the primary tumor. A 73-year-old female presented with dyspnea and dry cough of 4 weeks duration and a massive pleural effusion was found on a chest radiograph. Additionally, on physical examination a poorly defined mass was noted in the upper outer quadrant of the left breast. The patient underwent bronchoscopy, excisional breast biopsy and medical thoracoscopy. By cytology, histology and immunohistochemistry primary lung adenocarcinoma with metastasis to the breast and parietal pleura was diagnosed. Both the primary and metastatic anatomic sites demonstrated histologically extensive micropapillary component, which is recently recognized as an important prognostic factor. The patient received chemotherapy but passed away within 7 months. Accurate differentiation of metastatic from primary carcinoma is of crucial importance because the treatment and prognosis differ significantly

The complexity in DNA methylation analysis of allergic diseases

Purpose of reviewThis review aims to report all the recent studies that are implicated in DNA methylation analysis in the field of allergy and to underline the complexity of the study methodologies and results.Recent findingsAlthough the growing number of DNA methylation studies have yet to point to a specific mechanism, herein we provide an overview of the majority of pathways considered to be implicated and highlight particular genes, like KNH2, ATPAF2 and ZNF385A, for their potential as biomarkers.SummaryThe epigenetic profile of respiratory allergic diseases, and particularly DNA methylation, has been investigated in various populations, so as to gain a better understanding of its role in pathogenesis. Through our analysis, multiple links are presented between differential DNA methylation loci and IgE sensitization, lung functionality and severity of the disease. Additionally, associations of this epigenetic change with maternal asthma, age, sex and environmental factors are described, thus uncovering specific gene families that, after further examination could be used as methylation biomarkers in cases of allergic disease. © 2023 Lippincott Williams and Wilkins. All rights reserved

The influence of infaunal (Nereis diversicolor) abundance on degradation of organic matter in sandy sediments

The influence of the infaunal polychaete Nereis diversicolor on the degradation of aged detritus (Fucus sp.) deposited 3cm below the sediment surface was investigated as a function of worm density (0, 600, 1200 and 2400m-2) in manipulated laboratory microcosms. Benthic metabolism in the microcosms was determined as sediment-water fluxes of dissolved carbon and microbial sulfate reduction. In addition, the vertical distribution of key sediment parameters, such as porewater solutes and bacterial abundance and community fingerprint (based on 16S rDNA) were determined at the end of the experimental period. Porewater concentrations of TCO2, DOC, and NH4+ were negatively related to worm density as a result of irrigation mediated excess transport. Conversely, sediment-water fluxes increased linearly with increasing macrofaunal abundance. Total benthic metabolism (TCO2 and O2 flux) was stimulated by up to 75% in unamended and 175% in detritus enriched treatments. The high faunal stimulation of benthic metabolism in the Fucus enriched sediment was primarily due to increased aerobic microbial metabolism resulting in a more efficient mineralisation of the released DOC and thus faster decay of the aged detritus. Sediment bacteria in the detritus amended treatment seemed to rapidly assimilate NH4+ within the sediment when utilising the added nitrogen-deficient detritus. NH4+ fluxes were similar in both amended and unamended treatments but increased with animal density, suggesting that animal excretion contributed significantly to the NH4+ flux. Analysis of the bacterial community showed that the addition of detritus significantly changed both its abundance and composition compared to unamended treatments. These differences were gradually alleviated with increasing animal abundance. Our results show that N. diversicolor abundance is a significant factor that determines not only total benthic metabolism, but also organic matter degradation pathways and microbial community composition, and a possible reduction of natural populations would result to changes in sediment biogeochemistry. © 2010 Elsevier B.V

Impact of Pestarella tyrrhena on benthic metabolism in sediment microcosms enriched with seagrass and macroalgal detritus

The impact of Pestarella (= Callianasa) tyrrhena (Decapoda: Thalassinidea), a common burrowing shrimp in the Mediterranean Sea on sediment-water fluxes (O2, TCO2, NH4+ and NO 3-+ NO2-), sediment characteristics (organic matter, chlorophyll a) and porewater solutes (TCO2, NH 4+ and NO3- + NO2 -) was investigated in laboratory microcosms over a period of 42 d. Microcosms containing homogenised fine sandy sediment were amended with either dead Posidonia oceanica leaves or fresh Ulva lactuca thalli. Reworking activity by the animal resulted in a rapid burial of surface deposited organic matter into the sediment. Porewater profiles of both TCO2 and NH 4+ indicated that P. tyrrhena activities result in a significant flushing of porewater solutes. Total sediment metabolism and carbon mineralisation were enhanced in the presence of P. tyrrhena. Metabolism of P. tyrrhena individuals was approximately 3 times higher in Ulva-amended sediment, probably due to a high activity level when nutritious food sources are in excess. Accordingly, animal respiration explained approximately half of the total enhancement in Ulva-amended sediment, while microbial decomposition of refractory seagrass detritus contributed about 4 times more to the stimulated carbon mineralisation than animal respiration. Despite the higher initial addition of carbon in Posidonia-amended sediment compared to Ulva-amended sediment, the amount of excess carbon mineralised was 4.7 times higher in the latter, indicating that mineralisation processes depend on the degradability rather than the quantity of the organic pool. Although P. tyrrhena excretion constituted only a minor part of the total nitrogen mineralised, macrofaunal activities were the major factor affecting total nitrogen mineralisation, and not the enrichment with organic matter

DNA methylation biomarkers in asthma and rhinitis: Are we there yet?

The study of epigenetics has improved our understanding of mechanisms underpinning gene-environment interactions and is providing new insights in the pathophysiology of respiratory allergic diseases. We reviewed the literature on DNA methylation patterns across different tissues in asthma and/or rhinitis and attempted to elucidate differentially methylated loci that could be used to characterize asthma or rhinitis. Although nasal and bronchial epithelia are similar in their histological structure and cellular composition, genetic and epigenetic regulation may differ across tissues. Advanced methods have enabled comprehensive, high-throughput methylation profiling of different tissues (bronchial or nasal epithelial cells, whole blood or isolated mononuclear cells), in subjects with respiratory conditions, aiming to elucidate gene regulation mechanisms and identify new biomarkers. Several genes and CpGs have been suggested as asthma biomarkers, though research on allergic rhinitis is still lacking. The most common differentially methylated loci presented in both blood and nasal samples are ACOT7, EPX, KCNH2, SIGLEC8, TNIK, FOXP1, ATPAF2, ZNF862, ADORA3, ARID3A, IL5RA, METRNL and ZFPM1. Overall, there is substantial variation among studies, (i.e. sample sizes, age groups and disease phenotype). Greater variability of analysis method detailed phenotypic characterization and age stratification should be taken into account in future studies. © 2022 The Authors. Clinical and Translational Allergy published by John Wiley & Sons Ltd on behalf of European Academy of Allergy and Clinical Immunology

Malat1 as a versatile regulator of cancer: Overview of the updates from predatory role as competitive endogenous rna to mechanistic insights

The central dogma of molecular biology, has remained a cornerstone of classical molecular biology. However, serendipitously discovered microRNAs (miRNAs) in nematodes paradigmat-ically shifted our current knowledge of the intricate mechanisms during transitions from transcrip-tion to translation. Thediscovery of miRNA captured considerable attention and appreciation, and we had witnessed an explosion in the field of non-coding RNAs. Ground-breaking discoveries in the field of non-coding RNAs have helped in better characterization of microRNAs and long non-coding RNAs (LncRNAs). There is an ever-increasing list of miRNA targets that are regulated by MALAT1 to stimulate or repress the expression of target genes. However, in this review, our main focus is to summarize mechanistic insights on MALAT1-mediated regulation of oncogenic signaling pathways. We have discussed how MALAT1 modulated TGF/SMAD and Hippo pathways in various cancers. We have also comprehensively summarized how JAK/STAT and Wnt/β-catenin pathways stimulated MALAT1 expression and consequentially how MALAT1 potentiated these signaling cascades to promote cancer. MALAT1 research has undergone substantial broadening. However, there is still a need to identify additional mechanisms. MALAT1 is involved in the multi--layered regulation of multiple transduction cascades, and detailed analysis of different pathways will be advantageous in getting a step closer to individualized medicine. © 2021 Bentham Science Publishers

Psychoticism in patients with panic disorder with or without comorbid agoraphobia

Objective: A few case-reports have previously described transient psychotic-like symptoms in non-psychotic patients with panic disorder (PD). We aimed to systematically explore whether PD patients without any current or past psychosis can be differentiated according to the severity of ‘psychoticism’ as a dimension, comprising clinical features such as psychotic-like experiences, increased social alienation, hostility and suspiciousness. Methods: Sample included 35 (female = 26) medication-free, non-psychotic patients consecutively referred from our Department’s Outpatient Clinic for acute symptoms of DSM-5 PD with (PDA; N = 29) or without concurrent agoraphobia. Psychometric measures included the Symptom Checklist–90–Revised (SCL-90-R), Agoraphobic Cognitions Questionnaire (ACQ), Body Sensations Questionnaire (BSQ), and panic attacks during last 21 days PA-21d. Results: Multiple regression analysis (forward stepwise) revealed that, among all SCL-90-R subscales, the psychoticism-subscale was most significantly associated with panic-related beliefs included in the ACQ, while significant associations emerged between the paranoid ideation-subscale and the ACQ and BSQ measures. Moreover, significant correlations emerged between the SCL-90-R psychoticism-subscale and all three measures of PD symptoms (ACQ, BSQ, PA-21d) and between the SCL-90-R paranoid ideation-subscale and both the ACQ and BSQ. Conclusions: This significant association between levels of psychoticism and severity of panic symptoms may reflect a more severe subtype of PD. © 2017 Informa UK Limited, trading as Taylor & Francis Group