Weed evolution: Genetic differentiation among wild, weedy, and crop radish

Approximately 200 weed species are responsible for more than 90% of crop losses and these comprise less than one percent of all named plant species, suggesting that there are only a few evolutionary routes that lead to weediness. Agricultural weeds can evolve along three main paths: they can be escaped crops, wild species, or crop‐wild hybrids. We tested these three hypotheses in weedy radish, a weed of small grains and an emerging model for investigating the evolution of agricultural weeds, using 21 CAPS and SSR markers scored on 338 individuals from 34 populations representing all major species and sub‐species in the radish genus Raphanus. To test for adaptation of the weeds to the agricultural environment, we estimated genetic differentiation in flowering time in a series of common garden experiments with over 2,400 individuals from 43 populations (all but one of the genotyped populations plus 10 additional populations). Our findings suggest that the agricultural weed radish R. r. raphanistrum is most genetically similar to native populations of R. r. raphanistrum and is likely not a feral crop or crop hybrid. We also show that weedy radish flowers more rapidly than any other Raphanus population or cultivar, which is consistent with rapid adaptation to the frequent and severe disturbance that characterizes agricultural fields.

[Guidelines in medical imaging : objectives, limits and radiation protection]

CONTEXT

Guidelines in medical imaging are aimed at increasing the appropriateness of prescriptions, eliminating unnecessary examina- tions, reducing the exposure of the population and minimizing the costs to public health.

METHOD

Our analysis is based on a bibliographic search and the discussions of the " quality " working group of the BELMIP platform.

RESULTS

The introduction in 2004 and its 2014 revision of the guideliness in medical imaging in Belgium had no measurable effect on the imaging prescription. These recommendations are in fact unrecognized, incomplete, poorly constructed and often unusable.

CONCLUSION

Recommendations in medical imaging need to be reviewed and will be reviewed in the near future in order to be better structured and usable. The legal and medico-legal constraints should be integrated in order for Belgium to comply with the relevant European directive.

How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects

For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and among alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both the scalloped and vestigial genes, which influence wing development in Drosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development) of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis.

Different mutations in a gene, or in genes with related functions, can have effects of varying severity. Studying sets of mutations and analyzing how they interact are essential components of a geneticist's toolkit. However, the effects caused by a mutation depend not only on the mutation itself, but on additional genetic variation throughout an organism's genome and on the environment that organism has experienced. Therefore, identifying how the genomic and environmental context alter the expression of mutations is critical for making reliable inferences about how genes function. Yet studies on this context dependence have largely been limited to single mutations in single genes. We examined how the genomic and environmental context influence the expression of multiple mutations in two related genes affecting the fruit fly wing. Our results show that the genetic and environmental context generally affect the expression of related mutations in similar ways. However, the interactions between two different mutations in a single gene sometimes depended strongly on context. In addition, cell proliferation in the developing wing and adult wing size were not affected by the genetic and environmental context in similar ways in mutant flies, suggesting that variation in cell growth cannot fully explain how mutations affect wings. Overall, our findings show that context can have a big impact on the interpretation of genetic experiments, including how we draw conclusions about gene function and cause-and-effect relationships.

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Tuning of automatic exposure control strength in lumbar spine CT

OBJECTIVE

To investigate the impact of tuning the automatic exposure control (AEC) strength curve (specific to Care Dose 4D®; Siemens Healthcare, Forchheim, Germany) from "average" to "strong" on image quality, radiation dose and operator dependency during lumbar spine CT examinations.

METHODS

Two hospitals (H1, H2), both using the same scanners, were considered for two time periods (P1 and P2). During P1, the AEC curve was "average" and radiographers had to select one of two protocols according to the body mass index (BMI): "standard" if BMI <30.0 kg m(-2) (120 kV-330 mAs) or "large" if BMI >30.0 kg m(-2) (140 kV-280 mAs). During P2, the AEC curve was changed to "strong", and all acquisitions were obtained with one protocol (120 kV and 270 mAs). Image quality was scored and patients' diameters calculated for both periods.

RESULTS

497 examinations were analysed. There was no significant difference in mean diameters according to hospitals and periods (p > 0.801) and in quality scores between periods (p > 0.172). There was a significant difference between hospitals regarding how often the "large" protocol was assigned [13 (10%)/132 patients in H1 vs 37 (28%)/133 in H2] (p < 0.001). During P1, volume CT dose index (CTDIvol) was higher in H2 (+13%; p = 0.050). In both hospitals, CTDIvol was reduced between periods (-19.2% in H1 and -29.4% in H2; p < 0.001).

CONCLUSION

An operator dependency in protocol selection, unexplained by patient diameters or highlighted by image quality scores, has been observed. Tuning the AEC curve from average to strong enables suppression of the operator dependency in protocol selection and related dose increase, while preserving image quality.

ADVANCES IN KNOWLEDGE

CT acquisition protocols based on weight are responsible for biases in protocol selection. Using an appropriate AEC strength curve reduces the number of protocols to one. Operator dependency of protocol selection is thereby eliminated.

Reduced z-axis coverage in multidetector-row CT pulmonary angiography decreases radiation dose and diagnostic accuracy of alternative diseases

OBJECTIVE

To investigate the effect of a two-third reduction of the scanned length (i.e. 10 cm) on diagnosis of both pulmonary embolism (PE) and alternative diseases.

METHODS

247 consecutive patients suspected of acute PE had a CT pulmonary angiography (CTPA) of the thorax (standard length, L). Based on this acquisition, a second set of images was created to obtain a scan length of 10 cm caudally to the aortic arch (l). Images were anonymized, randomized and interpreted by two independent readers. The quality of enhancement, the presence of PE and the possible alternative and/or complementary diagnoses were recorded. A McNemar exact test investigated differences in discrepancies between readers and between scan lengths.

RESULTS

57 (23%) patients had an acute PE. Among l sets, PE was missed by both readers in one (1.8%) patient, because the unique clot was localized in a subsegmental artery out of the 10-cm range. There were discrepancies between L and l sets in 9 (3.6%) and 11 (4.5%) patients, by Readers 1 and 2 (p=0.820), respectively. Discrepancies between the readers of L sets and those between both sets were not different regardless of the reader (p>0.99). There were discrepancies between both sets for alternative and/or complementary diagnoses in 43 (17.2%) patients.

CONCLUSION

Although its performance in diagnosing PE is maintained, CTPA should not be restricted to a range of 10 cm centred over the pulmonary hilum, because alternative and/or complementary diagnoses could be missed.

ADVANCES IN KNOWLEDGE

(1) A 10-cm CTPA acquisition reduces the radiation dose by two-thirds as compared with a standard one, but does not impair the accuracy for the diagnosis of PE. (2) Significant alternative diagnoses are missed in 17.2% of patients when reducing the acquisition height to 10 cm.

Optimised z-axis coverage at multidetector-row CT in adults suspected of acute appendicitis

OBJECTIVE

To compare diagnostic performances of two reduced z-axis coverages to full coverage of the abdomen and pelvis for the diagnosis of acute appendicitis and alternative diseases at unenhanced CT.

METHODS

This study included 152 adults suspected of appendicitis who were enrolled in two ethical committee-approved previous prospective trials. Based on scans covering the entire abdomen and pelvis (set L), two additional sets of images were generated, each with reduced z-axis coverages: (1) from the top of the iliac crests to the pubis (set S) and (2) from the diaphragmatic crus to the pubis (set M). Two readers independently coded the visualisation of the appendix, measured its diameter and proposed a diagnosis (appendicitis or alternative). Final diagnosis was based on surgical findings or clinical follow-up. Fisher exact and McNemar tests and logistic regression were used.

RESULTS

46 patients had a definite diagnosis of appendicitis and 53 of alternative diseases. The frequency of appendix visualisation was lower for set S than set L for both readers (89% and 84% vs 95% and 91% by Readers A and B, respectively; p=0.021 and 0.022). The probability of giving a correct diagnosis was lower for set S (68%) than set L (78%; odds ratio, 0.611; p=0.008) for both readers, without significant difference between sets L and M (77%, p=0.771); z-axis coverage being reduced by 25% for set M.

CONCLUSION

Coverage from diaphragmatic crus to pubis, but not focused on pelvis only, can be recommended in adults suspected of appendicitis.

ADVANCES IN KNOWLEDGE

In suspected appendicitis, CT-coverage can be reduced from diaphragmatic crus to pubis.

Automatic computed tomography patient dose calculation using DICOM header metadata

The present work describes a method that calculates the patient dose values in computed tomography (CT) based on metadata contained in DICOM images in support of patient dose studies. The DICOM metadata is preprocessed to extract necessary calculation parameters. Vendor-specific DICOM header information is harmonized using vendor translation tables and unavailable DICOM tags can be completed with a graphical user interface. CT-Expo, an MS Excel application for calculating the radiation dose, is used to calculate the patient doses. All relevant data and calculation results are stored for further analysis in a relational database. Final results are compiled by utilizing data mining tools. This solution was successfully used for the 2009 CT dose study in Luxembourg. National diagnostic reference levels for standard examinations were calculated based on each of the countries' hospitals. The benefits using this new automatic system saved time as well as resources during the data acquisition and the evaluation when compared with earlier questionnaire-based surveys.

[Pain: thought about risks and benefits of imaging test in primary care]

In 2007, the budget of medical imaging in Belgium was of more than 920,000,000 Euro. A small part of this amount is attributed to prescription by general practitioners. The yearly costs of medical imaging generated by an individual general practitioner is approximately of 12,000 Euro. Pain is one of the most frequent clinical condition for which imaging tests are requested. The effectiveness of imaging in diagnosing acute painful disorders is well established. However, in case of subacute or chronic pain, the benefits of imaging tests are reduced or not clearly defined. The objective of this review is to highlight the balance between benefit, costs and risks (i.e. radiation risk) of imaging tests in case of acute, subacute and chronic pain. Four of the most frequently encountered clinical conditions illustrate this review.

Radiation dose in computed tomography of the chest

Since the beginning of the eighties, computed tomography (CT) has been more and more widely used as this technique provides precise anatomical details on the lungs, the mediastinum, and the chest wall. However, CT requires the use of ionizing radiations. The collective radiation from CT is therefore in constant increase. As evaluated on atomic bomb survivors, ionizing radiations increase the mortality by cancer. The risk is proportional to the dose and the dose related to CT is much higher than that related to a chest radiograph, both being in the field "of low-level radiations" a range of radiation dose from which no increase in cancer mortality could be demonstrated. This article outlines the risk estimation in the field of low-level radiations, the various methods to measure and estimate the radiation dose, the CT parameters influencing the radiation dose, dose comparisons between CT and most other imaging techniques of the chest, the newly developed so called "Low-Dose" CT techniques and highlights some of the unresolved questions related to radiation dose in clinical CT practice.

Cholecystoduodenal fistula in a porcelain gallbladder

Calcification of the gallbladder wall (porcelain gallbladder) is rare. Its appearance is quite characteristic on plain films, ultrasonography and computed tomography. Sporadic cases of cholecystitis have been described in porcelain gallbladders. Enterobiliary fistula may complicate acute or chronic cholecystitis in non-calcified gallbladder. We report a unusual case of acute cholecystitis with cholecystoduodenal fistula in a porcelain gallbladder.

[Multislice computed tomography in clinical practice]

This paper presents our first experience with multislice computed tomography emphasizing our technical protocols. Between November 1999 and October 2000, 8086 multislice computed tomographic examinations were performed. The choice in collimation, pitch, slice width and increment, multiplanar reconstructions and contrast enhancement were adapted to provide high resolution in the Z axis, high speed acquisitions and low exposure to the patient. Filming and archiving parameters are also detailed. Multislice CT provides excellent 3D imaging with high speed acquisitions and lower doses than previously reported with single slice CT.

[Unsuspected hepatic rupture with peritoneal extravasation of contrast media revealed by computed tomography]

Computed tomography (CT) plays a major role as the initial diagnostic tool in adult blunt abdominal trauma. Indications of CT are hemodynamical instability, abdominal defense and high-speed deceleration. We present the case of a 22 year-old man involved in a motor-vehicle accident admitted in our emergency department with headache but without clinical signs of intraabdominal trauma. The abdominal CT was asked because of the high-speed deceleration and because the patient had to come to the CT room for a head CT. The abdominal multislice helical CT performed with contrast bolus injection showed a massive intraperitoneal extravasation from a hepatic laceration and avulsion. The patient died during operation despite immediate management of the abdominal traumatic lesions detected by CT.

The CT fallen-lung sign

On chest radiograph, the diagnosis of tracheobronchial tear is usually suspected because of the persistence of a pneumothorax after chest tube insertion. Since this radiographic pattern is nonspecific, the diagnosis is usually made by bronchoscopy and delayed. The fallen-lung sign consists in the fall of the collapsed lung away from the mediastinum occurring when the normal central bronchial anchoring attachment of the lung is disrupted. In contrast to the persistent pneumothorax, this sign is specific but rarely observed. Our purpose is to present the corresponding CT patterns observed in two cases of right stem bronchus tear, consisting in a caudal-dependent displacement of the right upper lobe bronchus which becomes obliquely oriented.

Helmet accommodation analysis using 3D laser scanning

A method used to determine the probable population accommodation of a helmet sizing system is described. The method involves the use of 3D laser scanning, as a means of measuring helmet standoff distance (distance between the inside of the helmet and the skull), and the selection of a representative sample of test subjects. The laser scanner and the software developed to calculate standoff distance proved to be an excellent tool for the assessment of helmet fit. The main advantages include ease of use and visualization of problem areas. This 3D-analysis method gives designers objective evidence of the need for design changes as well as an idea of what these changes should be. A comparison was made between standoff distance results obtained from the scanner and those obtained using a physical measurement method (a probe). Although discrepancies were found between the two, sources of errors intrinsic to both methods make it difficult to determine which of the two methods yielded the truest standoff distance. Analysis of the comparison data shows laser scanning to be slightly more conservative than the probe method for standoff distance purposes, i.e. erring on the side of safety.

Spontaneous lung herniation after a single cough

Herniation of the lung is commonly caused by congenital rib abnormalities, blunt trauma, or thoracic surgery. Spontaneous hernias are rarely described in the literature. We report a case of a spontaneous intercostal pulmonary hernia following a single cough. In addition, a review of the literature is presented which outlines the classification, causes, and incidence of lung hernias. Some reference is made to possible methods of treatment.

[CT-xray demonstration of a vertical vein]

Congenital anomalies of the thoracic veins are infrequent but important developmental disorders. Anomalies of the systemic thoracic veins usually are asymptomatic but may be associated with other more serious cardiovascular abnormalities and complicate their management. We present a case of a vertical vein consisting in an abnormal venous drainage from the left upper pulmonary lobe to the superior vena cava, resulting in a non cyanotic shunt.

The SERRATE locus controls the formation of the early juvenile leaves and phase length in Arabidopsis

The development of the shoot can be divided into a series of distinct developmental phases based on leaf character-istics and inflorescence architecture. The relationship between phase length, defined by the number of organs produced, and the timing of the floral induction (V3-I1 transition) is relatively ill defined. Characterization of the serrate mutant (CS3257; Arabidopsis Biological Research Center) revealed defects in both vegetative and inflores-cence phase lengths, the timing of phase transitions, leaf number, the leaf initiation rate, and phyllotaxy. The timing of floral induction, however, is the same as in wild-type in extended short days as well as in short days, whereas the flowering time response to photoperiod is unaffected. SERRATE is shown to be required for the development of early juvenile leaves (V1) and to promote late juvenile leaf development (V2), while suppressing adult leaf (V3) and inflorescence development (I1 and I2). The se mutation supports the hypothesis that the timing of floral induction is independent of vegetative and inflorescence phase lengths. The role of SERRATE in the regulation of phase length and leaf identity is discussed.

[Spiral computed tomography of the renal arteries]

With the recent advent of spiral or helical CT, the ability to acquire large volume of imaging has become possible. Fast scanning of both kidneys, the aorta and the renal vessels can be accomplished during one breathhold. Early reports of CT angiography in the evaluation of renal artery stenosis indicated a sensitivity of 92% utilizing the MIP projection method and 59% utilizing the shaded surface display method. Specificity for both method was approximately 82%. More recent articles reports for hemodynamically relevant renal artery stenosis a sensitivity/sensibility of 96/99%. The introduction of a new multidetector CT technology will probably increase those results and the indication of CT angiography.

[Placing of a Nitiol Memotherm prosthesis: personal experience]

The authors report their experience in the placement of a new Nitinol stent. Thirty eight stents were placed in 28 iliac arteries, 3 superficial femoral arteries, 1 popliteal artery, 2 subclavian arteries, and 2 veins of hemodialysis fistulae. The primary success rate was 100%, but several angioplasty balloons have been ruptured due to the specific configuration of the stent. The mean follow-up period was 6 months. Memotherm placement is an easy procedure, but the specific structure of the device makes the manipulation of the angioplasty balloons delicate, especially in tortuous vessels.

[Persistent left superior vena cava. Apropos of 2 cases]

Double superior vena cava with persistence of a left superior vena cava is rarely encountered. The prevalence in the general population is 0.3% but may reach 3 to 10% in patients with inborn heart diseases. There are usually no clinical signs and the malformation is usually discovered fortuitiously. We describe the features of two cases observed in our institution and reviewed the literature on the subject.

[Diagnosis of an 'apple-core' lesion in the course of a small bowel enema]

We describe a case of gallbladder carcinoma observed fortuitously during small bowel enteroclysis as an "apple-core" lesion. This case illustrates the non-specificity of the clinical manifestations as well as the usual pitfalls in the diagnostic step.

[NMR evaluation of neoplastic invasion of the pulmonary artery]

Bronchial tumors that invade the mediastinum are not necessarily inoperable. Whether surgery is possible depends, among other things, on the extent of pulmonary artery invasion. The authors have studied the value of cardiac-gated MRI and compared it with CT and venous DSA for staging tumor invasion. CT demonstrated the areas of contact between tumor and mediastinum. The MRI planes were transverse and also in the main axis of the pulmonary arteries. Twenty-one patients were studied and in 16 the findings could be checked during surgery. In all cases the findings on MRI were confirmed. In eight patients MRI provided more information than CT and DSA combined and thereby showed its superiority for evaluating arterial invasion.

[Neoplastic invasion of the pulmonary arteries. Evaluation by MRI. Preliminary experience]

Bronchial tumors invading the mediastinum are no longer systematically regarded as inoperable. Curative surgery has produced a significant survival rate and led to the adaptation of the TNM classification. The degree of invasion of the pulmonary artery is a criterion of operability. The authors are trying to assess the role of MRI with regard to CT and DSA for the measurement of invasion. Their study deals with the prospective assessment of ten patients. The MRI examinations have been carried out with a 0.5 and 1.5 T supraconductive magnet (Philips Gyroscan). Cardiac gating has been used for acquisition. The planes of section are axial, transverse or oblique along the greater axis of the pulmonary arteries. CT examinations in 9-mm thick sections with and IV contrast injection demonstrate the contact of the tumor with the mediastinum. The digital angiograms have been taken with an intravenous injection into a vein of the bend of the elbow or into a femoral vein. Six cases have been verified at surgery. In all cases, the invasion predicted with MRI proved to be correctly assessed. In three cases, MRI provides additional information to the combined findings of CT and DSA. MRI is a good complement for the preoperative assessment of patients with large tumors invading the mediastinum but for which curative surgery is indicated.