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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.

Produced water (PW) is the largest by-product that comes out from wells during oil & gas (O&G) fields exploration. These waters contain high saline content along with other organic and inorganic composition. A mathematical model specifically for treatment of PW with electrocoagulation (EC) techniques has been developed. The mechanistic model considers the dominant Al species contribution to COD removal, multi-scale modelling of the EC reactor, the role of Al chloro complex species in impacting the COD removal and the development of mechanistic approach for the removal of COD by the Al complexes dominantly present in the system. The influence of experimental and model working parameters such as current density (10-20 mA/cm2), initial pH (3.1-8.6), interelectrode distance (1.35-4 cm), mixing speed (130-300 rpm) and scale up of EC reactor (0.3-1.5 L) on Al concentration and COD removal was investigated and modelled. The results showed that EC at the current density of 20 mA/cm2 enabled higher COD removal (78.3%) than at the current density of 10 mA/cm2 (68.3%) and 15 mA/cm2 (75%) and mathematical model prediction of COD removal fits well with the experimental data at 10 mA/cm2, and 15 mA/cm2 with R2 value of 0.96 and 0.97, respectively. The initial pH of 7.3 resulted in higher COD removal (95.85%) than the initial pH of 3.1 (64.5%), 6.1 (79.1%) and 8.6 (81.2%) and model reproduces 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. The variation of constants involved in the model formulation was optimized according to the effect of model working parameters.

Introduction – Ocular morbidities are frequently associated with closed head injury. These injuries are often ignored or treatment is delayed resulting in permanent visual loss. Aim- This study aimed to nd out the various Ophthalmic manifestation in patients of closed head injury and nd out an association between them. Method- A Prospective observational study was conducted with a total of 120 closed head injury patients in a tertiary care hospital for a period of 4 months. The initial ophthalmic examination was done within 12 hrs of admission and was reviewed daily. GCS was applied to grade the head injury and analysis was done to nd out the association. Results- Out of 120 enrolled patients, 88 cases were male and 32 were female patients in age group of 6 to70 years. Most common cause of sustaining head injury was road trafc accident followed by assault. Periorbital edema and ecchymosis was most common manifestation. RAPD was encountered as most common neuro-ophthalmic manifestation followed by disc edema and extraocular muscle restriction. Poor GCS is associated with frequent pupillary involvement. Conclusion – Young adult males are more vulnerable in sustaining ocular injury associated with head injury followed by road trafc accident. Poor GCS frequently involves pupil abnormality

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/.

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.

We report a case of MASC (mammary analogue of secretory carcinoma) in a 24-year-old male who presented with swelling in the parotid region and provisional diagnosed as pleomorphic adenoma and supercial parotidectomy was done. On histopathological examination and immunohistochemistry, it was diagnosed as MASC which is a less common variant of salivary gland tumor and completely a pathological diagnosis, not possible to diagnose preoperatively. It shows resemblance to pleomorphic adenoma both clinically and histopathologically. The treatment varies from simple excisions to radical surgery with or without neck dissections, adjuvant radiotherapy and or adjuvant systemic chemotherapy. Post-operative radiotherapy is reserved for patients with close surgical margins (5mm), incomplete resection, perineural invasion and / T3 or T4 tumours which are not present in our case.

In the past few decades, the role of nanotechnology has expanded into environmental remediation applications. In this regard, nanofibers have been reported for various applications in water treatment and air filtration. Nanofibers are fibers of polymeric origin with diameters in the nanometer to submicron range. Electrospinning has been the most widely used method to synthesize nanofibers with tunable properties such as high specific surface area, uniform pore size, and controlled hydrophobicity. These properties of nanofibers make them highly sought after as adsorbents, photocatalysts, electrode materials, and membranes. In this review article, a basic description of the electrospinning process is presented. Subsequently, the role of different operating parameters in the electrospinning process and precursor polymeric solution is reviewed with respect to their influence on nanofiber properties. Three key areas of nanofiber application for water treatment (desalination, heavy-metal removal, and contaminant of emerging concern (CEC) remediation) are explored. The latest research in these areas is critically reviewed. Nanofibers have shown promising results in the case of membrane distillation, reverse osmosis, and forward osmosis applications. For heavy-metal removal, nanofibers have been able to remove trace heavy metals due to the convenient incorporation of specific functional groups that show a high affinity for the target heavy metals. In the case of CECs, nanofibers have been utilized not only as adsorbents but also as materials to localize and immobilize the trace contaminants, making further degradation by photocatalytic and electrochemical processes more efficient. The key issues with nanofiber application in water treatment include the lack of studies that explore the role of the background water matrix in impacting the contaminant removal performance, regeneration, and recyclability of nanofibers. Furthermore, the end-of-life disposal of nanofibers needs to be explored. The availability of more such studies will facilitate the adoption of nanofibers for water treatment applications.

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., BMC Genomic Data, 22 (1)

Background: Laparoscopy is an established method to perform major surgeries, with many advantages over open surgeries. Hysterectomy is a common procedure performed with increased use of laparoscopy, having postoperative pain management is a major issue. Effective pain management promotes early ambulation, lowering the risk of DVT and PE.Methods: The present study aimed to assess effect of bupivacaine intraperitoneally during laparoscopic hysterectomy to reduce postoperative pain. 48 women undergoing laparoscopic hysterectomy under ASA I and II general anesthesia were included, divided into 2 groups, group A receiving 0.25% bupivacaine intraperitoneally; group B receiving saline. A blind observer observed both groups for 6 hours post-surgery or until the VAS was 4, whichever came first, need for rescue analgesia, side-effects, and total dose of analgesia required in 24 hours. Diclofenac sodium and paracetamol was used as rescue analgesia for both groups.Results: There was no significant difference reported in demographic parameters between two study groups. The VAS scores at 6, 12 and 24 hours after laparoscopy was significantly lower in group A than group B. There was significant increase in the time required for 1st analgesia, while amount of analgesia required was significantly low in group A as compared to group B. There were significantly more number of patients in group B who needed opioids than group A.Conclusions: Peritoneal bupivacaine instillation after laparoscopic hysterectomy was found to be useful to reduce the pain as compared to use of saline (placebo), significant reduction in need for analgesics in the postoperative period.

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.

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 (cytomegalovirus) 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 (coronary artery disease), 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.

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. Studying lncRNAs is challenging due to their low expression level, cell type-specific occurrence, poor sequence conservation between orthologs, and lack of information about RNA domains. LncRNAs direct the regulatory factors in the locations that are in cis to their transcription sites. We designed a model to predict if an lncRNA acts in cis based on its features and trained it using RNA-chromatin interaction data. The trained model is cell type-independent and does not require RNA-chromatin data. Combining RNA-chromatin and Hi-C data, we showed that lncRNA-chromatin binding sites are determined by chromosome conformation. For each lncRNA, the spatially proximal genes were identified as their potential targets by combining Hi-C and Cap Analysis Gene Expression (CAGE) data in 18 human cell types. RNA-protein and RNA-chromatin interaction data suggested that lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. We provide the data through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.

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., Highlights • The healthcare workers are under immense pressure and stress due to the COVID 19 pandemic. • The struggle to deliver in this new normal environment is making healthcare more prone to error. • Surgeons, should be aware of the wider perspectives and pitfalls during this pandemic to avoid costly mishaps.

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.

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 determined, for the first time, the global lineage-specific lncRNAome of human dermal blood and lymphatic endothelial cells (BECs and LECs), combining RNA-Seq and CAGE-Seq. A subsequent genome-wide antisense oligonucleotide-knockdown screen of a robust set of BEC- and LEC-specific lncRNAs identified LETR1 as a critical gatekeeper of the global LEC transcriptome. Deep RNA-DNA, RNA-protein, and phenotype rescue analyses revealed that LETR1 acts as 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 new evidence supporting the intriguing concept that every cell type expresses precise lncRNA signatures to control lineage-specific regulatory programs.

Tuberculosis (TB) is a infectious disease that can involve any organ system of the body. Abdominal TB can be gastrointestinal, lymphnodal, visceral or perironeal. Gall bladder(GB) is rarely involved as a primary organ in abdominal TB. On extensive research the literature on gall bladder TB is limited to case reports. There has been no review on this rare abdominal pathology. The GB tuberculosis is a difficult diagnosis preoperatively. It is a rare differential among the more common gall bladder pathologies like cholelithiasis, or a gall bladder malignancy. Typical histopathology of the resected specimen helps establish this rare diagnosis. Subjecting every specimen to histopathological examination followed by medical treatment offers the chance of cure. Through this review the authors are trying to provide an insight into this entity.

Tuberculosis (TB) is an infectious disease that can affect any organ system of the body. Abdominal TB can be gastrointestinal, lymph nodal, visceral or peritoneal. The gallbladder (GB) is rarely involved in abdominal TB as a primary organ. Extensive research literature on gallbladder TB is limited to case reports. There has been no review on this rare abdominal pathology. GB tuberculosis is a difficult diagnosis preoperatively. It is a rare differential among the more common gallbladder pathologies such as cholelithiasis, or a gallbladder malignancy. Typical histopathology of the resected specimen helps to establish this rare diagnosis. Subjecting every specimen to histopathological examination followed by medical treatment offers the chance of cure. Through this review, the authors attempt to provide an insight into this disease entity.

Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression 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 lncRNA 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 dataset with molecular phenotyping (over 1,000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

Introduction: Coronary microvascular disease (CMD) affects small arteries that feed the heart and is more prevalent in postmenopausal women. Since CMD and Coronary artery disease (CAD) have distinct pathologies, but are treated the same way, the majority of the patients with CMD do not receive a proper diagnosis and treatment, which in turn results in higher rates of adverse future events such as heart failure, sudden cardiac death, and acute coronary syndrome (ACS). Previously, we performed full metabolite profiling of plasma samples using GC-MS analysis and tested their classification performance using machine learning approaches. This initial proof-of-concept study showed that plasma metabolite profiles can be used to develop diagnostic signatures for CMD. In the current study, we hypothesize that plasma metabolite and protein composition is different for postmenopausal women with no heart disease, with CAD, or with CMD. Methods: We obtained plasma samples from 70 postmenopausal women who are healthy, women who have CMD, and women who have CAD at the time of blood collection. In addition to GC-MS metabolite profiles, we performed LC-MS metabolomic profiling, and proteomic profiling of a panel of 92 proteins that were implicated in cardiometabolic disease. We identified a combination of metabolites and proteins, and further tested their classification performance using machine learning approaches to identify potential circulating biomarkers for CMD. Results: We identified a comprehensive list of metabolites and proteins that were involved in endothelial cell function, nitric oxide metabolism and inflammation, which significantly different in plasma from women with CMD. We further validated difference in the level of several protein biomarkers, such as RAGE, PTX3, AGRP, CNTN1, and MMP-3, which are statistically significantly higher in postmenopausal women with CMD when compared with healthy women or women with CAD. Conclusion: Our research identified a group of potential molecules that can be used in the design of easy and low-cost blood biomarkers for the clinical diagnosis of CMD.

Produced water (PW), the largest waste stream generated in oil and gas industries, has the potential to be a harmless product rather than being a waste. Biological processes using microorganisms have proven useful to remediate PW contaminated by petroleum hydrocarbons, complex organic chemicals, and solvents. In particular, the bioremediation of PW using algae is an eco-friendly and low-cost approach due to algae’s ability to utilize certain pollutants as nutrient sources. Therefore, the utilization of PW as an algal growth medium has a great potential to eliminate chemicals from the PW and minimize the large volumes of freshwater needed for cultivation. Although several reviews describing the bioremediation of PW have been published, to the best of our knowledge, no review has exclusively focused on the algae-based PW treatment. Therefore, the present review is dedicated to filling this gap by portraying the many different facets of the algae cultivation in PW. Several algal species that are known to thrive in a wide range of salinity and the critical steps for their cultivation in hypersaline PW have been identified. Overall, this comprehensive review highlights the PW bioremediation using algae and brings attention to utilizing PW to grow biomass that can be processed to generate biofuels and useful bioproducts.

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.

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.

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 ribosomal RNA genes (rDNA) encode the major rRNA species of the ribosome, and thus are essential across life. These genes are highly repetitive in most eukaryotes, forming blocks of tandem repeats that form the core of nucleoli. The primary role of the rDNA in encoding rRNA has been long understood, but more recently the rDNA has been implicated in a number of other important biological phenomena, including genome stability, cell cycle, and epigenetic silencing. Noncoding elements, primarily located in the intergenic spacer region, appear to mediate many of these phenomena. Although sequence information is available for the genomes of many organisms, in almost all cases rDNA repeat sequences are lacking, primarily due to problems in assembling these intriguing regions during whole genome assemblies. Here, we present a method to obtain complete rDNA repeat unit sequences from whole genome assemblies. Limitations of next generation sequencing (NGS) data make them unsuitable for assembling complete rDNA unit sequences; therefore, the method we present relies on the use of Sanger whole genome sequence data. Our method makes use of the Arachne assembler, which can assemble highly repetitive regions such as the rDNA in a memory-efficient way. We provide a detailed step-by-step protocol for generating rDNA sequences from whole genome Sanger sequence data using Arachne, for refining complete rDNA unit sequences, and for validating the sequences obtained. In principle, our method will work for any species where the rDNA is organized into tandem repeats. This will help researchers working on species without a complete rDNA sequence, those working on evolutionary aspects of the rDNA, and those interested in conducting phylogenetic footprinting studies with the rDNA.

The ribosomal RNA genes (rDNA) encode the major rRNA species of the ribosome, and thus are essential across life. These genes are highly repetitive in most eukaryotes, forming blocks of tandem repeats that form the core of nucleoli. The primary role of the rDNA in encoding rRNA has been long understood, but more recently the rDNA has been implicated in a number of other important biological phenomena, including genome stability, cell cycle, and epigenetic silencing. Noncoding elements, primarily located in the intergenic spacer region, appear to mediate many of these phenomena. Although sequence information is available for the genomes of many organisms, in almost all cases rDNA repeat sequences are lacking, primarily due to problems in assembling these intriguing regions during whole genome assemblies. Here, we present a method to obtain complete rDNA repeat unit sequences from whole genome assemblies. Limitations of next generation sequencing (NGS) data make them unsuitable for assembling complete rDNA unit sequences; therefore, the method we present relies on the use of Sanger whole genome sequence data. Our method makes use of the Arachne assembler, which can assemble highly repetitive regions such as the rDNA in a memory-efficient way. We provide a detailed step-by-step protocol for generating rDNA sequences from whole genome Sanger sequence data using Arachne, for refining complete rDNA unit sequences, and for validating the sequences obtained. In principle, our method will work for any species where the rDNA is organized into tandem repeats. This will help researchers working on species without a complete rDNA sequence, those working on evolutionary aspects of the rDNA, and those interested in conducting phylogenetic footprinting studies with the rDNA.

Additional file 1. This file consists of four supplemental tables and six supplemental figures. Table S1 lists the components in the HS medium used to grow ANME-1 Mcr-producing M. acetivorans on methane and 0.1 mM or 10 mM FeCl3. Table S2 shows the fold changes of differentially expressed genes in M. acetivorans/pES1-MATmcr3 grown on methane and 0.1 mM FeCl3, in comparison to the same strain grown on methanol. Table S3 lists the strains and plasmids, and Table S4 lists the oligonucleotides, used in this study. Figure S1 shows the three promoters used to express ANME-1 mcrBGA genes. Figure S2 shows the detected McrA-FLAG in M. acetivorans/pES1-MATmcr3-flag grown on methane after five days. Figure S3 shows the detection of ANME-1 mcrA after 30 days of growth on methane. Figure S4 shows the GC/MS spectra of culture supernatants used to identify acetate from H13CO. Figure S5 shows the flux through the various reactions in the methanogenesis pathway of M. acetivorans estimated by 13C-metabolic flux analysis using 13C-labeled bicarbonate as the input tracer. Figure S6 shows a simplified methanogenesis pathway from CO2 and CH3OH of M. acetivorans.

The short arms of the five acrocentric human chromosomes harbor sequences that direct the assembly and function of the nucleolus, one of the key functional domains of the nucleus, yet they are absent from the current human genome assembly. Here we describe the genomic architecture of these human nucleolar organizers. Sequences distal and proximal to ribosomal gene arrays are conserved among the acrocentric chromosomes, suggesting they are sites of frequent recombination. Although previously believed to be heterochromatic, characterization of these two flanking regions reveals that they share a complex genomic architecture similar to other euchromatic regions of the genome, but they have distinct genomic characteristics. Proximal sequences are almost entirely segmentally duplicated, similar to the regions bordering centromeres. In contrast, the distal sequence is predominantly unique to the acrocentric short arms and is dominated by a very large inverted repeat. We show that the distal element is localized to the periphery of the nucleolus, where it appears to anchor the ribosomal gene repeats. This, combined with its complex chromatin structure and transcriptional activity, suggests that this region is involved in nucleolar organization. Our results provide a platform for investigating the role of NORs in nucleolar formation and function, and open the door for determining the role of these regions in the well-known empirical association of nucleoli with pathology.

Word alignment using recency-vector based approach has recently become popular. One major advantage of these techniques is that unlike other approaches they perform well even if the size of the parallel corpora is small. This makes these algorithms worth-studying for languages where resources are scarce. In this work we studied the performance of two very popular recency-vector based approaches, proposed in (Fung and McKeown, 1994) and (Somers, 1998), respectively, for word alignment in English-Hindi parallel corpus. But performance of the above algorithms was not found to be satisfactory. However, subsequent addition of some new constraints improved the performance of the recency-vector based alignment technique significantly for the said corpus. The present paper discusses the new version of the algorithm and its performance in detail.

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., Mammalian genomes encode tens of thousands of ncRNAs that have important roles in regulation of gene expression and chromatin organization. Here, the authors present RADICLseq to map RNA-chromatin interactions in intact nuclei to shed light on these fine-tuned processes.