Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date.

KEY MESSAGE: Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.

Mortality in British military participants in human experimental research into chemical warfare agents at Porton Down: cohort study.

OBJECTIVE: To investigate any long term effects on mortality in participants in experimental research related to chemical warfare agents from 1941 to 1989. DESIGN: Historical cohort study. Data sources Archive of UK government research facility at Porton Down, UK military personnel records, and national death and cancer records. Participants 18,276 male members of the UK armed forces who had spent one or more short periods (median 4 days between first and last test) at Porton Down and a comparison group of 17,600 non-Porton Down veterans followed to 31 December 2004. MAIN OUTCOME MEASURES: Mortality rate ratio of Porton Down compared with non-Porton Down veterans and standardised mortality ratio of each veteran group compared with the general population. Both ratios adjusted for age group and calendar period. RESULTS: Porton Down veterans were similar to non-Porton Down veterans in year of enlistment (median 1951) but had longer military service (median 6.2 v 5.0 years). After a median follow-up of 43 years, 40% (7306) of Porton Down and 39% (6900) of non-Porton Down veterans had died. All cause mortality was slightly greater in Porton Down veterans (rate ratio 1.06, 95% confidence interval 1.03 to 1.10, P<0.001), more so for deaths outside the UK (1.26, 1.09 to 1.46). Of 12 cause specific groups examined, rate ratios in Porton Down veterans were increased for deaths attributed to infectious and parasitic (1.57, 1.07 to 2.29), genitourinary (1.46, 1.04 to 2.04), circulatory (1.07, 1.01 to 1.12), and external (non-medical) (1.17, 1.00 to 1.37) causes and decreased for deaths attributed to in situ, benign, and unspecified neoplasms (0.60, 0.37 to 0.99). There was no clear relation between type of chemical exposure and cause specific mortality. The mortality in both groups of veterans was lower than that in the general population (standardised mortality ratio 0.88, 0.85 to 0.90; 0.82, 0.80 to 0.84). CONCLUSIONS: Mortality was slightly higher in Porton Down than non-Porton Down veterans. With lack of information on other important factors, such as smoking or service overseas, it is not possible to attribute the small excess mortality to chemical exposures at Porton Down.

Cancer morbidity in British military veterans included in chemical warfare agent experiments at Porton Down: cohort study.

OBJECTIVE: To determine cancer morbidity in members of the armed forces who took part in tests of chemical warfare agents from 1941 to 1989. DESIGN: Historical cohort study, with cohort members followed up to December 2004. DATA SOURCE: Archive of UK government research facility at Porton Down, UK military personnel records, and national death and cancer records. PARTICIPANTS: All veterans included in the cohort study of mortality, excluding those known to have died or been lost to follow-up before 1 January 1971 when the UK cancer registration system commenced: 17,013 male members of the UK armed forces who took part in tests (Porton Down veterans) and a similar group of 16,520 men who did not (non-Porton Down veterans). MAIN OUTCOME MEASURES: Cancer morbidity in each group of veterans; rate ratios, with 95% confidence intervals, adjusted for age group and calendar period. RESULTS: 3457 cancers were reported in the Porton Down veterans compared with 3380 cancers in the non-Porton Down veterans. While overall cancer morbidity was the same in both groups (rate ratio 1.00, 95% confidence interval 0.95 to 1.05), Porton Down veterans had higher rates of ill defined malignant neoplasms (1.12, 1.02 to 1.22), in situ neoplasms (1.45, 1.06 to 2.00), and those of uncertain or unknown behaviour (1.32, 1.01 to 1.73). CONCLUSION: Overall cancer morbidity in Porton Down veterans was no different from that in non-Porton Down veterans.

Exposures recorded for participants in the UK Chemical Warfare Agent Human Research Programme, 1941-1989.

OBJECTIVES: This study describes exposures to military veterans who participated between 1941 and 1989 in British research at Porton Down on the effects of exposure to chemical warfare agents and to defences against those agents. The study is part of a programme of epidemiological research initiated in response to service veterans' concerns about possible long-term health effects of their participation. METHODS: All entries in 97 books held in the Porton Down historical experimental archive covering the years 1939-1989 were reviewed. For tests between April 1941 and December 1989, data were abstracted on chemicals used, with additional detail abstracted for tests involving vesicants and nerve agents. For tests recorded during 1939-1941, similar data were abstracted for a representative sample of tests. RESULTS: Historical data were abstracted for 17 303 veterans included in the cohort study of 18,276 servicemen who took part in tests at Porton Down between 1941 and 1989. The median number of days per veteran on which tests were carried out was 2 days. The median difference between the last and first day of testing was 4 days. A large number of chemicals were tested over this period (n = 492). The type of chemical tested varied over time. Exposures were often modified by respirator use or use of protective clothing or protective equipment. It was possible to assign a quantitative measure of cumulative exposure to 73% of veterans exposed to the vesicant sulphur mustard--3491 (34%) of exposed veterans had cumulative exposures > or =10.63 mg and for 70% of veterans exposed to the nerve agent sarin--658 (29%) of exposed veterans had cumulative exposures > or =15.0 mg min m(-3). Ninety-three per cent of veterans exposed to sulphur mustard were classified to a semi-quantitative scale of dermal effect--3771 (37%) had a vesicle or necrosed area, and 69% of veterans exposed to sarin could be categorized by change in blood cholinesterase activity--1033 (31%) had a depression in cholinesterase activity of > or =30%. CONCLUSIONS: The experimental archive at Porton Down has proved to be a rich source of data on tests conducted between 1941 and 1989. It has been possible to categorize most veterans according to date of test, chemical group, chemical, type of protection and, for certain chemicals, level of exposure and/or degree of acute toxicity. These categorizations have been used to assign veterans to exposure groups for epidemiological analysis.

Strategies for the study of meiosis in rye.

We describe how we are furthering our understanding of meiosis in rye (Secale cereale L.) using a combination of cytogenetic and molecular biological approaches. Fluorescent in situ hybridisation, electron microscopy of synaptonemal complexes, sequencing of meiosis-specific genes, and the immunolocalisation of recombinogenic proteins are being combined to build up phenotypic "identikits" of wild type, asynaptic mutants sy1 and sy9, and desynaptic mutant sy10. From this information, we review the status of our current understanding of the genetic control of meiosis in rye, and consider strategies for determining more precisely the interrelationships between meiosis-specific genes and their products.

Notch signaling targets the Wingless responsiveness of a Ubx visceral mesoderm enhancer in Drosophila.

BACKGROUND: Members of the Notch family of receptors mediate a process known as lateral inhibition that plays a prominent role in the suppression of cell fates during development. This function is triggered by a ligand, Delta, and is implemented by the release of the intracellular domain of Notch from the membrane and by its interaction with the protein Suppressor of Hairless [Su(H)] in the nucleus. There is evidence that Notch can also signal independently of Su(H). In particular, in Drosophila, there is evidence that a Su(H)-independent activity of Notch is associated with Wingless signaling. RESULTS: We report that Ubx(VM)B, a visceral mesoderm-specific enhancer of the Ubx gene of Drosophila, is sensitive to Notch signaling. In the absence of Notch, but not of Su(H), the enhancer becomes activated earlier and over a wider domain than in the wild type. Furthermore, the removal of Notch reduces the requirement for Disheveled-mediated Wingless signaling to activate this enhancer. This response to Notch is likely to be mediated by the dTcf binding sites in the Ubx(VM)B enhancer. CONCLUSIONS: Our results show that, in Drosophila, an activity of Notch that is likely to be independent of Su(H) inhibits Wingless signaling on Ubx(VM)B. A possible target of this activity is dTcf. As dTcf has been shown to be capable of repressing Wingless targets, our results suggest that this repressive activity may be regulated by Notch. Finally, we suggest that Wingless signaling is composed of two steps, a down-regulation of a Su(H)-independent Notch activity that modulates the activity of dTcf and a canonical Wingless signaling event that regulates the activity of Armadillo and its interaction with dTcf.

Retrotransposon evolution in diverse plant genomes.

Retrotransposon or retrotransposon-like sequences have been reported to be conserved components of cereal centromeres. Here we show that the published sequences are derived from a single conventional Ty3-gypsy family or a nonautonomous derivative. Both autonomous and nonautonomous elements are likely to have colonized Poaceae centromeres at the time of a common ancestor but have been maintained since by active retrotransposition. The retrotransposon family is also present at a lower copy number in the Arabidopsis genome, where it shows less pronounced localization. The history of the family in the two types of genome provides an interesting contrast between "boom and bust" and persistent evolutionary patterns.

De novo evolution of satellite DNA on the rye B chromosome.

The most distinctive region of the rye B chromosome is a subtelomeric domain that contains an exceptional concentration of B-chromosome-specific sequences. At metaphase this domain appears to be the physical counterpart of the subtelomeric heterochromatic regions present on standard rye chromosomes, but its conformation at interphase is less condensed. In this report we show that the two sequence families that have been previously found to make up the bulk of the domain have been assembled from fragments of a variety of sequence elements, giving rise to their ostensibly foreign origin. A single mechanism, probably based on synthesis-dependent strand annealing (SDSA), is responsible for their assembly. We provide evidence for sequential evolution of one family on the B chromosome itself. The extent of these rearrangements and the complexity of the higher-order organization of the B-chromosome-specific families indicate that instability is a property of the domain itself, rather than of any single sequence. Indirect evidence suggests that particular fragments may have been selected to confer different properties on the domain and that rearrangements are frequently selected for their effect on DNA structure. The current organization appears to represent a transient stage in the evolution of a conventional heterochromatic region from complex sequences.

Subtle hydrophobic interactions between the seventh residue of the zinc finger loop and the first base of an HGATAR sequence determine promoter-specific recognition by the Aspergillus nidulans GATA factor AreA.

A change of a universally conserved leucine to valine in the DNA-binding domain of the GATA factor AreA results in inability to activate some AreA-dependent promoters, including that of the uapA gene encoding a specific urate-xanthine permease. Some other AreA-dependent promoters become able to function more efficiently than in the wild-type context. A methionine in the same position results in a less extreme, but opposite effect. Suppressors of the AreA(Val) mutation mapping in the uapA promoter show that the nature of the base in the first position of an HGATAR (where H stands for A, T or C) sequence determines the relative affinity of the promoter for the wild-type and mutant forms of AreA. In vitro binding studies of wild-type and mutant AreA proteins are completely consistent with the phenotypes in vivo. Molecular models of the wild-type and mutant AreA-DNA complexes derived from the atomic coordinates of the GATA-1-AGATAA complex account both for the phenotypes observed in vivo and the binding differences observed in vitro. Our work extends the consensus of physiologically relevant binding sites from WGATAR to HGATAR, and provides a rationale for the almost universal evolutionary conservation of leucine at the seventh position of the Zn finger of GATA factors. This work shows inter alia that the sequence CGATAGagAGATAA, comprising two almost adjacent AreA-binding sites, is sufficient to ensure activation of transcription of the uapA gene.

Nitrogen metabolite signalling involves the C-terminus and the GATA domain of the Aspergillus transcription factor AREA and the 3' untranslated region of its mRNA.

AREA is a GATA transcription factor which mediates nitrogen metabolite repression in Aspergillus nidulans in response to intracellular glutamine levels. We have identified and localized three elements important to modulation of AREA function: a region of 13 residues within the DNA-binding GATA domain which forms a putative extended loop structure, the 12 C-terminal residues, and sequences within a 218 nucleotide region of the 3' UTR. The 12 C-terminal residues are also required for transcriptional activation at a subset of loci under areA control. Specific deletions within the 3' UTR and the C-terminus cause similar levels of derepression and the mutations are additive, implicating two principal signal transduction pathways. The contribution of the 3' UTR to AREA modulation is effected at the level of transcript stability such that the areA mRNA is at least five times more stable under nitrogen-derepressing conditions than it is under repressing growth conditions.

Mutational analysis of the C-terminal region of AREA, the transcription factor mediating nitrogen metabolite repression in Aspergillus nidulans.

In Aspergillus nidulans the positive-acting, wide domain regulatory gene areA mediates nitrogen metabolite repression. Previous analysis demonstrated that the C-terminal 153 residues of the areA product (AREA) are inessential for at least partial expression of most genes subject to regulation by areA. Paradoxically, areAr2, a -1 frameshift replacing the wild-type 122 C-terminal residues with a mutant peptide of 117 amino acids, leads to general loss of function. To determine the basis for the areAr2 mutant phenotype, and as a means of delineating functional domains within the C-terminal region of AREA, we have selected and characterised areAr2 revertants. Deletion analysis, utilising direct gene replacement, extended this analysis. A mutant areA product truncated immediately after the last residue of the highly conserved GATA (DNA-binding) domain retains partial function. The areAr2 product retains some function with respect to the expression of uaZ (encoding urate oxidase) and the mutant allele is partially dominant with respect to nitrate reductase levels. Consistent with the areAr2 product having a debilitating biological activity, we have demonstrated that a polypeptide containing both the wild-type DNA-binding domain and the mutant C-terminus of AREA2 is able to bind DNA in vitro but no longer shows specificity for GATA sequences.

Mutational analysis reveals dispensability of the N-terminal region of the Aspergillus transcription factor mediating nitrogen metabolite repression.

Mutational analysis has enabled identification and localization of an upstream exon of the areA gene of Aspergillus nidulans mediating nitrogen metabolite repression. A mutation in the initiation codon and frameshift mutations, which revert by restoration of the reading frame, established the coding role of the exon and mutations affecting intron splicing in conjunction with DNA sequencing of reverse transcriptase polymerase chain reaction (RT-PCR) products localized the coding region intron. The resulting AREA translation product would have 876 residues. Deletion of the upstream exon such that translation of the remaining areA coding region would yield a protein containing only the 719 C-terminal residues has only a subtle phenotype, very similar to those resulting from single amino acid replacements in upstream exon-encoded regions of strong sequence similarity to the Neurospora crassa and Penicillium chrysogenum homologues. A number of areA mRNAs of different sizes are synthesised and appear to be functionally redundant. Synthesis of at least the smallest mRNA(s) is probably subject to autogenous activation. Suppression of frameshift mutations by compensating mutations preventing intron splicing suggests that insertion of a markedly hydrophobic sequence can impair AREA function. Finally, translational initiation for areA can occur within a region of at least 123 nucleotides.

Withdrawal of mechanical ventilation: ethical principles and guidelines for terminal weaning.

BACKGROUND: Discontinuation of mechanical ventilation because of the recognition of futility of continued treatment or because of patient or family request is an increasingly frequent occurrence in critical care. Although there is broad consensus about the patient's right to refuse life support, little has been written about the actual procedure of withdrawing mechanical ventilation. OBJECTIVE: The purposes of this article are: (1) to review ethical arguments supporting the view that it may be morally permissible to withdraw mechanical ventilation from patients who are neither terminally ill nor imminently dying and (2) to provide guidelines for the procedure of ventilator withdrawal. METHOD: Ethical principles supporting the position that ventilator withdrawal under these conditions can be morally justified and principles suggesting that ventilator withdrawal is morally objectionable are evaluated. Factors contributing to clinicians' ambivalence about this issue and guidelines for planning and implementing treatment withdrawal are discussed.

C-terminal truncation of the transcriptional activator encoded by areA in Aspergillus nidulans results in both loss-of-function and gain-of-function phenotypes.

Mutations truncating as many as 143 C-terminal residues from the transcriptional activator encoded by the areA gene, mediating nitrogen metabolite repression in Aspergillus nidulans, do not significantly reduce the ability of the areA product to activate expression of most genes under areA control. Such mutations can even have a gain-of-function, derepressed phenotype, consistent with a critical role for this region in modulating the activity of the areA protein. However, expression of a few genes under areA control is substantially impaired by such C-terminal truncations, indicating that regions of an activator protein can play differing roles in the control of different structural genes. This underlines the advantages of being able to monitor effects of areA mutations on expression of large numbers of structural genes. Additionally, it is shown that truncation of as many as 153 C-terminal residues, virtually all amino acids C-terminal to the DNA-binding region, is compatible with retention of some areA function.

The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans. Mutations affecting specificity of gene activation alter a loop residue of a putative zinc finger.

The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans has been sequenced and its transcript mapped and orientated. A single ORF can encode a protein of 719 amino acids. A 52 amino acid region including a putative 'zinc finger' strongly resembles putative DNA binding regions of the major regulatory protein of erythroid cells. The derived protein sequence also contains a highly acidic region possibly involved in gene activation and 22 copies of the motif S(T)PXX, abundant in DNA binding proteins. Analysis of chromosomal rearrangements and transformation with deletion clones identified 342 N-terminal and 124 C-terminal residues as inessential and localized a C-terminal region required for nitrogen metabolite repressibility. A -1 frameshift eliminating the inessential 122 C-terminal amino acids is a surprising loss-of-function mutation. Extraordinary basicity of the replacement C terminus might explain its phenotype. Mutant sequencing also identified a polypeptide chain termination and several missense mutations, but most interesting are sequence changes associated with specificity mutations. A mutation elevating expression of some structural genes under areA control whilst reducing or not affecting expression of others is a leucine to valine change in the zinc finger loop. It reverts to a partly reciprocal phenotype by replacing the mutant valine by methionine.

Operative factors, not hemodynamics, modify hormones in repair of coarctation.

This study was designed to evaluate separately the influence of restoration of distal pulse pressure and the influence of factors related to operation upon hemodynamic and hormonal alterations accompanying repair of canine aortic coarctation. Eight normal adult dogs underwent a sham operation and served as controls. In 10 dogs the thoracic aorta was transfected and reanastomosed. In 10 dogs aortic coarctation was created within 1 week of birth by banding the aorta just proximal to the ductus ligament, thereby fixing lumenal diameter at 1 to 2 mm. Studies were performed in the latter animals 18 months after operation. These dogs were subdivided into two groups: one (n = 6) underwent surgical repair of the coarctation; in the other (n = 4), the coarctation was repaired and an occluder was placed on the aorta to maintain distal aortic pulse pressure at its diminished preoperative level. Normal distal pulse pressure was restored in these animals by releasing the occluder 1 week after recovery from the repair of coarctation. Each dog was studied in the conscious state before the definitive procedure and again 24 hr later. Plasma renin activity increased significantly after operation in the sham and in the transection groups. Renin activity and proximal blood pressure were significantly elevated and distal pulse pressure was diminished preoperatively in both the repair and the occluder groups. After their respective definitive procedures, the elevation in renin activity and in proximal pressure persisted in the repair group but decreased in the occluder group.(ABSTRACT TRUNCATED AT 250 WORDS)

Treatment of blunt hepatic injuries: role of CT.

Serial dynamic upper abdominal computed tomography (CT) studies were performed on 20 patients as part of the conservative treatment of blunt hepatic injuries (hematoma, laceration, or fracture). Fourteen of these patients had either major or minor associated hemoperitoneum. In 13 patients, hemoperitoneum was either significantly reduced or absent by 1 week. A severe delayed hemorrhage occurred in one patient 7 1/2 days after admission; a large and unchanged volume of intraperitoneal fluid had been seen on a preceding abdominal CT scan. One other patient who had a satisfactory response underwent surgery for a pancreatic laceration. Serial abdominal CT studies are an integral part of the conservative treatment of blunt hepatic injuries and seem to be useful in monitoring resorption of hemoperitoneum and the pattern of healing of intrahepatic hematomas, lacerations, and fractures.

Multiple paradoxical emboli.

We report a case of multiple paradoxical emboli involving the common carotid, right subclavian, right renal, celiac, and superior mesenteric arteries. Paradoxical embolus is an uncommon but important cause of acute arterial occlusion. Successful management requires prompt recognition, prevention of further embolization, and treatment directed toward relief of the acute arterial occlusion.