A functional-structural model of ephemeral seagrass growth influenced by environment

Background and Aims

Ephemeral seagrasses that respond rapidly to environmental changes are important marine habitats. However, they are under threat due to human activity and are logistically difficult and expensive to study. This study aimed to develop a new functional-structural environmentally dependent model of ephemeral seagrass, able to integrate our understanding of ephemeral seagrass growth dynamics and assess options for potential management interventions, such as seagrass transplantation.

Methods

A functional-structural plant model was developed in which growth and senescence rates are mechanistically linked to environmental variables. The model was parameterized and validated for a population of Halophila stipulacea in the Persian Gulf.

Key Results

There was a good match between empirical and simulated results for the number of apices, net rhizome length or net number of internodes using a 330 d simulation. Simulated data were more variable than empirical data. Simulated structural patterns of seagrass rhizome growth qualitatively matched empirical observations.

Conclusions

This new model successfully simulates the environmentally dependent growth and senescence rates of our case-study ephemeral seagrass species. It produces numerical and visual outputs that help synthesize our understanding of how the influence of environmental variables on plant functional processes affects overall growth patterns. The model can also be used to assess the potential outcomes of management interventions like seagrass transplantation, thus providing a useful management tool. It is freely available and easily adapted for new species and locations, although validation with more species and environments is required.

Elucidating the clinical characteristics of patients captured using different definitions of massive transfusion

BACKGROUND AND OBJECTIVES

The type and clinical characteristics of patients identified with commonly used definitions of massive transfusion (MT) are largely unknown. The objective of this study was to define the clinical characteristics of patients meeting different definitions of MT for the purpose of patient recruitment in observational studies.

MATERIALS AND METHODS

Data were extracted on all patients who received red blood cell (RBC) transfusions in 2010 at three tertiary Australian hospitals. MT patients were identified according to three definitions: ≥10 units RBC in 24 h (10/24 h), ≥6 units RBC in 6 h (6/6 h) and ≥5 units RBC in 4 h (5/4 h). Clinical coding data were used to assign bleeding context. Data on in-hospital mortality were also extracted.

RESULTS

Five hundred and forty-two patients met at least one MT definition, with 236 (44%) included by all definitions. The most inclusive definition was 5/4 h (508 patients, 94%) followed by 6/6 h (455 patients, 84%) and 10/24 h (251 patients, 46%). Importantly, 40-55% of most types of critical bleeding events and 82% of all obstetric haemorrhage cases were excluded by the 10/24 h definition. Patients who met both the 5/4 h and 10/24 h definitions were transfused more RBCs (19 vs. 8 median total RBC units; P < 0·001), had longer ventilation time (120 vs. 55 h; P < 0·001), median ICU (149 vs. 99 h; P < 0·001) and hospital length of stay (23 vs. 18 h; P = 0·006) and had a higher in-hospital mortality rate (23·3% vs. 16·4%; P = 0·050).

CONCLUSION

The 5/4 h MT definition was the most inclusive, but combination with the 10/24 h definition appeared to identify a clinically important patient cohort.

A computational simulation study of the influence of helmet wearing on head injury risk in adult cyclists

Evidence for the effectiveness of cycle helmets has relied either on simplified experiments or complex statistical analysis of patient cohorts or populations. This study directly assesses the effectiveness of cycle helmets over a range of accident scenarios, from basic loss of control to vehicle impact, using computational modelling. Simulations were performed using dynamics modelling software (MADYMO) and models of a 50% Hybrid III dummy, a hybrid cross bicycle and a car. Loss of control was simulated by a sudden turn of the handlebars and striking a curb, side and rear-on impacts by a car were also simulated. Simulations were run over a representative range of cycle speeds (2.0-14.0 m s(-1)) and vehicle speeds (4.5-17.9 m s(-1)). Bicycle helmets were found to be effective in reducing the severity of head injuries sustained in common accidents. They reduced the risk of an AIS>3 injury, in cases with head impacts, by an average of 40%. In accidents that would cause up to moderate (AIS=2) injuries to a non-helmeted rider, helmets eliminated the risk of injury. Helmets were also found to be effective in preventing fatal head injuries in some instances. The effectiveness of helmets was demonstrated over the entire range of cycle speeds studied, up to and including 14 m s(-1). There was no evidence that helmet wearing increased the risk of neck injury, indeed helmets were found to be protective of neck injuries in many cases. Similarly, helmets were found to offer an increase in protection even when an increase in cycle speed due to risk compensation was taken into consideration.

Piloting the use of 2D barcode and patient safety-software in an Australian tertiary hospital setting

OBJECTIVES

Errors in administration of blood products can lead to poor patient outcomes including fatal ABO incompatible transfusions. This pilot study sought to establish whether the use of two-dimensional (2D) barcode technology combined with patient identification software designed to assist in blood administration improves the bedside administration of transfusions in an Australian tertiary hospital.

STUDY DESIGN AND METHODS

The study was conducted in a Haematology/Oncology Day Clinic of a major metropolitan hospital, to evaluate the use of 2D barcode technology and patient safety-software and hand-held PDAs to assist nursing staff in patient identification and blood administration. Comparative audits were conducted before and after the technology's implementation.

RESULTS

The preimplementation transfusion practice audits demonstrated a poor understanding of the blood checking process, with focus on the product rather than patient identification. Following the implementation of 2D barcode technology and patient safety-software, there was significant improvement in administration practice. Positive, verbal patient identification improved from 57% (51/90) to 94% (75/80). Similarly, the cross-referencing of the patient's identification with the patient's wristband improved from 36% (32/90) to 94% (75/80), and the cross-referencing of patient ID on the compatibility tag to wristbands improved from 48% (43/90) to 99% (79/80). Importantly, the 2D barcode technology and patient safety-software saw 100% (80/80) of checks being conducted at the patient bedside, compared with 76% (68/90) in the preimplementation audits.

CONCLUSION

This pilot study demonstrates that 2D barcode technology and patient safety-software significantly improves the bedside check of patient and blood product identification in an Australian setting.

The Sea Empress oil spill (Wales, UK): effects on Common Scoter Melanitta nigra in Carmarthen Bay and status ten years later

Carmarthen Bay, UK, regularly supports internationally important numbers (>16,000) of non-breeding Common Scoters Melanitta nigra. The spill of 72,000 tonnes of crude oil from the Sea Empress in 1996 affected birds both through direct mortality and likely pollution of key food resources. Numbers were greatly reduced following the spill, whilst changes in the distribution of birds within Carmarthen Bay suggested that potentially sub-optimal foraging zones were used. However, ten years after the incident, numbers of Common Scoter were no different to those recorded immediately before the spill. Compared to some other spills, rapid revival is evident. Numbers increased to pre-spill levels within three winters and distributional changes suggested a concurrent return to previously contaminated feeding areas, implying that the ecosystem had regenerated sufficiently to support its top predator. The importance of prolonged, standardised monitoring of bird numbers and distribution as indicators of ecological recovery from environmental damage is emphasised.

A 3-year prospective study of the effects of adjuvant treatments on cognition in women with early stage breast cancer

The neuropsychological performance of 85 women with early stage breast cancer scheduled for chemotherapy, 43 women scheduled for endocrine therapy and/or radiotherapy and 49 healthy control subjects was assessed at baseline (T1), postchemotherapy (or 6 months) (T2) and at 18 months (T3). Repeated measures analysis found no significant interactions or main effect of group after controlling for age and intelligence. Using a calculation to examine performance at an individual level, reliable decline on multiple tasks was seen in 20% of chemotherapy patients, 26% of nonchemotherapy patients and 18% of controls at T2 (18%, 14 and 11%, respectively, at T3). Patients who had experienced a treatment-induced menopause were more likely to show reliable decline on multiple measures at T2 (OR=2.6, 95% confidence interval (CI) 0.823–8.266 P=0.086). Psychological distress, quality of life measures and self-reported cognitive failures did not impact on objective tests of cognitive function, but were significantly associated with each other. The results show that a few women experienced objective measurable change in their concentration and memory following standard adjuvant therapy, but the majority were either unaffected or even improve over time.

Recovery from post-operative anaemia

Acceptance of lower transfusion thresholds and shorter post-operative stays results in patients leaving hospital after surgery with lower haemoglobin (Hb) than previously. We undertook a prospective observational study to assess the haematological response to post-operative anaemia and to determine the utility of quality of life (QoL) measures in assessing the impact of anaemia on such patients. Thirty patients undergoing unilateral hip arthroplasty had blood samples taken and QoL questionnaires administered pre-operatively and at 7, 28 and 56 days post-operatively. Increased erythropoiesis was evident at day 7 post-operatively. Approximately two-thirds of the post-operative Hb deficit was corrected by day 28. There was evidence of functional iron deficiency in more than one-quarter of patients at day 56. QoL scores used did not show any relationship with Hb in the post-operative period. Red cell 2,3-diphosphoglycerate (2,3DPG) levels increased in proportion to the degree of post-operative anaemia. We concluded that substantial recovery of Hb occurs between day 7 and day 28 post-operatively. Complete recovery of Hb may be delayed beyond day 56 due to development of iron deficiency. Patients are at significant risk of developing post-operative iron deficiency depending on operative blood loss and pre-operative iron stores. Increased red cell 2,3DPG may offset the effect of anaemia on oxygen delivery. We found no evidence that anaemia produces a measurable effect on chosen QoL scores in the post-operative period.

Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors

The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.

'Tag and label' system for checking and recording of blood transfusions

Guidelines for checking and recording of blood transfusion mandate the use of a blood transfusion compatibility form. We have introduced and assessed a 'tag and label' system that does away with the compatibility form. A compatibility tag with a peel-off self-adhesive label is attached to the unit for transfusion. No compatibility form is issued to the site of the transfusion. The peel-off label is signed and fixed in patient notes at the time of transfusion. We have found the system easier to use and to be preferred by nursing staff administering transfusions. During 2 years, we have transfused over 100,000 blood components, including 70,000 units of red cells, and have not recognized any episode during which the wrong blood was transfused to a patient. Recording in the patient notes of units transfused has significantly improved compared with local and national figures in a previous survey. We conclude that it is possible to dispense with the compatibility form without compromising the safety of the transfusion process.

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.

Providing feedback to users on unacceptable practice in the delivery of a hospital transfusion service--a pilot study

The Serious Hazards of Transfusion Scheme's (SHOT) annual report continues to emphasize the importance of investigating serious transfusion errors. It is now recognized that lessons can also be learnt from near-miss events as these occur more frequently than serious errors in transfusion. One of the key features in developing a culture that can promote safety in relation to transfusion is providing feedback to staff on what is acceptable and unacceptable practice. We have developed a scoring system based on the number of serious errors and near misses that occur in the transfusion service to provide feedback to staff on their performance in relation to the administration of blood components and blood products. This was developed as part of an ongoing error logging system that we have previously described. The implementation of this feedback has resulted in an increased awareness within our organization of safety issues in relation to transfusion, and has highlighted the importance of the detection and correction of less serious errors.

Eye position sense contributes to the judgement of slant

We measured monocular judgements of the slant of a cube face while varying eye position in the absence of stereoscopic and external lighting cues. Errors were found to be small, only 10% on average of the cube's eccentricity. Two factors appear to have contributed approximately equally to this error: an underestimate of cube slant as seen by the eye and an underestimate of eye position. When prism adaptation altered the sensed eye position, the pattern of slant judgements changed to reflect the altered sense of eye position.

The genome sequence of Schizosaccharomyces pombe

We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.

Genome sequence of Yersinia pestis, the causative agent of plague

The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.

Massive gene decay in the leprosy bacillus

Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.

Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491

Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen.

The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barré syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni.

An audit of error rates in a UK district hospital transfusion laboratory

We have audited the error rates of our transfusion laboratory and compared these with error rates reported in the transfusion literature. Error rates were calculated using workload data from the department. The majority of errors that were detected were preanalytical and related to inadequate or incomplete data provided on the sample or request form. These errors were all corrected prior to any further action being taken on that request. The main analytical errors were transcription errors in entering patient identification information into the laboratory computer by transfusion staff together with the incorrect performance of blood group testing. For postanalytical errors the main errors were failure of nursing staff to follow procedures for the collection of blood components prior to transfusion. There were no serious consequences identified of the errors detected in this study. It was difficult to compare these results with those published in the literature in view of the different methodologies that have been reported when error rates have been determined. A standard method should be developed in the UK for calculating error rates so that laboratories can benchmark their performance against comparable organizations.

The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum

Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes.

Beagle 2: a proposed exobiology lander for ESA's 2003 Mars Express mission

The aim of the proposed Beagle 2 small lander for ESA's 2003 Mars Express mission is to search for organic material on and below the surface of Mars and to study the inorganic chemistry and mineralogy of the landing site. The lander will have a total mass of 60kg including entry, descent, and landing system. Experiments will be deployed on the surface using a robotic arm. It will use a mechanical mole and grinder to obtain samples from below the surface, under rocks, and inside rocks. Sample analysis by a mass spectrometer will include isotopic analysis. An optical microscope, an X-ray spectrometer and a Mossbauer spectrometer will conduct in-situ rock studies.

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation.