Analysis of Germline Gene Copy Number Variants of Patients with Sporadic Pancreatic Adenocarcinoma Reveals Specific Variations

Objectives: The rapid fatality of pancreatic cancer is, in large part, the result of diagnosis at an advanced stage in the majority of patients. Identification of individuals at risk of developing pancreatic adenocarcinoma would be useful to improve the prognosis of this disease. There is presently no biological or genetic indicator allowing the detection of patients at risk. Our main goal was to identify copy number variants (CNVs) common to all patients with sporadic pancreatic cancer. Methods: We analyzed gene CNVs in leukocyte DNA from 31 patients with sporadic pancreatic adenocarcinoma and from 93 matched controls. Genotyping was performed with the use of the GeneChip Human Mapping 500K Array Set (Affymetrix). Results: We identified 431 single nucleotide polymorphism (SNP) probes with abnormal hy-bridization signal present in the DNA of all 31 patients. Of these SNP probes, 284 corresponded to 3 or more copies and 147 corresponded to 1 or 0 copies. Several cancer-associated genes were amplified in all patients. Conversely, several genes supposed to oppose cancer development were present as single copy. Conclusions: These data suggest that a set of 431 CNVs could be associated with the disease. This set could be useful for early diagnosis

Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2)

We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.Peer reviewe

Effect of Appendectomy on ClinicalCourse of Diverticulosis

Diverticulitis is a common condition where inflammation seems to play a key role in all forms of the disease. Since diverticular disease, in some cases, exhibits clinical and histopathologic similarities with the idiopathic inflammatory bowel disease, could have in common, with these some environmental risk factors, as appendectomy, that could interfere with the natural history of diverticular disease. Since the prevalence and the role of appendectomy in patients with colonic diverticula has not been defined, the aim of this study was to evaluate the prevalence of appendectomy, both in uncomplicated diverticular disease and in patients with diverticulitis. Two hundred and seven consecutive patients with verified diagnosis of diverticular disease of the colon were enrolled. Diagnosis of diverticulitis was defined by means of clinical, colonoscopic, and computerised tomography criteria. Logistic regression was used to describe the relation between the dependent variable (diverticulitis) and several covariates: sex, age (60), BMI (26), and history of appendectomy (emergency or elective appendectomy). We included the first order interactions in the model to assess the effect of each variable for a particular degree of the others covariates. Statistical analysis was performed using SPSS software. Results: The first order interactions did not show a relevant effect (p>0.10) and therefore were excluded from the logistic model. Sex (p=0.88), BMI (p=0.80), elective appendectomy (p=0.17), age (p=0,11), do not affect significantly, either as an independent variable or as a confounder, the risk of development of diverticulitis, and therefore were also excluded from the model. According to the final model the risk of diverticulitis is 4,94 fold higher (95% confidence interval: 1.98 to 12.37) in patients with history of appendectomy with emergency operative treatment, compared with patients without appendectomy or history of elective resection (p<0.001. Conclusions: The risk of diverticulitis does not increase in patients with elective appendectomy, therefore only patients with emergency appendectomy have an increased risk of diverticuliti

Amyand's hernia-a vermiform appendix presenting in an inguinal hernia: a case series

<p>Abstract</p> <p>Introduction</p> <p>A vermiform appendix in an inguinal hernia, inflamed or not, is known as Amyand's hernia. Here we present a case series of four men with Amyand's hernia.</p> <p>Case presentations</p> <p>We retrospectively studied 963 Caucasian patients with inguinal hernia who were admitted to our surgical department over a 12-year period. Four patients presented with Amyand's hernia (0.4%). A 32-year-old Caucasian man had an inflamed vermiform appendix in his hernial sac (acute appendicitis), presenting as an incarcerated right groin hernia, and underwent simultaneous appendectomy and Bassini suture hernia repair. Two patients, Caucasian men aged 36 and 43 years old, had normal appendices in their sacs, which clinically appeared as non-incarcerated right groin hernias. Both underwent a plug-mesh hernia repair without appendectomy. The fourth patient, a 25-year-old Caucasian man with a large but not inflamed appendix in his sac, had a plug-mesh hernia repair with appendectomy.</p> <p>Conclusion</p> <p>A hernia surgeon may encounter unexpected intraoperative findings, such as Amyand's hernia. It is important to be prepared and apply the appropriate treatment.</p

Pressure dependent yield criteria for polymers

Different criteria have been proposed to include the influence of pressure (or mean normal stress) on the yield behavior of polymers. It is difficult to distinguish among them using the type of experiments that produce data used in two-dimensional plots of yield loci. This is due to the fact that the maximum range of values of mean normal stress is relatively small in such experiments. Marked differences between these criteria do occur however as the hydrostatic pressure or mean stress is altered substantially. Experiments that show the effect of applied pressure on tensile and/or compressive yield strength provide one means for describing such differences. This paper considers two forms of a pressure modified von Mises criterion and shows a comparison with available experimental information.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22415/1/0000865.pd

Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)

<p>Abstract</p> <p>Background</p> <p>The present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete <it>Streptomyces coelicolor </it>A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset.</p> <p>Findings</p> <p>A microarray dataset using samples from two replicate cultures for each nutrient limitation was generated. In this report our analysis has focused on the genes which are significantly differentially expressed, as determined by Rank Products Analysis, between samples from matched time points correlated by growth phase for the three pairs of differently limited culture datasets. With a few exceptions, genes are only significantly differentially expressed between the N6/N7 time points and their corresponding time points in the C and P-limited cultures, with the vast majority of the differentially expressed genes being more highly expressed in the N-limited cultures. Our analysis of these genes indicated expression of several members of the GlnR regulon are induced upon nitrogen limitation, as assayed for by [NH₄⁺] measurements, and we are able to identify several additional genes not present in the GlnR regulon whose expression is induced in response to nitrogen limitation. We also note SCO3327 which encodes a small protein (32 amino acid residues) unusually rich in the basic amino acids lysine (31.25%) and arginine (25%) is significantly differentially expressed in the nitrogen limited cultures. Additionally, we investigate the expression of known members of the GlnR regulon and the relationship between gene organization and expression for the SCO2486-SCO2487 and SCO5583-SCO5585 operons.</p> <p>Conclusions</p> <p>We provide a list of genes whose expression is differentially expressed in low nitrogen culture conditions, including a putative nitrogen storage protein encoded by SCO3327. Our list includes several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation. These genes represent likely targets for future studies into the nitrogen starvation response in <it>Streptomyces coelicolor</it>.</p

nocoRNAc: Characterization of non-coding RNAs in prokaryotes

<p>Abstract</p> <p>Background</p> <p>The interest in non-coding RNAs (ncRNAs) constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. However, for most organisms the non-coding transcriptome still remains unexplored to a great extent. Various experimental techniques for the identification of ncRNA transcripts are available, but as these methods are costly and time-consuming, there is a need for computational methods that allow the detection of functional RNAs in complete genomes in order to suggest elements for further experiments. Several programs for the genome-wide prediction of functional RNAs have been developed but most of them predict a genomic locus with no indication whether the element is transcribed or not.</p> <p>Results</p> <p>We present <smcaps>NOCO</smcaps>RNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. <smcaps>NOCO</smcaps>RNAc incorporates various procedures for the detection of transcriptional features which are then integrated with functional ncRNA loci to determine the transcript coordinates. We applied RNAz and <smcaps>NOCO</smcaps>RNAc to the genome of <it>Streptomyces coelicolor </it>and detected more than 800 putative ncRNA transcripts most of them located antisense to protein-coding regions. Using a custom design microarray we profiled the expression of about 400 of these elements and found more than 300 to be transcribed, 38 of them are predicted novel ncRNA genes in intergenic regions. The expression patterns of many ncRNAs are similarly complex as those of the protein-coding genes, in particular many antisense ncRNAs show a high expression correlation with their protein-coding partner.</p> <p>Conclusions</p> <p>We have developed <smcaps>NOCO</smcaps>RNAc, a framework that facilitates the automated characterization of functional ncRNAs. <smcaps>NOCO</smcaps>RNAc increases the confidence of predicted ncRNA loci, especially if they contain transcribed ncRNAs. <smcaps>NOCO</smcaps>RNAc is not restricted to intergenic regions, but it is applicable to the prediction of ncRNA transcripts in whole microbial genomes. The software as well as a user guide and example data is available at <url>http://www.zbit.uni-tuebingen.de/pas/nocornac.htm</url>.</p

The macroscopic yield behaviour of polymers

A yield criterion, not previously compared with the actual macroscopic behaviour of polymers, is herein compared with the pressure-modified octahedral shear stress criterion earlier suggested by others. This new relation, which is a version of the von Mises criterion, accommodates differences in tensile and compressive yield strengths and accounts for any dependence of yielding on the hydrostatic component of the applied stress state.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44784/1/10853_2004_Article_BF00550671.pd

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described