Systems-biology dissection of eukaryotic cell growth

A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth.

See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

Effects of manipulating the amount of social-evaluative threat on the cortisol stress response in young healthy women

Psychological stress is known to activate the hypothalamic-pituitary-adrenal axis, resulting in the release of cortisol from the adrenal cortex into the bloodstream. Cortisol is the major human stress hormone and its health correlates continue to be investigated by laboratories around the world. One line of research suggests that specific situational variables play a role in the creation of a stressful situation. The current study examined the effects of systematically varying several situational characteristics on the cortisol stress response in 80 healthy young women exposed to a public speaking task. Three main factors and its interactions were investigated by locating the expert panel either inside or outside of the room, having the subjects speak either about themselves or somebody else, and by asking half of the subjects to perform a distractor task in addition to performing the public speaking. We interpreted these manipulations as variations of social evaluative threat, ego-involvement, and divided attention. We hypothesized that the variations and their interactions would cause differences in endocrine stress responses. The results showed that only the manipulation of social-evaluative threat had a significant main effect on the cortisol stress response in women. There was a further trend (p = 0.07) for a four-way interaction effect. No other main or interaction effects could be observed. We conclude that in women, social-evaluative threat affects the endocrine stress response. This is in contrast to a previous study showing no effects of this variation in men. Thus, future studies should more closely investigate sex or gender effects that might be interacting with the situational aspects of a stressful task.

Investigations and control measures following a non-travel-associated case of toxigenic Cornyebacterium diphtheriae, London, United Kingdom, December 2009-January 2010

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Investigations and control measures following a non-travel-associated case of toxigenic Cornyebacterium diphtheriae, London, United Kingdom, December 2009-January 2010

This article reports the investigation and control measures undertaken following the identification of a toxigenic strain of Cornyebacterium diphtheriae var gravis, designated ribotype Minsk , in a partially vaccinated teenager born in the United Kingdom with no recent history of travel or known contact with a case of diphtheria or a carrier. This case highlights the need for ongoing work to improve vaccine uptake rates to ensure children receive all scheduled vaccinations.

Adhesional small bowel obstruction following anti-reflux surgery in children--comparison of 232 laparoscopic and open fundoplications

AIM

Adhesions are a major cause of morbidity following abdominal surgery. There is debate whether laparoscopic abdominal surgery results in a lower incidence of adhesional small bowel obstruction (ASBO) compared with the equivalent open procedure. The aim of this study was to study the incidence of ASBO following laparoscopic and open anti-reflux surgery.

METHODS

The case notes of all patients undergoing fundoplication (open or laparoscopic) between November 1997 and November 2005 were reviewed retrospectively. Laparotomy due to ASBO was chosen as the endpoint as it was a clearly identifiable and incontrovertible endpoint. The incidence of ASBO following each operation was compared using Fisher's exact test (p<0.05 was considered significant).

RESULTS

A total of 232 patients were analysed. There were no ASBO following 170 laparoscopic fundoplications. There were 5 episodes (8.1%) of ASBO in 3 patients (4.8%) following 62 open procedures. Two of the three patients who developed ASBO after open fundoplication had undergone concomitant Ladd's procedure. There was no significant difference in the rate of ASBO following laparoscopic and open fundoplication alone.

CONCLUSIONS

ASBO is a serious complication following any abdominal surgery. The data from this study indicate that the risk of ASBO following laparoscopic fundoplication is negligible. Although there is a suggestion that the risk of ASBO is lower following laparoscopic fundoplication compared with open fundoplication, there was no significant difference between the two groups as Ladd's procedure was performed in 2 of the open cases.

Study of 962 patients indicates progressive muscular atrophy is a form of ALS

BACKGROUND

Progressive muscular atrophy (PMA) is clinically characterized by signs of lower motor neuron dysfunction and may evolve into amyotrophic lateral sclerosis (ALS). Whether PMA is actually a form of ALS has important consequences clinically and for therapeutic trials. We compared the survival of patients with PMA or ALS to analyze the clinical features that influence survival in PMA.

METHODS

We reviewed the medical records of patients with PMA (n = 91) or ALS (n = 871) from our ALS Center and verified survival by telephoning the families or using the National Death Index.

RESULTS

In PMA, patients were more likely to be male (p < 0.001), older (p = 0.007), and lived longer (p = 0.01) than in ALS. Cox model analysis suggested that the risk of death increased with age at onset in both patient groups (p < 0.005). Upper motor neuron (UMN) signs developed in 22% of patients with PMA within 61 months after diagnosis. Demographic and other clinical variables did not differ at diagnosis between those who did or did not develop UMN signs. In PMA, the factors present at diagnosis that predicted shorter survival were greater number of body regions affected, lower forced vital capacity, and lower ALS Functional Rating Scale-Revised score. Noninvasive ventilation and gastrostomy were used frequently in PMA.

CONCLUSION

Although patients with progressive muscular atrophy (PMA) tended to live longer than those with amyotrophic lateral sclerosis (ALS), shorter survival in PMA is associated with the same risk factors that predict poor survival in ALS. Additionally, PMA is relentlessly progressive, and UMN involvement can occur, as also reported in imaging and postmortem studies. For these reasons, PMA should be considered a form of ALS.

EST and microarray analysis of horn development in Onthophagus beetles

Background

The origin of novel traits and their subsequent diversification represent central themes in evo-devo and evolutionary ecology. Here we explore the genetic and genomic basis of a class of traits that is both novel and highly diverse, in a group of organisms that is ecologically complex and experimentally tractable: horned beetles.

Results

We developed two high quality, normalized cDNA libraries for larval and pupal Onthophagus taurus and sequenced 3,488 ESTs that assembled into 451 contigs and 2,330 singletons. We present the annotation and a comparative analysis of the conservation of the sequences. Microarrays developed from the combined libraries were then used to contrast the transcriptome of developing primordia of head horns, prothoracic horns, and legs. Our experiments identify a first comprehensive list of candidate genes for the evolution and diversification of beetle horns. We find that developing horns and legs show many similarities as well as important differences in their transcription profiles, suggesting that the origin of horns was mediated partly, but not entirely, by the recruitment of genes involved in the formation of more traditional appendages such as legs. Furthermore, we find that horns developing from the head and prothorax differ in their transcription profiles to a degree that suggests that head and prothoracic horns are not serial homologs, but instead may have evolved independently from each other.

Conclusion

We have laid the foundation for a systematic analysis of the genetic basis of horned beetle development and diversification with the potential to contribute significantly to several major frontiers in evolutionary developmental biology.

Functional anatomy and muscle moment arms of the pelvic limb of an elite sprinting athlete: the racing greyhound (Canis familiaris)

We provide quantitative anatomical data on the muscle-tendon architecture and geometry of the pelvic limb of an elite sprint athlete, the racing greyhound. Specifically, muscle masses, muscle lengths, fascicle lengths, pennation angles and muscle moment arms were measured. Maximum isometric force and power of muscles, the maximum muscle torque at joints and tendon stress and strain were estimated. We compare data with that published for a generalized breed of canid, and other cursorial mammals such as the horse and hare. The pelvic limb of the racing greyhound had a relatively large volume of hip extensor muscle, which is likely to be required for power production. Per unit body mass, some pelvic limb muscles were relatively larger than those in less specialized canines, and many hip extensor muscles had longer fascicle lengths. It was estimated that substantial extensor moments could be created about the tarsus and hip of the greyhound allowing high power output and potential for rapid acceleration. The racing greyhound hence possesses substantial specializations for enhanced sprint performance.

Is return to professional rugby union likely after anterior cervical spinal surgery?

We have examined the outcome in 19 professional rugby union players who underwent anterior cervical discectomy and fusion between 1998 and 2003. Through a retrospective review of the medical records and telephone interviews of all 19 players, we have attempted to determine the likelihood of improvement, return to professional sport and the long-term consequences. We have also attempted to relate the probability of symptoms in the neck and radicular pain in the arm to the position of play. Neck and radicular pain were improved in 17 patients, with 13 returning to rugby, the majority by six months after operation. Of these, 13 returned to their pre-operative standard of play, one to a lower level and five have not played rugby again. Two of those who returned to the game have subsequently suffered further symptoms in the neck, one of whom was obliged to retire. The majority of the players with problems in the neck were front row forwards.

A return to playing rugby union after surgery and fusion of the anterior cervical spine is both likely and safe and need not end a career in the game.

A machine-learning approach to combined evidence validation of genome assemblies

MOTIVATION

While it is common to refer to 'the genome sequence' as if it were a single, complete and contiguous DNA string, it is in fact an assembly of millions of small, partially overlapping DNA fragments. Sophisticated computer algorithms (assemblers and scaffolders) merge these DNA fragments into contigs, and place these contigs into sequence scaffolds using the paired-end sequences derived from large-insert DNA libraries. Each step in this automated process is susceptible to producing errors; hence, the resulting draft assembly represents (in practice) only a likely assembly that requires further validation. Knowing which parts of the draft assembly are likely free of errors is critical if researchers are to draw reliable conclusions from the assembled sequence data.

RESULTS

We develop a machine-learning method to detect assembly errors in sequence assemblies. Several in silico measures for assembly validation have been proposed by various researchers. Using three benchmarking Drosophila draft genomes, we evaluate these techniques along with some new measures that we propose, including the good-minus-bad coverage (GMB), the good-to-bad-ratio (RGB), the average Z-score (AZ) and the average absolute Z-score (ASZ). Our results show that the GMB measure performs better than the others in both its sensitivity and its specificity for assembly error detection. Nevertheless, no single method performs sufficiently well to reliably detect genomic regions requiring attention for further experimental verification. To utilize the advantages of all these measures, we develop a novel machine learning approach that combines these individual measures to achieve a higher prediction accuracy (i.e. greater than 90%). Our combined evidence approach avoids the difficult and often ad hoc selection of many parameters the individual measures require, and significantly improves the overall precisions on the benchmarking data sets.

Data pushing: a fly-centric guide to bioinformatics tools

Bioinformatics tools can be invaluable resources to Drosophila researchers; however, the sheer number of applications and databases can be overwhelming. We present a broad overview of common bioinformatics tasks and the resources used to do them, with a specific focus on resources for Drosophila. The topics covered include: Genome Databases, Sequence Analysis, Comparative Genomics, Gene Expression Databases and Analysis Tools, Function-Based Data and Analysis, Pathways, Networks, and Interactions; and finally, tools to stay current with resources and literature. We also present a compilation of URLs and short descriptions that correspond to the topics and resources mentioned in this review.

Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex

Background

Sexual reproduction is a core biological function that is conserved throughout eukaryotic evolution, yet breeding systems are extremely variable. Genome-wide comparative studies can be effectively used to identify genes and regulatory patterns that are constrained to preserve core functions from those that may help to account for the diversity of animal reproductive strategies. We use a custom microarray to investigate gene expression in males and two reproductive stages of females in the crustacean Daphnia pulex. Most Daphnia species reproduce by cyclical parthenogenesis, alternating between sexual and clonal reproduction. Both sex determination and the switch in their mode of reproduction is environmentally induced, making Daphnia an interesting comparative system for the study of sex-biased and reproductive genes.

Results

Patterns of gene expression in females and males reveal that 50% of assayed transcripts show some degree of sex-bias. Female-biased transcription is enriched for translation, metabolic and regulatory genes associated with development. Male-biased expression is enriched for cuticle and protease function. Comparison with well studied arthropods such as Drosophila melanogaster and Anopheles gambiae suggests that female-biased patterns tend to be conserved, whereas male-biased genes are evolving faster in D. pulex. These findings are based on the proportion of female-biased, male-biased, and unbiased genes that share sequence similarity with proteins in other animal genomes.

Conclusion

Some transcriptional differences between males and females appear to be conserved across Arthropoda, including the rapid evolution of male-biased genes which is observed in insects and now in a crustacean. Yet, novel patterns of male-biased gene expression are also uncovered. This study is an important first step towards a detailed understanding of the genetic basis and evolution of parthenogenesis, environmental sex determination, and adaptation to aquatic environments.

Comparison of CT and positron emission tomography/CT coregistered images in planning radical radiotherapy in patients with non-small-cell lung cancer

Imaging with F-18 fluorodeoxyglucose positron emission tomography (PET) significantly improves lung cancer staging, especially when PET and CT information are combined. We describe a method for obtaining CT and PET images at separate acquisitions, which allows coregistration and incorporation of PET information into the radiotherapy (RT) planning process for non-small-cell lung cancer. The influence of PET information on RT planning was analysed for 10 consecutive patients. Computed tomography and PET images were acquired with the patient in an immobilization device, in the treatment position. Using specially written software, PET and CT data were coregistered using fiducial markers and imported into our RT planning system (Cadplan version 6). Treatment plans were prepared with and without access to PET/CT coregistered images and then compared. PET influenced the treatment plan in all cases. In three cases, geographic misses (gross tumour outside planning target volume) would have occurred had PET not been used. In a further three cases, better planning target volume marginal coverage was achieved with PET. In four patients, three with atelectasis, there were significant reductions in V20 (percentage of the total lung volume receiving 20 Gy or more). Use of coregistered PET/CT images significantly altered treatment plans in a majority of cases. This method could be used in routine practice at centres without access to a combined PET/CT scanner .