Annotation of nuclear lncRNAs based on chromatin interactions.

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.

A mechanistic mathematical model for the treatment of synthetic oil-field wastewater (produced water) by electrocoagulation process using aluminium electrodes.

Produced water (PW) is the largest by-product that comes out of the oil wells during oil and gas (O&G) field exploration. PW contains high-salt concentration along with other organic and inorganic components; therefore, PW must be treated before disposal. Electrocoagulation (EC) is an effective treatment method to remove pollutants from PW which has been the focus of many experimental studies; however, a mathematical model specifically for PW treatment by EC has not been developed yet. In this work, a comprehensive mathematical model has been developed to elucidate the role of EC operating parameters on the PW treatment performance and determine the mechanism for COD (Chemical Oxygen Demand) removal. The present model considers and identifies the dominant Al-hydroxy complex species and their contribution to the COD removal from synthetic PW samples by estimating their rate constants and comparing their magnitudes and investigates multi-scale modelling of the EC reactor. The influence of working parameters such as current density, initial pH, interelectrode distance, mixing speed and solution volume of PW on Al coagulant production and COD removal was investigated and modelled. The study estimates the rate constants of the reactions taking place for COD removal by EC process and by comparing their magnitudes identifies the dominant reactions and coagulant species involved in the process. The mathematical model prediction of COD removal fits well with the experimental data at 10 mA cm-2, 15 mA cm-2 and 20 mA cm-2 current density with R2 value of 0.96, 0.97 and 0.92, respectively and for dissolved Al concentration R2 value of 0.96, 0.99, and 0.97, respectively. The simulated results reproduced a good fit at initial pH of 6.1, 7.3 and 8.6 with R2 value of 0.92, 0.96 and 0.98, respectively for COD removal. The mathematical model and the experimental results showed the role of dominant Al-hydroxy complex species such as Al OH 2 + , Al OH 2 + , Al OH 3 , Al 2 OH 2 + 4 and Al OH 4 - in controlling the COD removal process. Under different operating conditions considered in the study, the model also predicted the COD removal performance of the EC reactors at different reactor volumes with R2 value of 0.96 for higher solution volume and larger reactor. The model presented and rate constants determined in the study will provide a theoretical basis for designing, scaling up and operating the EC reactor for oil-field PW treatment.

ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data.

In the genomic era, data dissemination and visualization is an integral part of scientific publications and research projects involving international consortia producing massive genome-wide data sets, intra-organizational collaborations, or individual labs. However, creating custom supporting websites is oftentimes impractical due to the required programming effort, web server infrastructure, and data storage facilities, as well as the long-term maintenance burden. ZENBU-Reports (https://fantom.gsc.riken.jp/zenbu/reports) is a web application to create interactive scientific web portals by using graphical interfaces while providing storage and secured collaborative sharing for data uploaded by users. ZENBU-Reports provides the scientific visualization elements commonly used in supplementary websites, publications and presentations, presenting a complete solution for the interactive display and dissemination of data and analysis results during the full lifespan of a scientific project both during the active research phase and after publication of the results.

Indoor Bacterial and Fungal Burden in "Moldy" versus "Non-Moldy" Homes: A Case Study Employing Advanced Sequencing Techniques in a US Metropolitan Area.

The presence of fungi in the indoor environment is associated with allergies and other respiratory symptoms. The aim of this study was to use sequencing and molecular methods, including next-generation sequencing (NGS) approaches, to explore the bacterial and fungal communities and their abundance in the indoor environment of houses (n = 20) with visible "moldy" (HVM) and nonvisible "non-moldy" (HNM) in Memphis, TN, USA. Dust samples were collected from air vents and ground surfaces, and the total DNA was analyzed for bacteria and fungi by amplifying 16S rRNA and ITS genes on the Illumina Miseq. Results indicated that Leptosphaerulina was the most abundant fungal genus present in the air vent and ground samples from HNM and HVM. At the same time, the most abundant bacterial genera in the air vent and ground samples were Propionibacterium and Streptococcus. The fungi community diversity was significantly different in the air vent samples. The abundance of fungal species known to be associated with respiratory diseases in indoor dust samples was similar, regardless of the visibility of fungi in the houses. The existence of fungi associated with respiratory symptoms was compared with several parameters like dust particulate matter (PM), CO2 level, temperature, and humidity. Most of these parameters are either positively or negatively correlated with the existence of fungi associated with respiratory diseases; however, none of these correlations were significant at p = 0.05. Our results indicate that implementing molecular methods for detecting indoor fungi may strengthen common exposure and risk assessment practices.

Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.

Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

BACKGROUND: The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism's physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. RESULTS: To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. CONCLUSION: In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types.

Identification of Circulating Diagnostic Biomarkers for Coronary Microvascular Disease in Postmenopausal Women Using Machine-Learning Techniques.

Coronary microvascular disease (CMD) is a common form of heart disease in postmenopausal women. It is not due to plaque formation but dysfunction of microvessels that feed the heart muscle. The majority of the patients do not receive a proper diagnosis, are discharged prematurely and must go back to the hospital with persistent symptoms. Because of the lack of diagnostic biomarkers, in the current study, we focused on identifying novel circulating biomarkers of CMV that could potentially be used for developing a diagnostic test. We hypothesized that plasma metabolite composition is different for postmenopausal women with no heart disease, CAD, or CMD. A total of 70 postmenopausal women, 26 healthy individuals, 23 individuals with CMD and 21 individuals with CAD were recruited. Their full health screening and tests were completed. Basic cardiac examination, including detailed clinical history, additional disease and prescribed drugs, were noted. Electrocardiograph, transthoracic echocardiography and laboratory analysis were also obtained. Additionally, we performed full metabolite profiling of plasma samples from these individuals using gas chromatography-mass spectrometry (GC-MS) analysis, identified and classified circulating biomarkers using machine learning approaches. Stearic acid and ornithine levels were significantly higher in postmenopausal women with CMD. In contrast, valine levels were higher for women with CAD. Our research identified potential circulating plasma biomarkers of this debilitating heart disease in postmenopausal women, which will have a clinical impact on diagnostic test design in the future.

Unusual Complication of Intercostal Tube Drainage of Penetrating Chest Injury: A Case Report.

Penetrating chest injuries can lead to diaphragmatic injuries, which are often missed easily on initial assessments, especially in patients with polytrauma. We are usually more focused and biased towards other evident, immediately life-threatening injuries. The fact that clinical and radiological findings are subtle, especially on chest X-rays, which is sometimes the only investigation performed, highlights the importance of using higher imaging modalities in stable patients and that a clinician should be suspicious of this entity with the corresponding history. Intervening in such patients with the placement of intercostal drain can contribute to morbidity and mortality, as in our case, by causing inadvertent injury to the herniating structures. The case report briefs the same and emphasizes that thoracic injuries, especially penetrating ones, should ring a bell and should be carefully investigated further before the intervention.

LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C.

Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. There is ample evidence that distinct types of vasculature undergo tight transcriptional control to preserve their structure, identity, and functions. We determine a comprehensive map of lineage-specific lncRNAs in human dermal lymphatic and blood vascular endothelial cells (LECs and BECs), combining RNA-Seq and CAGE-Seq. Subsequent antisense oligonucleotide-knockdown transcriptomic profiling of two LEC- and two BEC-specific lncRNAs identifies LETR1 as a critical gatekeeper of the global LEC transcriptome. Deep RNA-DNA, RNA-protein interaction studies, and phenotype rescue analyses reveal that LETR1 is a nuclear trans-acting lncRNA modulating, via key epigenetic factors, the expression of essential target genes, including KLF4 and SEMA3C, governing the growth and migratory ability of LECs. Together, our study provides several lines of evidence supporting the intriguing concept that every cell type expresses precise lncRNA signatures to control lineage-specific regulatory programs.

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

Covid-19 and surgery: Challenging issues in the face of new normal - A narrative review.

This review aims to outline the current perspectives of surgery in the COVID 19 pandemic associated with the pitfalls in implementing the emerging guidelines to continue patient care without compromising safety, both from the surgeons' and the patients' points of view. The fight between the surgeon and the pandemic will be a dragging one since the post-pandemic infflux of surgical patients coupled with the 'new normal' practices to prevent COVID 19 spread requires pertinent resources, well-trained personnel, and co-operation among different departments. Emergency surgeries and cancer care have continued all this while, undoubtedly, with unwanted delays and distress. While we continue to prepare ourselves and work in a whole new environment, surgeons are facing the increased chances of litigations and compromised safety. We review what we have come to understand about safe surgical practices during and after the pandemic and the unanswered questions.

Role of carbohydrate antigen 19-9, carcinoembryonic antigen, and carbohydrate antigen 125 as the predictors of resectability and survival in the patients of Carcinoma Gall Bladder.

INTRODUCTION: Carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9) have been reported in previous studies to assess the prognosis of gall bladder cancer (GBC) individually and in combination. However, the evidence of utility of preoperative CA 19-9, CEA and carbohydrate antigen 125 (CA 125) in determining the resectability and prognosis of GBC is still lacking. In the present study we correlated the serum levels of tumor markers CA 19-9, CEA and CA 125 individually and combined to determine the resectability and prognosis of the GBC. MATERIALS AND METHODS: Seventy one diagnosed patients of GBC between January 2018 and September 2019 were included in the present study. Serum CA 19-9, CEA and CA 125 were determined by chemiluminescence. Receiver operating characteristic (ROC) curve was used to evaluate the role of tumor markers in determining the resectability of GBC. The Kaplan Meier survival curves were made and log rank analysis was performed to assess the prognostic role of tumor markers in terms of overall median survival. RESULTS: All the three tumor markers CA19-9, CEA and CA 125 showed high discriminatory power in determining the resectability with respective area under curve of 0.76, 0.68 and 0.78 as determined by ROC. Median survival in patients with high serum CA 19-9, CA 125 was significantly lower than patients with normal serum CA 19-9, CA 125 whereas no significant difference was observed in case of CEA. CONCLUSION: The present study suggested that CA 19-9, CEA and CA 125 can predict resectability in GBC and raised levels of CA 19-9 and CA 125 can predict poor prognosis in patients with elevated levels.

Evaluation of platelet distribution width as novel biomarker in gall bladder cancer.

INTRODUCTION: Gall bladder cancer (GBC) tends to present in advanced stages, therefore, early diagnosis of GBC is necessary. There is no ideal single tumor marker available presently for the diagnosis and prognosis of GBC. Platelet distribution width (PDW) is an early marker for activated platelets and has been used in a variety of tumors to assess prognosis. This study was designed to evaluate the utility of PDW in identifying GBC patients and its association with tumor markers, staging and resectability of GBC. MATERIALS AND METHODS: This cross sectional study was done on 100 patients of GBC and 100 age- and sex- matched healthy controls. PDW was evaluated and compared between GBC and healthy controls. Receiver-operating characteristics was plotted to determine optimal cut-off for identifying GBC patients and to determine sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of PDW. Correlation between serum tumor markers (carbohydrate antigen 19-9, carcinoembryonic antigen, and carbohydrate antigen 125) and PDW were evaluated. Association of PDW with hyperbilirubinemia, staging and resectability of GBC was also studied. RESULTS: A significantly higher PDW with a median of 18.1 was observed in GBC as compared to healthy controls with median value of 13. PDW was found to have a very high sensitivity (90%), specificity (95%), PPV (94%) and NPV (90%) in identifying GBC at cut-off of 16 with area under the curve (AUC) of 0.97. An increase of PDW was observed with increasing stage and unresectable GBC. However, it was not statistically significant. Significant positive correlation was observed between PDW and all three serum tumor markers and good positive correlation with r = 0.61 was observed with CA 19-9. CONCLUSION: PDW was associated with GBC and may be considered as a cost- effective marker in adjunct to other investigations for the diagnosis of GBC.

Comparative transcriptomics of primary cells in vertebrates.

Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure.

Post-traumatic necrotising fasciitis of the breast: a case study with literature review.

Necrotising fasciitis is a rare infection of the skin and underlying soft tissue. It primarily involves the extremities and rarely the breast. Primary necrotising fasciitis of the breast in a non-lactating, healthy female is rarer still. The authors present the case report of a patient presenting with primary necrotising fasciitis of the breast after sustaining a penetrating injury. The patient was managed successfully with serial debridement and negative pressure wound therapy (NPWT). To our knowledge only 19 such cases have been reported in the indexed literature so far. This is also the eighth case globally of primary necrotising fasciitis of the breast in a non-lactating female without any associated immunosuppression, which is the basis of reporting this case.

Red Cell Distribution Width: A Surrogate Biomarker to Predict Tumor Burden in Carcinoma Gallbladder.

AIM: To assess the role of red cell distribution width as a marker to predict tumor burden in gallbladder cancer (GBC). METHODS: One hundred and twenty-eight patients with newly diagnosed GBC were included in the study. Peripheral blood samples were obtained, and red cell distribution width (RDW) was assessed. Tumor markers and other biochemical parameters were also recorded. STATISTICAL ANALYSIS: Quantitative variables were summarized using mean and standard deviation or median and interquartile range based on the normality of the distribution. The association of RDW with stage of tumor was analyzed using Chi-square test. All statistical tests were interpreted for significance using a cutoff value of P < 0.05. RESULTS: RDW showed a positive correlation with total bilirubin, total leukocyte count, and erythrocyte sedimentation rate (P < 0.002), but not with platelet count (P < 0.643). RDW showed a significant correlation with tumor markers CA 19-9 (P < 0.003), carcinoembryonic antigen (P < 0.003), and CA 125 (P < 0.002). In Stage IVB, there were significantly more patients with high RDW (78%) than normal RDW (21.8%). However, the results were not statistically significant (P < 0.073). CONCLUSION: In the present study, we have utilized RDW for correlation with tumor markers in carcinoma gallbladder and as a predictor of stage. We demonstrated higher levels of RDW with advanced stages of GBC. Overall, the study suggested that RDW may be utilized as a surrogate biomarker to predict tumor burden and disease in patients with GBC.

The conservation landscape of the human ribosomal RNA gene repeats.

Ribosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed using de novo whole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.