A human ubiquitin conjugating enzyme,L-UBC,maps in the Alzheimer's disease locus on Chromosome 14q24.3

We have identified a novel ubiquitin conjugating enzyme gene, L-UBC, which maps to human Chromosome (Chr) 14q24.3. This is also the location of the major early onset familial Alzheimer's disease gene (FAD3). L-UBC encodes a protein that demonstrates homology to the yeast ubiquitin conjugating enzyme, UBC-4, and human UbcH5. Their functions are to ubiquitinate specific proteins targeted for degradation. The protein also exhibits very strong homology to a rabbit protein, E2-F1, which mediates p53 degradation driven by papilloma virus E6 protein in vitro. The accumulation of specific proteins that have undergone aberrant processing in neurofibrillary tangles and amyloid plaques is the classic pathological feature in brains of Alzheimer's disease patients. Abnormal ubiquitination has previously been suggested to play a role in the etiology of Alzheimer's disease. This gene therefore represents a plausible candidate gene for FAD3.     

The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments

As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of related measurements. The common property among these high-dimensional biological studies is that the measured features have a rich and largely unknown underlying structure. One example of much recent interest is identifying differentially expressed genes in comparative microarray experiments. We propose a new approach aimed at optimally performing many hypothesis tests in a high-dimensional study. This approach estimates the optimal discovery procedure (ODP), which has recently been introduced and theoretically shown to optimally perform multiple significance tests. Whereas existing procedures essentially use data from only one feature at a time, the ODP approach uses the relevant information from the entire data set when testing each feature. In particular, we propose a generally applicable estimate of the ODP for identifying differentially expressed genes in microarray experiments. This microarray method consistently shows favorable performance over five highly used existing methods. For example, in testing for differential expression between two breast cancer tumor types, the ODP provides increases from 72% to 185% in the number of genes called significant at a false discovery rate of 3%. Our proposed microarray method is freely available to academic users in the open-source, point-and-click EDGE software package.     

Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

Background

With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated.

Results

We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.

Conclusions

ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.     

Negotiating decisions during informed consent for pediatric Phase I oncology trials

During informed consent conferences (ICCs) for Phase I trials, oncologists must present complex information while addressing concerns. Research on communication that evolves during ICCs remains largely unexplored. We examined communication during ICCs for pediatric Phase I cancer trials using a stratified random sample from six pediatric cancer centers. A grounded theory approach identified key communication steps and factors influencing the negotiation of decisions for trial participation. Analysis suggests that during ICCs, families, patients, and clinicians exercise choice and control by negotiating micro-decisions in two broad domains: drug logic and logistics, and administration/scheduling. Micro-decisions unfold in a four-step communication process: (1) introduction of an issue; (2) response; (3) negotiation of the issue; and (4) resolution and decision. Negotiation over smaller micro-decisions is prominent in ICCs and merits further study.     

The Ischemic Stroke Genetics Study (ISGS) Protocol

Background  

The molecular basis for the genetic risk of ischemic stroke is likely to be multigenic and influenced by environmental factors. Several small case-control studies have suggested associations between ischemic stroke and polymorphisms of genes that code for coagulation cascade proteins and platelet receptors. Our aim is to investigate potential associations between hemostatic gene polymorphisms and ischemic stroke, with particular emphasis on detailed characterization of the phenotype.     

A comparison of the illness beliefs of people with angina and their peers: a questionnaire study

Background

Systolic compression of a coronary artery by overlying myocardial tissue is termed myocardial bridging. Myocardial bridging usually has a benign prognosis, but some cases resulting in myocardial ischemia, infarction and sudden cardiac death have been reported. We are reporting a case of myocardial bridging which was complicated with acute myocardial infarction associated with inappropriate blood donation.

Case presentation

A 33 year-old-man was admitted to our emergency with acute anteroseptal myocardial infarction after a blood donation. The electrocardiography showed sinus rhythm and was consistent with an acute anteroseptal myocardial infarction. We decided to perform primary percutanous intervention (PCI). Myocardial bridging was observed in the mid segment of the left anterior descending coronary artery on coronary angiogram. PCI was canceled and medical follow up was decided. Blood transfusion was made because he had a deep anemia. A normal hemaglobin level and clinical reperfusion was achieved after ten hours by blood transfusion. At the one year follow up visit, our patient was healthy and had no cardiac complaints.

Conclusions

Myocardial bridging may cause acute myocardial infarction in various clinical conditions. Although the condition in this case caused profound anemia related acute myocardial infarction, its treatment and management was unusual.     

The influence of diet crude protein level on odour and ammonia emissions from finishing pig houses

Feed trials were carried out to assess the influence of crude protein content in finishing pig diets on odour and ammonia emissions. Eight pigs (4 boars and 4 gilts), average initial weight 70.8 kg (s.e. 3.167) were housed in two pens that were isolated from the rest of a pig house at University College Dublin Research Farm, Newcastle, Dublin, Ireland. Four diets containing 130, 160, 190 and 220 g x kg(-1) crude protein were fed during six four-week feeding periods (one treatment per room). The first week of the feeding periods served to allow odour build up in the pens and as a dietary adjustment period. The pens had partially slatted floors that were cleaned and had all the manure removed after each four-week period. Odour and ammonia concentrations were measured on days 9, 14, 16, 21 and 23 of each trial period. Odour samples were collected in Nalophan bags and analysed for odour concentration using an ECOMA Yes/No olfactometer. The odour threshold concentration was calculated according to the response of the olfactometry panel members and was displayed in Ou(E)m(-3), which referred to the physiological response from the panel equivalent to that elicited by 40 ppbv(-1) n-butanol evaporated in 1 m(3) of neutral gas. Ammonia concentrations in the ventilation air were measured using Dr?ger tubes. The odour emission rates per animal for the 130, 160, 190 and 220 g x kg(-1) crude protein diets were 12.1, 13.2, 19.6 and 17.6 Ou(E)s(-1)animal(-1), respectively (P<0.01). The odour emission rate per livestock unit (500 kg) for the 130, 160, 190 and 220 g x kg(-1) crude protein diets were 77.6, 80.0, 115.8 and 102.9 Ou(E)s(-1)LU(-1), respectively (P<0.01). The ammonia emission rates per animal for the 130, 160, 190 and 220 g x kg(-1) crude protein diets were 3.11, 3.89, 5.89 and 8.27 g x d(-1)animal(-1), respectively (P0.05). Manipulation of dietary crude protein levels would appear to offer a low cost alternative, in relation to end-of-pipe treatments, for the abatement of odour and ammonia emissions from finishing pig houses.