Single-cell resolution of longitudinal blood transcriptome profiles in rheumatoid arthritis, systemic lupus erythematosus and healthy control pregnancies

OBJECTIVES

Comparative longitudinal analyses of cellular composition and peripheral blood gene expression in Rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and healthy pregnancies.

METHODS

In total, 335 whole blood samples from 84 RA, SLE and healthy controls before pregnancy, at each trimester, 6 weeks, 6 months and 12 months post partum were analysed. We combined bulk and single cell RNA analyses for cell-type estimation, validated by flow cytometry, before combining this in a cell-type adjusted analysis for an improved resolution of unrecognised gene expression changes associated with RA and SLE pregnancies.

RESULTS

Patients were well regulated throughout pregnancy, and few had pregnancy complications. In SLE, the interferon signature was augmented during pregnancy, and the pregnancy signature was continued post partum. An altered cell type composition strongly influences the profile. In the pregnancy signature, transcripts involved in galactosylation potentially altering the effector functions of autoantibodies became more evident. Several genes in the adjusted RA signature are expressed in mucosal associated invariant T cells.

CONCLUSION

We found distinct RA, SLE and pregnancy signatures, and no expression patterns could be attributed to medication or disease activity. Our results support the need for close postpartum follow-up of patients with SLE. Gene expression patterns in RA were closer to healthy controls than to SLE, and primarily became evident after cell-type adjustment. Adjusting for cell abundance unravelled gene expression signatures less associated with variation in cell-composition and highlighted genes with expression profiles associated with changes in specialised cell populations.

RPA guides UNG to uracil in ssDNA to facilitate antibody class switching and repair of mutagenic uracil at the replication fork

Activation-induced cytidine deaminase (AID) interacts with replication protein A (RPA), the major ssDNA-binding protein, to promote deamination of cytosine to uracil in transcribed immunoglobulin (Ig) genes. Uracil-DNA glycosylase (UNG) acts in concert with AID during Ig diversification. In addition, UNG preserves genome integrity by base-excision repair (BER) in the overall genome. How UNG is regulated to support both mutagenic processing and error-free repair remains unknown. UNG is expressed as two isoforms, UNG1 and UNG2, which both contain an RPA-binding helix that facilitates uracil excision from RPA-coated ssDNA. However, the impact of this interaction in antibody diversification and genome maintenance has not been investigated. Here, we generated B-cell clones with targeted mutations in the UNG RPA-binding motif, and analysed class switch recombination (CSR), mutation frequency (5' Ig Sμ), and genomic uracil in clones representing seven Ung genotypes. We show that the UNG:RPA interaction plays a crucial role in both CSR and repair of AID-induced uracil at the Ig loci. By contrast, the interaction had no significant impact on total genomic uracil levels. Thus, RPA coordinates UNG during CSR and pre-replicative repair of mutagenic uracil in ssDNA but is not essential in post-replicative and canonical BER of uracil in dsDNA.

TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat

Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. This is reflected by the many publications and database resources describing knowledge about TFs. We previously launched the TFCheckpoint database, an integrated resource focused on human, mouse and rat dbTFs, providing users access to a comprehensive overview of these proteins. Here, we describe TFCheckpoint 2.0 (https://www.tfcheckpoint.org/index.php), comprising 13 collections of dbTFs, coTFs and GTFs. TFCheckpoint 2.0 provides an easy and versatile cross-referencing system for users to view and download collections that may otherwise be cumbersome to find, compare and retrieve.

MicroRNA profiling of psoriatic skin identifies 11 miRNAs associated with disease severity

MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as central regulators of gene expression and powerful biomarkers of disease. Much is yet unknown about their role in psoriasis pathology. To globally characterize the miRNAome of psoriatic skin, skin biopsies were collected from psoriatic cases (n = 75) and non-psoriatic controls (n = 46) and RNA sequenced. Count data were meta-analysed with a previously published dataset (cases, n = 24, controls, n = 20), increasing the number of psoriatic cases fourfold from previously published studies. Differential gene expression analyses were performed comparing lesional psoriatic (PP), non-lesional psoriatic (PN) and control (NN) skin. Further, functional enrichment and cell-specific analyses were performed. Across all contrasts, we identified 439 significantly differentially expressed miRNAs (DEMs), of which 85 were novel for psoriasis and 11 were related to disease severity. Meta-analyses identified 20 DEMs between PN and NN, suggesting an inherent change in the constitution of all skin in psoriasis. By integrating the miRNA transcriptome with mRNA target interactions, we identified several functionally enriched terms, including "thyroid hormone signalling," "insulin resistance" and various infectious diseases. Cell-specific expression analyses revealed that the upregulated DEMs were enriched in epithelial and immune cells. This study provides the most comprehensive overview of the miRNAome in psoriatic skin to date and identifies a miRNA signature related to psoriasis severity. Our results may represent molecular links between psoriasis and related comorbidities and have outlined potential directions for future functional studies to identify biomarkers and treatment targets.

Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation

Proper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 57 lncRNAs. We selected four of these lncRNAs-SNHG26, EMSLR, ZFAS1, and EPB41L4A-AS1-for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.

Non-Coding RNAs in Human Breast Milk: A Systematic Review

Breast milk is the primary source of nutrition and hydration for the newborn infant but also plays an important role in the child’s first immune defense. Additionally, several breast milk factors have been implicated in immune-related health outcomes later in life, including immunoglobulins, cytokines, chemokines, growth factors and, more recently, non-coding RNA (ncRNA) species. In this systematic review, we provide a comprehensive summary of the current literature on endogenous ncRNAs found in human breast milk. Thirty (30) relevant studies were identified and, whilst the majority studies focused on microRNAs (miRNAs), there is evidence that breast milk contains high quantities of RNA which also include long-coding RNAs, circular RNAs, as well as other short RNAs and fragmented tRNA and rRNAs. Among studies investigating miRNAs, miR-148a-3p, miR-30a/d-5p, miR-22-3p, miR-146b-5p, miR-200a/c-3p, and the 5p end of the let-7 miRNAs were commonly reported among the top 10 miRNAs in the cell, lipid, and skim milk fractions of breast milk. Methodological difference and small sample sizes limit the possibility of conclusively identifying which maternal and infant characteristics affect the miRNA profile. The highly expressed miRNAs were generally reported to be similar across lactational stage, milk fraction, maternal and infant characteristics, or infant growth and health. All the same, individual studies identify potential differences in miRNA expression levels which should be confirmed by future studies. Stability, uptake, and physiological functions of miRNAs were also considered in several studies. Breast milk miRNAs are relatively resistant to a range of harsh conditions and uptake experiments suggest that extracellular vesicles containing miRNAs and circular RNAs can be taken up by intestinal epithelial cells. Although the evidence regarding the functional effect of breast milk miRNAs is limited, the predicted functions range from metabolic and biosynthetic processes to signaling pathways, cellular adhesion, communication, growth, and differentiation. Finally, this systematic review highlights some of the methodological challenges and knowledge gaps which can help direct future research in this field. In particular, it is important to further investigate the bioavailability of miRNAs in different milk fractions, and to characterize other ncRNAs which are largely unstudied.

Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients

BACKGROUND

The expression of microRNAs (miRNAs) is a promising prognostic and diagnostic tool in hepatocellular carcinoma (HCC). Here we performed small RNA sequencing (sRNA-seq) of tissue, serum and serum exosomes to investigate changes in miRNA expression between the different sample types and correlated the expression with clinical parameters. We also performed gene expression arrays on tumor and normal tissue.

RESULTS

Paired tissue, serum and serum exosomes sequencing revealed consistent positive correlation of miR-21 between serum exosomes and tumor tissue, indicating that miR-21 could be exported from tissue to circulation via exosomes. We found that let-7 miRNAs are generally upregulated in serum exosomes compared to whole serum, indicating that these miRNAs could be preferentially loaded into exosomes. Comparing serum from HCC patients with serum from healthy individuals revealed a global increase of miRNAs in serum from HCC patients, including an almost 4-fold increase of several miRNAs, including the liver-specific miR-122. When correlating miRNA expression with clinical parameters we detected significant association between hepatitis B virus (HBV) infection and miR-122 in serum as well as several serum and tissue-miRNAs that correlated with surgery type. We found that miR-141 and miR-146 correlated with cirrhosis in tumor tissue and normal tissue, respectively. Finally, high expression of miR-21 in tumors were associated with poor survival. Focusing on gene expression we found several significant messenger RNAs (mRNAs) between tumor and normal tissue and a Gene Ontology (GO) analysis revealed that these changes were mainly related to cell cycle and metabolism. Further, we detected mRNAs that correlated with cirrhosis and HBV infection in tissue. Finally, GO analysis of predicted targets for miRNAs down-regulated in tumor found that these were enriched for functions related to collagen synthesis.

CONCLUSIONS

Our combined data point to altered miRNA and mRNA expression contributing to both generally impaired lipid metabolism and increased cell proliferation and a miRNA-driven increase in collagen synthesis in HCC. Our results further indicate a correlation in miRNA expression between exosomes, serum, and tissue samples suggesting export from tumors via exosomes. This correlation could provide a basis for a more tumor-specific miRNA profile in serum.

Nephronectin mediates p38 MAPK-induced cell viability via its integrin-binding enhancer motif

Nephronectin (NPNT) is an extracellular matrix (ECM) protein involved in kidney development. We recently reported intracellular NPNT as a potential prognostic marker in breast cancer and that NPNT promotes metastasis in an integrin-dependent manner. Here, we used reverse-phase protein array (RPPA) to analyze NPNT-triggered intracellular signaling in the 66cl4 mouse breast cancer cell line. The results showed that the integrin-binding enhancer motif is important for the cellular effects upon NPNT interaction with its receptors, including phosphorylation of p38 mitogen-activated protein kinase (MAPK). Furthermore, analysis using prediction tools suggests involvement of NPNT in promoting cell viability. In conclusion, our results indicate that NPNT, via its integrin-binding motifs, promotes cell viability through phosphorylation of p38 MAPK.

Strain diversity and relative transmission of Mycobacterium tuberculosis in south coastal Karnataka, India

BACKGROUND

There are no published reports on the strain diversity and relative transmission of Mycobacterium tuberculosis isolates circulating in Karnataka State, India.

OBJECTIVE

To explore the strain diversity of M. tuberculosis isolates and their relative transmission in south coastal Karnataka using spoligotyping and mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing.

DESIGN

A total of 108 clinical isolates of M. tuberculosis were processed for spoligotyping, and 12-locus MIRU-VNTR typing and cluster analysis was performed.

RESULTS

Spoligotyping data of 108 isolates revealed 63 spoligotype patterns: 36 (80 isolates, 74.1%) patterns corresponded to spoligotype international types (SITs), whereas 27 (28 isolates, 25.9%) patterns were orphans. A further 57 (52.8%) isolates were clustered into 12 clusters; 51 (47.2%) isolates were unique. The largest spoligotype cluster comprised SIT 48 (L1.2.2), followed by SIT 1942 (L3) and SIT 11 (L1.1.2). Combined MIRU-VNTR typing and spoligotyping analysis further differentiated these 108 isolates into five clusters of two isolates each and 98 individual patterns.

CONCLUSIONS

Combined use of spoligotyping and MIRU-VNTR typing is best suited for genotyping studies in this region. Very high genetic diversity was observed among the clinical isolates. Further elaborate studies are required for a better understanding of the genetic diversity and transmission dynamics of the strains circulating in this region.

Genes2GO: A web application for querying gene sets for specific GO terms

Gene ontology annotations have become an essential resource for biological interpretations of experimental findings. The process of gathering basic annotation information in tables that link gene sets with specific gene ontology terms can be cumbersome, in particular if it requires above average computer skills or bioinformatics expertise. We have therefore developed Genes2GO, an intuitive R-based web application. Genes2GO uses the biomaRt package of Bioconductor in order to retrieve custom sets of gene ontology annotations for any list of genes from organisms covered by the Ensembl database. Genes2GO produces a binary matrix file, indicating for each gene the presence or absence of specific annotations for a gene. It should be noted that other GO tools do not offer this user-friendly access to annotations.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process.

Database URL: http://www.tfcheckpoint.org

The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms

Background

The gastrointestinal peptide hormones cholecystokinin and gastrin exert their biological functions via cholecystokinin receptors CCK1R and CCK2R respectively. Gastrin, a central regulator of gastric acid secretion, is involved in growth and differentiation of gastric and colonic mucosa, and there is evidence that it is pro-carcinogenic. Cholecystokinin is implicated in digestion, appetite control and body weight regulation, and may play a role in several digestive disorders.

Results

We performed a detailed analysis of the literature reporting experimental evidence on signaling pathways triggered by CCK1R and CCK2R, in order to create a comprehensive map of gastrin and cholecystokinin-mediated intracellular signaling cascades. The resulting signaling map captures 413 reactions involving 530 molecular species, and incorporates the currently available knowledge into one integrated signaling network. The decomposition of the signaling map into sub-networks revealed 18 modules that represent higher-level structures of the signaling map. These modules allow a more compact mapping of intracellular signaling reactions to known cell behavioral outcomes such as proliferation, migration and apoptosis. The integration of large-scale protein-protein interaction data to this literature-based signaling map in combination with topological analyses allowed us to identify 70 proteins able to increase the compactness of the map. These proteins represent experimentally testable hypotheses for gaining new knowledge on gastrin- and cholecystokinin receptor signaling. The CCKR map is freely available both in a downloadable, machine-readable SBML-compatible format and as a web resource through PAYAO (http://sblab.celldesigner.org:18080/Payao11/bin/).

Conclusion

We have demonstrated how a literature-based CCKR signaling map together with its protein interaction extensions can be analyzed to generate new hypotheses on molecular mechanisms involved in gastrin- and cholecystokinin-mediated regulation of cellular processes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-015-0181-z) contains supplementary material, which is available to authorized users.

Atypical Presentations of Melioidosis in North India: Report of Two Cases

Melioidosis is an infection caused by Gram-negative bacterium, Burkholderia pseudomallei. This is a rare disease in India, more so in North India. We present two cases of melioidosis with unusual sites of infection. The first patient was a young diabetic male presenting to us with history of prolonged fever and upper abdominal discomfort, subsequently diagnosed as a case of pyogenic liver abscess. The second patient was a middle aged diabetic complaining of prolonged fever and headache and found to have right frontal lobe brain abscess.The pus cultured from the lesion in both cases showed growth of Burkholderia pseudomallei. These two cases are described to consider melioidosis as a differential diagnosis amongst pyrexia of unknown origin cases.

EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom

Plant essential oils are complex mixtures of volatile organic compounds, which play indispensable roles in the environment, for the plant itself, as well as for humans. The potential biological information stored in essential oil composition data can provide an insight into the silent language of plants, and the roles of these chemical emissions in defense, communication and pollinator attraction. In order to decipher volatile profile patterns from a global perspective, we have developed the ESSential OIL DataBase (EssOilDB), a continually updated, freely available electronic database designed to provide knowledge resource for plant essential oils, that enables one to address a multitude of queries on volatile profiles of native, invasive, normal or stressed plants, across taxonomic clades, geographical locations and several other biotic and abiotic influences. To our knowledge, EssOilDB is the only database in the public domain providing an opportunity for context based scientific research on volatile patterns in plants. EssOilDB presently contains 123 041 essential oil records spanning a century of published reports on volatile profiles, with data from 92 plant taxonomic families, spread across diverse geographical locations all over the globe. We hope that this huge repository of VOCs will facilitate unraveling of the true significance of volatiles in plants, along with creating potential avenues for industrial applications of essential oils. We also illustrate the use of this database in terpene biology and show how EssOilDB can be used to complement data from computational genomics to gain insights into the diversity and variability of terpenoids in the plant kingdom. EssOilDB would serve as a valuable information resource, for students and researchers in plant biology, in the design and discovery of new odor profiles, as well as for entrepreneurs—the potential for generating consumer specific scents being one of the most attractive and interesting topics in the cosmetic industry.

Database URL: http://nipgr.res.in/Essoildb/

TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors

SUMMARY

Gene regulatory network assembly and analysis requires high-quality knowledge sources that cover functional aspects of the various components of the gene regulatory machinery. A multiplicity of resources exists with information about mammalian transcription factors (TFs); yet, only few of these provide sufficiently accurate classifications of the functional roles of individual TFs, or standardized evidence that would justify the information on which these functional classifications are based. We compiled the list of all putative TFs from nine different resources, ignored factors such as general TFs, mediator complexes and chromatin modifiers, and for the remaining factors checked the available literature for references that support their function as a true sequence-specific DNA-binding RNA polymerase II TF (DbTF). The results are available in the TFcheckpoint database, an exhaustive collection of TFs annotated according to experimental and other evidence on their function as true DbTFs. TFcheckpoint.org provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies.

AVAILABILITY

The TFcheckpoint database is freely available at www.tfcheckpoint.org

Molecular resurfacing of cartilage with proteoglycan 4

Early loss of proteoglycan 4 (PRG4), a lubricating glycoprotein implicated in boundary lubrication, from the cartilage surface has been associated with degeneration of cartilage and early onset of osteoarthritis. Viscosupplementation with hyaluronic acid and other macromolecules has been proposed as a treatment of osteoarthritis. However, the efficacy of viscosupplementation is variable and may be influenced by the short residence time of lubricant in the knee joint after injection. Recent studies have demonstrated the use of aldehyde (CHO) modified extracellular matrix proteins for targeted adherence to a biological tissue surface. It is hypothesized that CHO could be exploited to enhance the binding of lubricating proteoglycans to the surface of PRG4-depleted cartilage. The objective of this study was to determine the feasibility of molecular resurfacing of cartilage with CHO-modified PRG4. PRG4 was chemically functionalized with aldehyde (PRG4-CHO) and aldehyde plus Oregon Green (OG) fluorophore (PRG4-OG-CHO) to allow for differentiation of endogenous and exogenous PRG4. Cartilage disks depleted of native PRG4 were then treated with solutions of PRG4, PRG4-CHO, or PRG4-OG-CHO and then assayed for the presence of PRG4 by immunohistochemistry, ELISA, and fluorescence imaging. Repletion of cartilage surfaces was significantly enhanced with the inclusion of CHO compared with repletion with unmodified PRG4. These findings suggest a generalized approach which may be used for molecular resurfacing of tissue surfaces with PRG4 and other lubricating biomolecules, perhaps leading in the future to a convenient method for overcoming loss of lubrication during the early stages of osteoarthritis.

Pulmonary melioidosis in febrile neutropenia: the rare and deadly duet

We present the first two fulminant cases of pulmonary melioidosis in febrile neutropenic patients with acute and varied presentations seen in our institution and their fatal outcome. A high index of suspicion coupled with microbiological confirmation can facilitate the administration of the appropriate therapy in cases of melioidosis that differ from other bacterial infections in terms of presentation and the response to antimicrobials.

ZifBASE: a database of zinc finger proteins and associated resources

Background

Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP) to identify the potential binding sites and its location, which reduce the time of in vivo task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence.

Description

ZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available) and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones), the number of finger units in each of the zinc finger proteins (with multiple fingers), the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public databases like UniprotKB, PDB, ModBase and Protein Model Portal and PubMed for making it more informative.

Conclusion

A database is established to maintain the information of the sequence features, including the class, framework, number of fingers, residues, position, recognition site and physio-chemical properties (molecular weight, isoelectric point) of both natural and engineered zinc finger proteins and dissociation constant of few. ZifBASE can provide more effective and efficient way of accessing the zinc finger protein sequences and their target binding sites with the links to their three-dimensional structures. All the data and functions are available at the advanced web-based search interface .

Emerging extra-intestinal infections with Aeromonas hydrophila in coastal region of southern Karnataka

BACKGROUND

Aeromonas species are gram-negative rods usually isolated from the gastrointestinal tract. They have been occasionally reported as a cause of extra-intestinal infections such as cellulitis, cholangitis, necrotizing fascitis, meningitis, bacteremia, or peritonitis in both immunocompetent and immunocompromised patients.

AIM

To determine the role and possible pathogenesis of Aeromonas in extra-intestinal infections.

SETTINGS AND DESIGN

Retrospective analysis carried out at Kasturba Hospital Manipal, Karnataka in the months of January and February 2007.

MATERIALS AND METHODS

Clinical manifestations and management of eight cases of extra-intestinal infections caused by A. hydrophila , from the south Karnataka coastal region were reviewed. The isolates were identified with the help of biochemical tests using standard guidelines.

RESULTS

All patients acquired Aeromonas infections in the community. Five (62.5%) had underlying illnesses, such as liver disease, diabetes mellitus or malignancy. Five (62.5%) had polymicrobial infections, and three (37.5%) were complicated with bacteremia. These included three patients with ulcers or abscess over the lower leg, two with cellulitis due to snake bite and one each with pelvic inflammatory disease, spontaneous bacterial peritonitis and pneumonia. A. hydrophila was found to be a causative agent of pelvic inflammatory disease or cellulitis following sea snake bite, and such a clinical scenario has not been previously described. Seven patients survived the illness.

CONCLUSIONS

Isolation of A. hydrophila from extra-intestinal specimens demands utmost clinical and microbiological vigilance in diagnosis, since the organism can cause serious infections among immunocompromised as well as immunocompetent individuals.

Correlation of antioxidants and fitness levels in undergraduate medical students

Fitness is the ability of the organism to maintain the various internal equilibriums as closely as possible to the resting state during strenuous exercise and to restore promptly after exercise. The aim of the present study was to evaluate the fitness and correlate it with anti-oxidant levels of 50 male medical students in the age group of 18 to 25 years. Fitness was assessed by Harvard Step Test. The antioxidant status was assessed by Vitamin C and Vitamin E levels in the blood. Three groups were formed on the basis of fitness score. The mean values of fitness scores were 95.33 +/- 7.66, 68.5 +/- 9.22 and 37 +/- 10.9, in-group A, B and C, respectively. Between the three groups, Vitamin E values were significantly different but not the Vitamin C levels. Thus, it is concluded that Vitamin E levels influence the fitness state of an individual.

Castleman's disease and superior vena cava thrombi: a rare presentation and a review of the literature

Castleman's disease is a clinicopathological entity in which growth of lymphoid tissue is unregulated. It may present as asymptomatic involvement of one lymph node group or as a multicentric disease with systemic symptoms. Unlike localized disease, for which surgical excision is curative regardless of the histological type, multicentric disease often necessitates aggressive systemic therapy and portends a poor outcome. Superior vena caval thrombosis is an uncommon manifestation associated with Castleman's disease.

An unusual case of neonatal brain abscess following Klebsiella pneumoniae septicemia

A case of solitary brain abscess in a term neonate caused by Kiebsiella pneumoniae is described. K. pneumoniae, although a common cause of neonatal septicemia, is rarely implicated as an etiological agent for cerebral abscess in this age-group. The interest of this case lies in the rarity of the causative organism and atypical features. In the absence of predisposing factors in the neonate, we suspect that the infection was transmitted vertically from the mother before or at the time of delivery since there was evidence of asymtomatic urinary tract infection in the antenatal period.

Isolation and characterization of MC3T3-E1 preosteoblast subclones with distinct in vitro and in vivo differentiation/mineralization potential

A series of subclonal cell lines with high or low differentiation/mineralization potential after growth in the presence of ascorbic acid (AA) were derived from murine MC3T3-E1 cells. Subclones were characterized in terms of their ability to mineralize a collagenous extracellular matrix both in vitro and in vivo and express osteoblast-related genes. When compared with nonmineralizing cells, mineralizing subclones selectively expressed mRNAs for the osteoblast markers, bone sialoprotein (BSP), osteocalcin (OCN), and the parathyroid hormone (PTH)/parathyroid hormone-related protein (PTHrP) receptor. In contrast, alkaline phosphatase mRNA was present in certain nonmineralizing as well as mineralizing subclones, suggesting that its expression may be subject to different controls from other osteoblast markers. Only highly differentiating subclones exhibited strong AA-dependent induction of a transiently transfected OCN promoter-luciferase reporter gene, indicating that there was a good correlation between mRNA levels and transcriptional activity. Consistent with its postulated role in biomineralization, BSP as measured by Western blotting was only present in mineralizing subclones. After implantation into immunodeficient mice, highly differentiating subclones formed bone-like ossicles resembling woven bone, while poorly differentiating cells only produced fibrous tissue. Interestingly, subclones with both high and low differentiation potential produced similar amounts of collagen in culture and expressed comparable basal levels of mRNA encoding Osf2/Cbfa1, an osteoblast-related transcription factor. Although some strongly differentiating cells exhibited a modest AA-dependent up-regulation of Osf2/Cbfa1 mRNA, there was no clear relationship between levels of this message and induction of mRNAs for other differentiation markers. Thus, the mere presence of Osf2/Cbfa1 in a subclone was not sufficient for osteoblast differentiation. These subclones will be very useful for studying critical events in osteoblast differentiation and mineralization.

Dual-beam imaging for online verification of radiotherapy field placement

PURPOSE

Due to the poor quality of megavoltage (MV) radiographs, detection and assessment of discrepancies in radiation field placement are difficult. Furthermore, the high imaging dose required to produce the megavoltage radiograph prohibits frequent image acquisition, particularly for those fields that require the use of an "open-field" exposure. For these small, or conformal, radiation fields, an alternate method of verifying field placement is required if the out-of-field dose is to be minimized. An open-field image acquired with a kilovoltage (kV) source would (a) deliver a very low patient dose, (b) increase the visibility of bony landmarks, and (c) simplify intercomparison of portal and prescription images. This article describes the development of a dual-beam imaging system that produces diagnostic quality "double-exposure" portal images for verifying radiation field placement.

METHODS AND MATERIALS

The dual-beam system consists of a kV x-ray tube mounted on the gantry of a medical linear accelerator. The kV beam shares the same isocenter (+/- 1 mm) as the treatment beam but is at 45 degrees to the central axis. Both the kilovoltage and megavoltage images are collected with a fluoroscopic imaging system that uses a low-noise CCD camera to accumulate the light emitted from a phosphor screen. Two 45 degrees mirrors are used to remove the CCD camera from the x-ray beam. The light integration on the CCD array is controlled by a mechanical shutter, allowing easy synchronization with the radiation exposures. The camera is shielded by a lead housing to reduce the number of x-rays reaching the CCD array. A conventional thickness phosphor screen is used for both the kV and MV exposures. In the dual-beam imaging procedure, an open-field kV radiograph is acquired with the patient in treatment position. Immediately following, a MV image is acquired with the beam-defining blocks in position. Summation of the two images produces an online double-exposure image. The anatomical information in either the kV or MV image can be emphasized by weighting the images appropriately. This system was used to acquire MV and kV images of both a contrast-detail phantom and a Rando head phantom. Dual-beam images were also acquired for a pituitary treatment, demonstrating the feasibility and usefulness of the dual-beam technique.

RESULTS

Analysis of the contrast-detail images produced with the MV and kV beams shows the expected advantage of using the kV x-ray beam. Images of a Rando head phantom confirm these results. A clinical demonstration of the dual-beam system for verifying the delivery of a pituitary field is shown. The quality of the dual-beam image is similar to the prescription (simulation) image, contains a larger anatomical region, and delivers a lower integral dose to the patient. In addition, the kV beam also enhances the visibility of small markers implanted in the prostate.

CONCLUSIONS

A dual-beam imaging system has been developed for the radiographic verification of small, conformal fields. This development demonstrates the advantages and feasibility of using a kV x-ray beam in combination with the treatment beam to improve the accuracy of detecting patient setup errors.

Complete recovery from renal infarcts in a patient with mixed connective tissue disease

We report the case of a 66-year-old woman with mixed connective tissue disease (MCD) who had recurrent renal infarcts and renal insufficiency with only mildly increased serum anticardiolipin antibodies. After low-dose aspirin therapy, the renal lesions resolved, and renal function returned to normal within 3 weeks.

Paraneoplastic hypercalcemia associated with uterine papillary serous carcinoma

Hypercalcemia associated with endometrial carcinoma is rare. We report a patient with serous papillary endometrial carcinoma with paraneoplastic hypercalcemia due to parathyroid hormone-related peptide (PTHrP). To the best of our knowledge this is the first report of hypercalcemia due to PTHrP in this type of tumor.

Postpartum ovarian vein thrombosis

Ovarian vein thrombosis is a rare occurrence in the postpartum period. Two cases of postpartum ovarian vein thrombosis are presented. The differential diagnosis is extensive because many diseases can present with similar symptoms. Early diagnosis is essential for appropriate treatment and prevention of the potential sequelae that can occur. Computerized tomography with contrast is the optimal imaging modality for the diagnosis.

Progressive Bochdalek hernia with unusual ureteral herniation

An asymptomatic case of a Bochdalek hernia with progressive herniation of the right ureter is presented. The diagnosis was made by computed tomography (CT).

Branchiogenic cyst of larynx

An extremely rare case of branchiogenic cyst of the larynx in young adult male is reported. Relevant literature is reviewed.

Ruptured pyogenic Baker's cyst

The authors present the case of a patient who developed a ruptured Baker's cyst. Methods of diagnosis and treatment are discussed.