CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

MOTIVATION: Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signalling information, focus on capturing, organizing and displaying signalling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources. RESULTS: Aware of the enormous benefits of standardization efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions. Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated PSI-MITAB 2.8. We define the new term 'causal interaction', and related child terms, which are children of the PSI-MI 'molecular interaction' term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signalling networks more precisely and with higher coverage than before. AVAILABILITY AND IMPLEMENTATION: PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available online (https://psicquic.github.io/ and https://psicquic.github.io/MITAB28Format.html). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Adjuvant hepatic arterial infusion pump chemotherapy and resection versus resection alone in patients with low-risk resectable colorectal liver metastases - the multicenter randomized controlled PUMP trial.

BACKGROUND: Recurrences are reported in 70% of all patients after resection of colorectal liver metastases (CRLM), in which half are confined to the liver. Adjuvant hepatic arterial infusion pump (HAIP) chemotherapy aims to reduce the risk of intrahepatic recurrence. A large retrospective propensity score analysis demonstrated that HAIP chemotherapy is particularly effective in patients with low-risk oncological features. The aim of this randomized controlled trial (RCT) --the PUMP trial-- is to investigate the efficacy of adjuvant HAIP chemotherapy in low-risk patients with resectable CRLM. METHODS: This is an open label multicenter RCT. A total of 230 patients with resectable CRLM without extrahepatic disease will be included. Only patients with a clinical risk score (CRS) of 0 to 2 are eligible, meaning: patients are allowed to have no more than two out of five poor prognostic factors (disease-free interval less than 12 months, node-positive colorectal cancer, more than 1 CRLM, largest CRLM more than 5 cm in diameter, serum Carcinoembryonic Antigen above 200 µg/L). Patients randomized to arm A undergo complete resection of CRLM without any adjuvant treatment, which is the standard of care in the Netherlands. Patients in arm B receive an implantable pump at the time of CRLM resection and start adjuvant HAIP chemotherapy 4-12 weeks after surgery, with 6 cycles of floxuridine scheduled. The primary endpoint is progression-free survival (PFS). Secondary endpoints include overall survival, hepatic PFS, safety, quality of life, and cost-effectiveness. Pharmacokinetics of intra-arterial administration of floxuridine will be investigated as well as predictive biomarkers for the efficacy of HAIP chemotherapy. In a side study, the accuracy of CT angiography will be compared to radionuclide scintigraphy to detect extrahepatic perfusion. We hypothesize that adjuvant HAIP chemotherapy leads to improved survival, improved quality of life, and a reduction of costs, compared to resection alone. DISCUSSION: If this PUMP trial demonstrates that adjuvant HAIP chemotherapy improves survival in low-risk patients, this treatment approach may be implemented in the standard of care of patients with resected CRLM since adjuvant systemic chemotherapy alone has not improved survival. TRIAL REGISTRATION: The PUMP trial is registered in the Netherlands Trial Register (NTR), number: 7493 . Date of registration September 23, 2018.

Lactate, lactate clearance and outcome after cardiac arrest: A post-hoc analysis of the TTM-Trial.

BACKGROUND: Admission lactate and lactate clearance are implemented for risk stratification in sepsis and trauma. In out-of-hospital cardiac arrest, results regarding outcome and lactate are conflicting. METHODS: This is a post-hoc analysis of the Target Temperature Management trial in which 950 unconscious patents after out-of-hospital cardiac arrest were randomized to a temperature intervention of 33°C or 36°C. Serial lactate samples during the first 36 hours were collected. Admission lactate, 12-hour lactate, and the clearance of lactate within 12 hours after admission were analyzed and the association with 30-day mortality assessed. RESULTS: Samples from 877 patients were analyzed. In univariate logistic regression analysis, the odds ratio for death by day 30 for each mmol/L was 1.12 (1.08-1.16) for admission lactate, P < .01, 1.21 (1.12-1.31) for 12-hour lactate, P < .01, and 1.003 (1.00-1.01) for each percentage point increase in 12-hour lactate clearance, P = .03. Only admission lactate and 12-hour lactate levels remained significant after adjusting for known predictors of outcome. The area under the receiver operating characteristic curve was 0.65 (0.61-0.69), P < .001, 0.61 (0.57-0.65), P < .001, and 0.53 (0.49-0.57), P = .15 for admission lactate, 12-hour lactate, and 12-hour lactate clearance, respectively. CONCLUSIONS: Admission lactate and 12-hour lactate values were independently associated with 30-day mortality after out-of-hospital cardiac arrest while 12-hour lactate clearance was not. The clinical value of lactate as the sole predictor of outcome after out-of-hospital cardiac arrest is, however, limited.

Transient versus persistent acute kidney injury and the diagnostic performance of fractional excretion of urea in critically ill patients.

AIMS: To evaluate the performance of fractional excretion of urea (FeU) for differentiating transient (T) from persistent (P) acute kidney injury (AKI) and to assess performance of FeU in predicting AKI in patients admitted to the ICU. METHODS: We performed secondary analysis of a multicenter prospective observational cohort study on the predictive performance of biological markers for AKI in critically ill patients. AKI was diagnosed according to RIFLE staging. RESULTS: Of 150 patients, 51 and 41 patients were classified as having T-AKI and P-AKI, respectively. The diagnostic performance for FeU to discriminate T-AKI from P-AKI on the day of AKI was poor (AUC-ROC = 0.61; 95% CI: 0.49-0.73). The diagnostic performance of FeU to predict AKI 1 and 2 days prior to AKI was poor as well (AUC-ROC = 0.61; 95% CI: 0.47-0.74, and 0.58; 95% CI: 0.43-0.73, respectively). CONCLUSIONS: FeU does not seem to be helpful in differentiating T- from P-AKI in critically ill patients and it is a poor predictor of AKI.

Selection of monitoring locations for storm water quality assessment.

Storm water runoff is a major contributor to the pollution of receiving waters. Storm water characteristics may vary significantly between locations and events. Hence, for each given location, this necessitates a well-designed monitoring campaign prior to selection of an appropriate storm water management strategy. The challenge for the design of a monitoring campaign with a given budget is to balance detailed monitoring at a limited number of locations versus less detailed monitoring at a large number of locations. This paper proposes a methodology for the selection of monitoring locations for storm water quality monitoring, based on (pre-)screening, a quick scan monitoring campaign, and final selection of locations and design of the monitoring setup. The main advantage of the method is the ability to prevent the selection of monitoring locations that turn out to be inappropriate. In addition, in this study, the quick scan resulted in a first useful dataset on storm water quality and a strong indication of illicit connections at one of the monitoring locations.

Inflation and deflation timing of the AutoCAT 2 WAVE intra-aortic balloon pump using the autoPilot mode in a clinical setting.

The primary goal of this observational clinical study was to register the occurrence of incorrect inflation and deflation timing of an intra-aortic balloon pump in autoPilot mode. The secondary goal was to identify possible causes of incorrect timing. During IABP assistance of 60 patients, every four hours a strip was printed with the IABP frequency set to 1:2. Strips were examined for timing discrepancies beyond 40 ms from the dicrotic notch (inflation) and the end of the diastolic phase (deflation). In this way, 320 printed strips were examined. A total of 52 strips (16%) showed incorrect timing. On 24 of these strips, the incorrect timing was called incidental, as it showed on only one or a few beats. The other 28 cases of erroneous timing were called consistent, as more than 50% of the beats on the strip showed incorrect timing. We observed arrhythmia in 69% of all cases of incorrect timing. When timing was correct, arrhythmia was found on 13 (5%) of 268 strips. A poor quality electrocardiograph (ECG) signal showed on 37% of all strips with incorrect timing and 11% of all strips with proper timing. We conclude that inflation and deflation timing of the IABP is not always correct when using the autoPilot mode. The quality of the ECG input signal and the occurrence of arrhythmia appear to be related to erroneous timing. Switching from autoPilot mode to operator mode may not always prevent incorrect timing.

In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding.

The Menkes (ATP7A) P(1B)-type ATPase is a transmembrane copper-translocating protein. It contains six similar high-affinity metal-binding domains (MBDs) in the N-terminal cytoplasmic tail that are important for sensing intracellular copper and regulating ATPase function through the transfer of copper between domains. Molecular characterization of copper-binding and transfer is predominantly dependent on NMR structures derived from E. coli expression systems. A limitation of these models is the exclusion of post-translational modifications. We have previously shown that the third copper-binding domain, MBD3, uniquely contains two phosphorylated residues: Thr-327, which is phosphorylated only in the presence of elevated copper; and Ser-339, which is constitutively phosphorylated independent of copper levels. Here, using molecular dynamic simulations, we have incorporated these phosphorylated residues into a model based on the NMR structures of MBD3. Our data suggests that constitutively phosphorylated Ser-339, which is in a loop facing the copper-binding site, may facilitate the copper transfer process by exposing the CxxC copper-binding region of MBD3. Copper-induced phosphorylation of Thr327 is predicted to stabilize this change in conformation. This offers new molecular insights into how cell signaling (phosphorylation) can affect MBD structure and dynamics and how this may in turn affect copper-binding and thus copper-translocation functions of ATP7A.

[Resuscitation among patients with out-of-hospital cardiac arrest; intra-arrest transport, or not?] / Reanimatie bij hartstilstand buiten het ziekenhuis.

A prospective cohort study recently published in JAMA looked at the difference in survival to hospital discharge between intra-arrest transport vs continued on-scene resuscitation among patients with out-of-hospital cardiac arrest (OHCA). The conclusion of this study is that intra-arrest transport is associated with a lower survival compared to continuous on-site treatment. Research by the Amsterdam Resuscitation Study (ARREST) shows that in OHCA patients who are transported intra-arrest, survival decreases significantly if the time on-scene increases. Patients who are transported within 20 minutes have the highest chance of survival. This suggests that the decision for transport should be made early in the resuscitation process. National and regional circumstances (availability of a mobile medical team, distance to hospital etc.), and pre-hospital resuscitation treatments may make that different scenarios can be considered. In some scenarios extracorporeal cardiopulmonary resuscitation (eCPR) can be brought to the patient; in other scenarios the patient can be transported to the eCPR.

Fed-batch operation of an industrial cell culture process in shaken microwells.

Recently we have demonstrated batch suspension culture of mammalian cells in microwell plates. Here we describe a method for fed-batch culture of an industrially relevant GS-CHO (Glutamine Synthetase-Chinese Hamster Ovary) cell line in shaken 24-standard round well (24-SRW) plates. Use of a commercially available 'sandwich lid' and appropriate dilution of the bolus feeds counteracted liquid evaporation from the wells resulting in similar cell growth and antibody formation kinetics in both 24-SRW plates (800 mul) and shaken flasks (50 ml). Peak viable cell densities obtained were 8 +/- 0.5 x 10(6) and 9 +/- 1.3 x 10(6) ml(-1), respectively, while comparable final titres of a whole IgG of approximately 1.5 g l(-1) were recorded. Use of microwells provides at least a 50-fold reduction in medium requirements compared to shake-flask and other culture devices currently used in early stage cell culture process development. The ability to run multiple wells in parallel and to automate culture operation also offers considerable enhancements in experimental throughput.

Dyskinesia Impairment Scale scores in Dutch pre-school children after neonatal therapeutic hypothermia.

BACKGROUND: Neonatal therapeutic hypothermia (TH) can ameliorate or prevent the development of dyskinetic cerebral palsy (CP) after hypoxic-ischemic encephalopathy (HIE). The Dyskinesia Impairment Scale (DIS) was recently launched to quantify dyskinetic (dystonic and choreatic) motor features in patients with CP. In TH treated children, who are at risk of developing dyskinetic CP, we aimed to determine DIS-scores at pre-school age. METHOD: In 21 Dutch pre-school children (3-6 years of age) who had received TH according to the Dutch-Flemish treatment protocol, we determined DIS-scores. We associated DIS-scores with 1. age-matched control values (Kuiper et al., 2018) [1], and 2. previously reported DIS-score range in dyskinetic CP (Monbaliu E et al., 2015). RESULTS: The motor phenotype was determined as: normal (n = 18/21), mildly impaired (reduced coordination (n = 2/21)) and abnormal (dyskinetic CP; n = 1/21). In absence of CP (n = 20/21), DIS-scores were lower (more favorable) than in dyskinetic CP, without any overlapping group scores (mean difference: 71 points; p < .05). However, the obtained DIS-scores were still higher than previously reported in healthy age-matched controls (mean difference: 14 points; p < .05). There was an association between DIS-scores and retrospective neonatal MRI (basal ganglia and thalamus injury on diffusion weighted imaging (DWI)) and (a)EEG parameters (p < .05). CONCLUSION: In the vast majority (95%) of Dutch TH-HIE treated pre-school children, the phenotypic motor outcome was favorable. However, DIS-scores were moderately increased compared with healthy age-matched controls. Future studies may elucidate the significance of moderately increased DIS-scores should to further extent.

Immediate impact of COVID-19 on transplant activity in the Netherlands.

The rapid emergence of the COVID-19 pandemic is unprecedented and poses an unparalleled obstacle in the sixty-five year history of organ transplantation. Worldwide, the delivery of transplant care is severely challenged by matters concerning - but not limited to - organ procurement, risk of SARS-CoV-2 transmission, screening strategies of donors and recipients, decisions to postpone or proceed with transplantation, the attributable risk of immunosuppression for COVID-19 and entrenched health care resources and capacity. The transplant community is faced with choosing a lesser of two evils: initiating immunosuppression and potentially accepting detrimental outcome when transplant recipients develop COVID-19 versus postponing transplantation and accepting associated waitlist mortality. Notably, prioritization of health care services for COVID-19 care raises concerns about allocation of resources to deliver care for transplant patients who might otherwise have excellent 1-year and 10-year survival rates. Children and young adults with end-stage organ disease in particular seem more disadvantaged by withholding transplantation because of capacity issues than from medical consequences of SARS-CoV-2. This report details the nationwide response of the Dutch transplant community to these issues and the immediate consequences for transplant activity. Worrisome, there was a significant decrease in organ donation numbers affecting all organ transplant services. In addition, there was a detrimental effect on transplantation numbers in children with end-organ failure. Ongoing efforts focus on mitigation of not only primary but also secondary harm of the pandemic and to find right definitions and momentum to restore the transplant programs.

Spatial contrast sensitivity from star- to sunlight in healthy subjects and patients with glaucoma.

Glaucoma is traditionally considered an asymptomatic disease until later stages. However, questionnaire studies revealed visual complaints related to various tasks, especially under extreme luminance conditions (such as outdoor at night on an unlit road or outside in the sun). We measured contrast sensitivity (CS) over a luminance range of 6 log units spanning the scotopic to photopic range and we aimed (1) to determine whether Weber's law also holds under extremely high luminance conditions and (2) to compare CS as a function of spatial frequency and luminance between glaucoma patients and healthy subjects. We included 22 glaucoma patients and 51 controls, all with normal visual acuity. For the second aim, we used a subgroup of 22 age-similar controls. Vertically oriented sine-wave gratings were generated with a projector-based setup (stimulus size 8x5 degrees). CS was measured monocularly at 1, 3, and 10 cycles per degree (cpd); mean luminance ranged from 0.0085 to 8500 cd/m2. ANOVA was used to analyze the effect of glaucoma, luminance, and spatial frequency on logCS. In controls, Weber's law held for 3 and 10 cpd; for 1 cpd, CS dropped above 1000 cd/m2 (P = 0.003). The logCS versus log luminance curves did not differ grossly between patients and controls (P = 0.14; typically 0-0.2 log units); the difference became larger with decreasing luminance (P = 0.003) but did not depend clearly on spatial frequency (P = 0.27). We conclude that differences between glaucoma and healthy were relatively modest for the spatially redundant, static stimulus as used in the current study.

Characterization of a second Rhodococcus erythropolis SQ1 3-ketosteroid 9alpha-hydroxylase activity comprising a terminal oxygenase homologue, KshA2, active with oxygenase-reductase component KshB.

Previously we have characterized 3-ketosteroid 9alpha-hydroxylase (KSH), a key enzyme in microbial steroid degradation in Rhodococcus erythropolis strain SQ1, as a two-component iron-sulfur monooxygenase, comprised of the terminal oxygenase component KshA1 and the oxygenase-reductase component KshB. Deletion of the kshA1 gene resulted in the loss of the ability of mutant strain RG2 to grow on the steroid substrate 4-androstene-3,17-dione (AD). Here we report characteristics of a close KshA1 homologue, KshA2 of strain SQ1, sharing 60% identity at the amino acid level. Expression of the kshA2 gene in mutant strain RG2 restored growth on AD and ADD, indicating that kshA2 also encodes KSH activity. The functional complementation was shown to be dependent on the presence of kshB. Transcriptional analysis showed that expression of kshA2 is induced in parent strain R. erythropolis SQ1 in the presence of AD. However, promoter activity studies, using beta-lactamase of Escherichia coli as a convenient transcription reporter protein for Rhodococcus, revealed that the kshA2 promoter in fact is highly induced in the presence of 9alpha-hydroxy-4-androstene-3,17-dione (9OHAD) or a metabolite thereof. Inactivation of kshA2 in parent strain SQ1 by unmarked gene deletion did not affect growth on 9OHAD, cholesterol, or cholic acid. We speculate that KshA2 plays a role in preventing accumulation of toxic intracellular concentrations of ADD during steroid catabolism. A third kshA homologue was additionally identified in a kshA1 kshA2 double gene deletion mutant strain of R. erythropolis SQ1. The developed degenerate PCR primers for kshA may be useful for isolation of kshA homologues from other (actino) bacteria.

How to manage organisational change and create practice teams: experiences of a South African primary care health centre.

BACKGROUND: In South Africa, first-contact primary care is delivered by nurses in small clinics and larger community health centres (CHC). CHCs also employ doctors, who often work in isolation from the nurses, with poor differentiation of roles and little effective teamwork or communication. Worcester CHC, a typical public sector CHC in rural South Africa, decided to explore how to create more successful practice teams of doctors and nurses. This paper is based on their experience of both unsuccessful and successful attempts to introduce practice teams and reports on their learning regarding organisational change. METHODS: An emergent action research study design utilised a co-operative inquiry group. The first nine months of inquiry focused on understanding the initial unsuccessful attempt to create practice teams. This paper reports primarily on the subsequent nine months (four cycles of planning, action, observation and reflection) during which practice teams were re-introduced. The central question was how more effective practice teams of doctors and nurses could be created. The group utilised outcome mapping to assist with planning, monitoring and evaluation. Outcome mapping defined a vision, mission, boundary partners, outcome challenges, progress markers and strategies for the desired changes and supported quantitative monitoring of the process. Qualitative data were derived from the co-operative inquiry group (CIG) meetings and interviews with doctors, nurses, practice teams and patients. FINDINGS: The CIG engaged effectively with 68% of the planned strategies, and more than 60% of the progress markers were achieved for clinical nurse practitioners, doctors, support staff and managers, but not for patients. Key themes that emerged from the inquiry group's reflection on their experience of the change process dealt with the amount of interaction, type of communication, team resilience, staff satisfaction, leadership style, reflective capacity, experimentation and evolution of new structures. CONCLUSION: The group's learning supported a view of change that sees the organisation as a living system in which information flow, participation and the development of resilience are key aspects. These themes fit well into an understanding of change based on complexity theory. If managers of the health system wish to enhance organisational change, then their goal may need to shift from optimising health care delivery in a mechanistic model to optimising health care workers in a living system.

[Dissection of the carotid artery following blunt trauma: still a pitfall]. / Dissectie van de A. carotis door een stomp trauma: nog altijd een valkuil.

Two young patients, an 18-year-old woman and a 25-year-old man, were admitted to hospital after accidents with a car. They developed very severe complications as a consequence of blunt carotid artery dissection. This diagnosis was delayed in both patients until serious cerebral ischaemia had occurred. Despite current awareness of carotid dissection as a possible result of blunt trauma, this injury is often overlooked. Early diagnosis by means of Doppler ultrasonography and CT-angiography is important in adequate management of this injury and may reduce morbidity and mortality. The treatment of carotid dissection consists of antithrombotic, endovascular or surgical therapy and needs to be individualized.

[Subarachnoid haemorrhage presenting clinically as circulatory arrest in acute myocardial infarction]. / Subarachnoïdale bloeding met de klinische presentatie van een circulatiestilstand bij acuut myocardinfarct.

A 59-year-old woman and a 41-year-old man were both brought to the Cardiac Emergency Clinic with circulatory arrest on the basis ofpulseless electrical activity. The first patient had had no prodromal symptoms and the second patient had visited his general practitioner 2 weeks earlier because of pain in the head and neck. In both patients, electrocardiography and echocardiography suggested acute myocardial infarction. However, both patients proved to be suffering from a subarachnoid haemorrhage (SAH) and both died. One-third ofthe patients with SAH are comatose at presentation. Cardiac manifestations such as ECG-abnormalities, cardiac arrhythmias, cardiopulmonary arrest, elevated troponin values, and signs of left ventricular dysfunction are common. These findings can be misleading and may have catastrophic consequences if anticoagulant therapy is initiated because of a presumed myocardial infarction. Low-threshold CT-scanning of the brain is therefore advised for patients who remain comatose after resuscitation for cardiac arrest in the presence of an atypical anamnesis.

Physiological movement disorder-like features during typical motor development.

AIM: To compare physiological age-relatedness between dyskinesia (dystonia/choreoathetosis), dystonia and ataxia rating scale scores in healthy children. METHOD: Three movement disorders specialists quantified dyskinetic-like features in healthy children (n = 52; 4-16 years) using the Dyskinesia Impairment Scale (DIS = DIS-choreoathetosis (DIS-C) + DIS-dystonia (DIS-D)). We compared the age-related regression coefficients of the DIS with data processed from previous studies on dystonia and ataxia rating scales (Burke-Fahn-Marsden Movement and Disability Scales (BFMMS and BFMDS) and Scale for Assessment and Rating of Ataxia (SARA), International Cooperative Ataxia Rating Scale (ICARS) and Brief Ataxia Rating Scale (BARS)). RESULTS: Dyskinetic scores were obtained in 79% (DIS); 65% (DIS-D) and 17% (DIS-C) versus dystonic and ataxic scores in 98% (BFMMS) and 89% (SARA/ICARS/BARS) of the children. Age-related DIS and DIS-D scores (B = -0.90 and 0.77; p < 0.001) were correlated with age-related BFMMS scores (B = -0.49; p < 0.001; r = 0.87; p < 0.001), whereas DIS-C scores were age-independent. Ataxic scores revealed stronger age-related regression coefficients than dyskinetic and dystonic scores (4-8 years; p < 0.05). INTERPRETATION: In healthy children, comparison between physiological dyskinesia, dystonia and ataxia rating scale scores revealed: 1. inverse age-relatedness for dystonic and ataxic scores, but not for choreoathetotic scores, 2. interrelated dystonic DIS-D and BFMMS scores, 3. the strongest age-related expression by ataxic scores. In healthy children, these physiological movement disorder-like features are interpreted as an expression of the developing underlying motor centres.

The Mauriceville plasmid of Neurospora crassa: characterization of a novel reverse transcriptase that begins cDNA synthesis at the 3' end of template RNA.

The Mauriceville and Varkud plasmids are retroid elements that propagate in the mitochondria of some Neurospora spp. strains. Previous studies of endogenous reactions in ribonucleoprotein particle preparations suggested that the plasmids use a novel mechanism of reverse transcription that involves synthesis of a full-length minus-strand DNA beginning at the 3' end of the plasmid transcript, which has a 3' tRNA-like structure (M. T. R. Kuiper and A. M. Lambowitz, Cell 55:693-704, 1988). In this study, we developed procedures for releasing the Mauriceville plasmid reverse transcriptase from mitochondrial ribonucleoprotein particles and partially purifying it by heparin-Sepharose chromatography. By using these soluble preparations, we show directly that the Mauriceville plasmid reverse transcriptase synthesizes full-length cDNA copies of in vitro transcripts beginning at the 3' end and has a preference for transcripts having the 3' tRNA-like structure. Further, unlike retroviral reverse transcriptases, the Mauriceville plasmid reverse transcriptase begins cDNA synthesis directly opposite the 3'-terminal nucleotide of the template RNA. The ability to initiate cDNA synthesis directly at the 3' end of template RNAs may also be relevant to the mechanisms of reverse transcription used by LINEs, group II introns, and other non-long terminal repeat retroid elements.

Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana.

The major difference between annual and biennial cultivars of oilseed Brassica napus and B. rapa is conferred by genes controlling vernalization-responsive flowering time. These genes were compared between the species by aligning the map positions of flowering time quantitative trait loci (QTLs) detected in a segregating population of each species. The results suggest that two major QTLs identified in B. rapa correspond to two major QTLs identified in B. napus. Since B. rapa is one of the hypothesized diploid parents of the amphidiploid B. napus, the vernalization requirement of B. napus probably originated from B. rapa. Brassica genes also were compared to flowering time genes in Arabidopsis thaliana by mapping RFLP loci with the same probes in both B. napus and Arabidopsis. The region containing one pair of Brassica QTLs was collinear with the top of chromosome 5 in A. thaliana where flowering time genes FLC, FY and CO are located. The region containing the second pair of QTLs showed fractured collinearity with several regions of the Arabidopsis genome, including the top of chromosome 4 where FRI is located. Thus, these Brassica genes may correspond to two genes (FLC and FRI) that regulate flowering time in the latest flowering ecotypes of Arabidopsis.