Senescence is integral to the flowering plant life-cycle. Senescence-like processes occur also in non-angiosperm land plants, algae and photosynthetic prokaryotes. Increasing numbers of genes have been assigned functions in the regulation and execution of angiosperm senescence. At the same time there has been a large expansion in the number and taxonomic spread of plant sequences in the genome databases. The present paper uses these resources to make a study of the evolutionary origins of angiosperm senescence based on a survey of the distribution, across plant and microbial taxa, and expression of senescence-related genes.Arabidopsis was profiled for coexpression patterns and developmental relationships and revealed a clear carotenoid metabolism grouping, coordinated expression of genes for anthocyanin and flavonoid enzymes and regulators and a cluster pattern of genes for chlorophyll catabolism consistent with functional and evolutionary features of the pathway.Phylogeny analyses were carried out on protein sequences corresponding to genes with demonstrated functions in angiosperm senescence. They include proteins involved in chlorophyll catabolism and its control, homeoprotein transcription factors, metabolite transporters, enzymes and regulators of carotenoid metabolism and of anthocyanin biosynthesis. Evolutionary timelines for the origins and functions of particular genes were inferred from the taxonomic distribution of sequences homologous to those of angiosperm senescence-related proteins. Turnover of the light energy transduction apparatus is the most ancient element in the senescence syndrome. By contrast, the association of phenylpropanoid metabolism with senescence, and integration of senescence with development and adaptation mediated by transcription factors, are relatively recent innovations of land plants. An extended range of senescence-related genes of The expression and phylogenetic characteristics of senescence-related genes allow a framework to be constructed of decisive events in the evolution of the senescence syndrome of modern land-plants. Combining phylogenetic, comparative sequence, gene expression and morphogenetic information leads to the conclusion that biochemical, cellular, integrative and adaptive systems were progressively added to the ancient primary core process of senescence as the evolving plant encountered new environmental and developmental contexts. We present evidence that the genes and metabolism representing the core of the process of senescence in modern land-plants can be traced back to primaeval unicellular photoautotrophs and that specific elaborations and regulatory mechanisms have been progressively added to the senescence program at decisive points during plant evolution. Senescence is a prominent characteristic of angiosperm morphogenesis and ecology. The term is applied at all levels of plant biology, from processes at the biome-wide scale that define the season of autumn in temperate climates ,2 througA challenging question sometimes asked of biologists by children and physicists is: if leaves are solar panels, why are they green and not black -12? ThisPhylogenetic analysis of genes for Mg-tetrapyrrole biosynthesis indicates that anoxygenic photosynthetic organisms are ancestral to oxygen-evolving cyanobacteria and that the pathway in purple bacteria may be closest to that of the most ancient phototrophs . By contAuxenochlorella (formerly Chlorella) protothecoides. Cells turn yellow, accompanied by changes in protein and enzyme activities that resemble those of senescing mesophyll cells [Chlamydomonas mutant [Pyrocystis lunula is also a bilin degradation product of chlorophyll, though in this case the chlorin macrocycle is opened between rings A and D [Euphausia pacifica [The significant early events in the evolution of the photosynthetic apparatus comprised diversification of reaction centre and antenna structure, based on chlorophyll and isoprenoids, and organisation and delineation of oxygenic and anoxygenic photosynthesis. According to Strother  'the endll cells , and a rll cells -31. Chemll cells . This stll cells . Similars mutant . The luc A and D . A lucifpacifica ,36, presAuxenochlorella is an amino acid permease, dee4 [Arabidopsis homologue of dee4, At1g44100, were identified in isolated nuclei of Arabidopsis phloem cells, suggesting a role in nitrogen translocation from sources to sinks [Arabidopsis rosette leaves [Amongst the genes expressed during the auto- to hetero-trophic transition in se, dee4 . Transcrto sinks . Bleecketo sinks  considerto sinks ,40. To ae leaves , was incFrom endosymbiont origins of photosynthetic eukaryotes to angiosperms is a sequence of major events including differentiation of two- and three-dimensional body plans and emergence from the aquatic environment onto land . Cell spAuxenochlorella during the switch from auto- to hetero-trophy [As well as promoting diversification of structure, and adaptation to terrestrial ecological niches, achieving landfall eventually exposed plants to new biotic and abiotic interactions. The ancient role of carotenoids as quenchers of excess light energy intercepted by photosystems  acquiredo-trophy . Plastogo-trophy . Existino-trophy ,53,54. Wo-trophy .Carotenoid metabolism in senescence and ripening is closely integrated with the transdifferentiation of chloroplasts into gerontoplasts and chromoplasts. Chromoplast development is regulated by Or (dnaJ-type) chaperone/transcription factors , two of Arabidopsis homologue At4g32940.Another major class of pigments in land-plants comprises products of phenylpropanoid metabolism . AnthocyArabidopsis genes with likely functions in senescence, with the object of identifying common regulatory units. It is also of interest to seek evidence for homologies between terminal physiological changes in different organs, which in turn would begin to answer the question as to whether there is a common senescence program which operates, with variations, in all plant cells, tissues and organs.As well as analysing the distribution across plant and microbial taxa of the selection of senescence-related protein sequences described above, we applied the clustering tools in Genevestigator to an extended group of Gene expression profiles, protein structures and molecular phylogenies are discussed in relation to chlorophyll catabolism and its control, homeoprotein transcription factors with known functions in senescence, metabolite transporters, carotenoid metabolism and anthocyanin biosynthesis Table . Many seIn most cases the trees are presented in unrooted radial form and are based on global alignments of protein sequences from one or two representative genera of each major taxon. Tree topologies for individual proteins often deviated from those predicted by the evolutionary relationships between the corresponding taxa. The non-congruence of gene and species trees is a well-described feature of molecular phylogenies and indeed is statistically to be expected . BootstrArabidopsis genes whose protein trees are reported in the present paper, including RCCR and PaO (AGI accession numbers respectively At4g37000 and At3g44880). Expression of RCCR is not particularly strong in senescing leaves. It gives a noticeably weak signal in roots and other non-green structures like pollen. PaO is also largely undetectable in non-green tissues but exhibits clear differential expression during development, being most prominent in senescing leaf, cauline leaf and sepal.The observation of bilin products of chlorophyll catabolism in unicellular algae focuses attention on the enzymes responsible for opening the chlorin macrocycle, namely PaO and RCCR. Figure Anabaena protein, recording an extremely low E score of 4.80e-159. Protein and DNA BLAST searches, both of general databases and of the JGI Chlamydomonas reinhardtii site, failed to record a single hit within the green algae. The significance of the discontinuity in the distribution of RCCR across phyla is considered in the Discussion section.Sequence similarities to the protein corresponding to RCCR gene At4g37000  were anArabidopsis PaO gene At3g44880  was aligned with similar proteins from other species and the results were used to generate the tree shown in Figure Clostridium ancestor, possibly something like the firmicute Heliobacterium. The rRNA [Clostridium (11 of 44 genomes) and Bacillus (3 of 41 genomes) and there was no obvious conservation of genome context of Sgr between these organisms. We therefore conclude that Sgr is either an ancestral feature, which has been lost in all but a few remaining lineages; or, more likely, a feature that has been acquired more than once via horizontal gene transfer  is a post-translational regulator of chlorophyll-protein complex degradation ,69,70. TThe rRNA ,72 and SNematostella and the choanoflagellate Monosiga when BLASTed against Arabidopsis WBC23  is also upregulated in senescing leaves  is upregulated when s Figure  and has s Figure .Arabidopsis PAP-Fibrillin , a plastoglobule-associated protein [Ostreococcus sequence with a high E score appears to be a chimeric protein comprising two additional FHA  domains, separated from each other and the Fibrillin domain by regions of low complexity  to angiosperms  has a regulatory function in branch production, root growth, flower development and leaf senescence . It is ms Figure  and a seBrassica encode proteins of the dnaJ chaperone class that play an important role in the differentiation of chromoplasts [Arabidopsis gene corresponding to the cauliflower Or protein ABH07405 (UniProt), and is referred to here as OrI. It is expressed in floral parts, cotyledons and in cauline and senescent leaves  was aligned with similar sequences; the homologous Arabidopsis gene is AGI At5g17050. The anthocyanin pathway is under the control of myb transcription factor C1 . Both genes are widely expressed in different organs and tissues  is most strongly expressed in senescent and cauline leaf, with some significant signal in petal, sepal, xylem and cork  is the product of a nescence . It is anescence . The Arak Figure . A distaArabidopsis genes comprising those listed in Table In the evolution of the senescence program, genes would be expected to show a degree of coordinate expression in groupings that reflect phylogenetic trends. Similarly, a consequence of the differentiation of plant tissues and organs from ancestral structures is the sharing of common senescence programs. We used the Genevestigator Clustering Analysis tool to look for relationships between a collection of The present account of the evolutionary origins of plant senescence seeks to follow the major features of the syndrome in angiosperms through the lineage of organisms leading from the earliest phototrophs, as revealed by analysing sequence relationships among key proteins. Additional File Arabidopsis: mutants deficient in CYP38 make normal amounts of photosystem structural components but these fail to assemble correctly and are turned over. Significantly, the CYP38 gene (At3g01480) is strongly down-regulated in senescing compared with mature and juvenile Arabidopsis leaves (data not shown). Xiong [The Archaeozoic and Mesoproterozoic eons lasted from 3800-1000 mya. Although the detailed phylogeny of this period is difficult to infer from molecular analysis of contemporary prokaryotes , it is p). Xiong  describe). Xiong  and of p). Xiong  shows coCharge-separation is hazardous for pigment-protein reaction centres and here again there will be a requirement for turnover systems to maintain functioning structures . Genes sAuxenochlorella protothecoides is transferred from auto- to hetero-trophic culture conditions; the Arabidopsis homologue is also upregulated in senescing leaves  from the published study of O tauri by Derelle et al. [O lucimarinus database . In both cases the E value for alignment with See2 is better than 1e-13 and for the C13 peptidase superfamily conserved domain E scores were of the order of 1e-80. We conclude that VPE-like proteases are present in Ostreococcus  have been implicated in a cell death program in diatoms . It is dAuxenochlorella protothecoides by light and nitrogen limitation is associated with excretion of bilin products of chlorophyll catabolism [Arabidopsis and the corresponding genes  are upregulated during senescence  saw the rise of the charophytes, which are considered to link the unicellular chlorophytes with the first land-plants. The lack of sequence data for members of the Charophyta is a major gap in the phylogenetic record, but it is possible to identify features within charophyte algae likely to be relevant to senescence evolution, notably the elaboration of multicellular morphology, branching, 3-D cell division and interconnection of cells by plasmodesmata . A key gyophytes .Coleochaete [The presence of lignin-like compounds in eochaete  is evideeochaete . Long-raChara and Nitella show them to perform sophisticated functions in ionic regulation, hydraulic maintenance of tissue morphology and turgor-driven cell wall growth [The development of multicellular two- and three-dimensional forms changes the relationship between the plant body and the external medium. Direct exchange of materials across the plasmalemma has to be subordinated to the structural and physiological requirements of the tissue. It seems likely that this was the impetus for the evolution of more complex roles for the cell vacuole, which took on the status of 'inner space', in a sense adopting the role of a remnant of the ancestral aquatic milieu inside each vegetative cell. Extensive studies of the vacuoles of l growth -118. Thel growth -121. Thel growth .2 assimilation within chloroplasts are regulated by systems present in Chlamydomonas and other unicellular chlorophyceans [2 concentration 410 mya is believed to have been around 3000 to 4000 ppmv [Archaeopteris (359-349 mya) probably controlled canopy morphology through abscission of lower megaphylls [Glossopteris flora was already well established in Gondwanaland during the Carboniferous era [Green plants made landfall in the Silurian-Jurassic period, more than 410 mya. In this new and hostile environment, desiccation was avoided and ionic homeostasis maintained by the early development of an all-enveloping epidermal and cuticular 'space suit'  and a waphyceans . Atmosph000 ppmv . This, c000 ppmv  'the gregaphylls . Abscissgaphylls , and a drous era . Preservrous era . Thomas rous era  discusseAuxenochlorella expel RCC, the product of the PaO reaction, directly into the medium, possibly via an MRP2/4-like transporter as discussed above. Land plants, on the other hand, have requisitioned a detoxification pathway to redirect the products of chlorophyll catabolism to the cell vacuole. The two activities that make the link between the evolutionarily ancient first section of the catabolic pathway and the cytosolic-vacuolar steps are RCCR and the envelope transporter WBC23. The presence of the latter in Chlamydomonas and Ostreococcus is identified by BLAST; BLAST analysis also records hits on similar choanoflagellate and cnidarian sequences  revealed weak similarity with phycoerythrobilin ferredoxin oxidoreductases, which may conceivably have been the distant ancestral sources of plant RCCRs. BLASTing the Nostoc punctiforme genome database reveals two genes located side-by-side (Npun_R3279 and Npun_R3277). They are highly similar and may represent a duplication. Pfam recognises both proteins as possessing the conserved domains of RCCR. Global transcription data are available for Nostoc and show that 3277 is strongly expressed during hormogonia differentiation but not in other developmental stages. By contrast 3279 was down-regulated during hormogonia differentiation [Nostoc is an extracellular symbiont or endophyte in the hornwort Anthoceros [Gunnera [Anabaena genome (A variabilis) has only one RCCR-homologous sequence. Anabaena is symbiotic with the water fern Azolla [Using site-specific mutagenesis methods, Pružinská et al.  have shontiation . Nostoc thoceros , but an [Gunnera . The horn Azolla .Nostoc at least) are those that form symbioses with green plants in tissues which are exposed to light. In these associations , the normal option of excreting RCC into an aqueous medium would not be available. We speculate that this is the reason for the anomalous occurrence of RCCR genes in symbiotic Nostoc and Anabaena. The source of these genes remains problematical. Did land plants acquire RCCR by gene transfer between a cyanobacterium and a hornwort-like early colonizer host; or  did a cyanobacterial symbiont pick up the gene from its host? The possibility of gene transfer between hosts and symbionts as a factor in the adaptation of early land plants to the new environment merits further study.It is significant that the only cyanobacteria known to have RCCR homologues  to the macrophyllous and euphyllous ferns, conifers and angiosperms. Beerling points out that the genes for leaf morphogenesis were to a large extent already present in clubmosses, spikemosses and quillworts and proposes that high CO2 constrained the expression of this morphogenetic potential. The elaboration of megaphyllous laterals from the Carboniferous onward led directly to the evolution of the specialised reproductive and propagative structures of the angiosperms according to long-established ontogenetic principles [2 fixation by (cyano)bacteria and archea and nitrogen oxide fertilization by electrical storms could have contributed to the formation of skeletal oligotrophic soils as far back as 1200 mya [Beerling  has propinciples ,141. Alt1200 mya . The req1200 mya ,142.Physcomitrella patens online database at the time of writing yields more than 330 hits with high sequence similarity to senescence-related genes in Arabidopsis, rice and Medicago, and proteomics studies, such as the analysis of responses of the P patens phosphoproteome to cytokinin treatment described by Heintz et al. [Efficient internal nitrogen recycling requires cell integrity and metabolic regulation in the senescing source tissue, a directional translocation system connecting the source to the developing sink, means of signalling supply and demand status between the different regions of the plant body and a morphogenetic context that maintains structural and functional fitness ,143,144.z et al. , also id2O2, and autoregulates its own synthesis by feedback inhibition. Salicylic acid and jasmonic acid, via the regulatory protein ESR, control Wrky53 functions in senescence and resistance responses to pathogens [The senescence program is integral to strategies for dealing with the biotic and abiotic stresses of the terrestrial environment. Wrky53, member of a family of regulatory genes that diversified greatly with the evolution of the tracheophytes ; Figure , encodesathogens . Acclimaathogens . Miao etathogens  reportedAngiosperms appeared in the Jurassic period, 150 mya. Carpels, flowers and tectate pollen occur in the fossil record at around this time and within 30 my angiosperms had become the dominant component of global floras. Before evolution of the angiosperms the colour world of vegetation would have consisted largely of greens, yellows and browns, much as it does in modern conifer-dominated forest ecosystems. A rapid increase in the profusion of natural pigmentation accompanied the Cretaceous explosion in angiosperm evolution and was likely to have been an adaptive response to a combination of abiotic and biotic factors ,153. RadPhotoinhibition and the damaging effect of excess light energy within assimilatory tissues is a common factor in the experience of abiotic stresses ,156. TheCoevolution with pollinators and dispersers is an important factor in establishing carotenoid- and phenylpropanoid-based pigmentation of floral organs and propagating structures such as seeds and fruits ,160-163.Arabidopsis and rice and placed At1g69490 and three other closely related sequences  in the NAP subgroup of Group I. Genevestigator expression profiling shows that each of the four AtNAPs in this family has a distinctly different tissue specificity: highest abundance of At1g69490 transcripts is in senescing leaves, with petals and sepals also giving a strong signal , a lineThis schematic description of the homologous interrelationships of organ senescence has important implications when considered together with the molecular relationships described in the present study. It is clear that the competence to transdifferentiate chloroplasts into gerontoplasts was already well established in the bryophytes and ferns, whereas chromoplasts appeared later when coevolution with the visual systems of interacting animals began to drive diversification of the colours and morphologies of reproductive structures , bu, buformated see -182) as  as formated  as representative of the genomic status of its newly-evolved ancestral form. Many more sequences from many more species, particularly covering the span between the cyanobacteria and the angiosperms, are needed before this belief can be held with full confidence. For the specific case of plant senescence, the scarcity of sequences from ferns and charophytes is a particular limitation. Even so, the present study has allowed a feasible scheme to be proposed that accounts for much of the available information on senescence-related genes, their functions and interactions.In recent times the quantity and quality of DNA sequence information from plants across the taxonomic and evolutionary range has increased greatly. At the same time our understanding of the molecular and cell biology of plant senescence has developed to the point where we can assign functions to some enzymes and regulatory proteins. In the present paper we have taken the first steps towards a synthesis that allows us to frame, and begin to test, hypotheses about the evolutionary origins of angiosperm senescence, its control and integration into plant development and adaptation. Because major gaps remain in the taxonomic spread of sequenced species, and the assignment of functions to senescence-associated genes, the arguments presented here include a number of conjectural interpolations and extrapolations. For example, it is something of an article of faith for molecular evolution studies to consider a modern member of an ancient phylum  systemChlamydomonas reinhardtii v 3.0 BLASTJGI CYANOBASEPhyscomitrella patens online databaseJGI Gramene data resource for comparative genome analysis in the grassesTree of Life web projectBLAST, including protein BLAST (blastp), nucleotide BLAST , blastx, tblastn, tree viewer and BLINK precomputed BLASTEBI FASTA fast protein comparisonEBI ClustalW2 sequence alignment toolGENEDOC sequence alignment editorEMBL SMART domain architecture toolPfam protein domain databaseAll protein trees reported here were generated using, as appropriate, BLASTP and FASTA for local alignments, ClustalW2 for global alignment, and TREE-PUZZLE, PUZZLEBOOT and the PHYLIP Phylogeny Inference Package ,186 for . Input files for PROML, consisting of multiple sequence alignments, were created using ClustalW2. The Jones-Taylor-Thornton model was used to compute probabilities of changes between amino acid sequences.Protein sequence trees were constructed from amino acid sequence data using PROML (Protein Maximum Likelihood Program) in PHYLIP 3.62 for inferring evolutionary trees. PHYLIP  is distributed by the author, J Felsenstein, Department of Genome Sciences, University of Washington, Seattle. For all amino acid sequence data sets, PROML was run with three different settings for the R (rate variation among sites) parameter: Gamma distribution , Hidden . High bootstrapping values mean uniform support; a support value of less than 50 is treated as giving no support. Support values generated in this study are presented in Additional File  package was also performed on all datasets and the output of support values from this analysis is consistent with the support values presented in this study.Bootstrapping analyses were carried out on all datasets to measure how consistently the data support given taxon bipartitions. The bootstrapping majority-rule consensus tree and support values were generated through the use of SEQBOOT, NEIGHBOR and CONSENSE programs in PHYLIP, and PUZZLEBOOT  was run, using alignments created in ClustalW2, to generate the parameters such as the alpha (Gamma rate heterogeneity parameter) values, number of rate categories, individual rates and their respective probabilities to specify, as appropriate, coefficient of variation for a Gamma distribution model and how many categories of substitution rate there would be in a HMM of rate variation.To estimate the degree of rate heterogeneity, TREE-PUZZLE 5.2 ,190 was Protein trees were displayed using the TreeView visualisation tool:Arabidopsis using the Genevestigator reference expression database and meta-analysis system for Affymetrix® expression arrays [We profiled the expression of senescence-related genes in n arrays . Figure n arrays . The expThe authors declare that they have no competing interests.Clostridium. HO devised the bioinformatics strategy, contributed to alignment and expression analyses and carried out the investigations of CCD8, NAC and cyanobacterial RCCR-like sequences. All authors read and approved the final manuscript.HT conceived of the study, participated in sequence alignments and analyses of expression profiles and substantially drafted the manuscript. LH carried out the phylogeny and bootstrap analyses. MY was responsible for alignment and interpretation of Sgr-like sequences in Outfiles from Consensus tree program, version 3.67. Bootstrapping support values for protein consensus trees generated through the use of SEQBOOT, NEIGHBOR and CONSENSE and PUZZLEBOOT programs.Click here for fileOutfiles from PROML. Amino acid sequence Maximum Likelihood method, version 3.67. Tree branch lengths with error estimates, generated using PROML with Gamma distribution.Click here for fileSynopsis of significant events in the evolution of plant senescence in relation to the geological timeline. Innovations in the geological time-line relevant to the evolution of a senescence program integrated into plant development and adaptation.Click here for fileLog Likelihood (Ln) values corresponding to Hidden Markov Model, Gamma Distribution Model and Constant Rate Variation options in PHYLIP for phylogenetic analysis of senescence-related protein sequences. Results of analysing all amino acid sequence data with the PROML program run with three different settings for the R (rate variation among sites) parameter.Click here for file


Plasmodium falciparum malaria significantly lower patient infectiousness and have the potential to reduce population-level transmission of the parasite. With the increased interest in malaria elimination, understanding the impact on transmission of ACT and other antimalarial drugs with different pharmacodynamics becomes a key issue. This study estimates the reduction in transmission that may be achieved by introducing different types of treatment for symptomatic P. falciparum malaria in endemic areas.Artemisinin derivatives used in recently introduced combination therapies (ACTs) for We developed a mathematical model to predict the potential impact on transmission outcomes of introducing ACT as first-line treatment for uncomplicated malaria in six areas of varying transmission intensity in Tanzania. We also estimated the impact that could be achieved by antimalarials with different efficacy, prophylactic time, and gametocytocidal effects. Rates of treatment, asymptomatic infection, and symptomatic infection in the six study areas were estimated using the model together with data from a cross-sectional survey of 5,667 individuals conducted prior to policy change from sulfadoxine-pyrimethamine to ACT. The effects of ACT and other drug types on gametocytaemia and infectiousness to mosquitoes were independently estimated from clinical trial data. Predicted percentage reductions in prevalence of infection and incidence of clinical episodes achieved by ACT were highest in the areas with low initial transmission. A 53% reduction in prevalence of infection was seen if 100% of current treatment was switched to ACT in the area where baseline slide-prevalence of parasitaemia was lowest (3.7%), compared to an 11% reduction in the highest-transmission setting . Estimated percentage reductions in incidence of clinical episodes were similar. The absolute size of the public health impact, however, was greater in the highest-transmission area, with 54 clinical episodes per 100 persons per year averted compared to five per 100 persons per year in the lowest-transmission area. High coverage was important. Reducing presumptive treatment through improved diagnosis substantially reduced the number of treatment courses required per clinical episode averted in the lower-transmission settings although there was some loss of overall impact on transmission. An efficacious antimalarial regimen with no specific gametocytocidal properties but a long prophylactic time was estimated to be more effective at reducing transmission than a short-acting ACT in the highest-transmission setting.Our results suggest that ACTs have the potential for transmission reductions approaching those achieved by insecticide-treated nets in lower-transmission settings. ACT partner drugs and nonartemisinin regimens with longer prophylactic times could result in a larger impact in higher-transmission settings, although their long term benefit must be evaluated in relation to the risk of development of parasite resistance. Lucy Okell and colleagues predict the impact on transmission outcomes of ACT as first-line treatment for uncomplicated malaria in six areas of varying transmission intensity in Tanzania. Plasmodium falciparum, a mosquito-borne parasite that causes malaria, kills nearly one million people every year. When an infected mosquito bites a person, it injects a life stage of the parasite called sporozoites, which invade human liver cells where they initially develop. The liver cells then release merozoites (another life stage of the parasite). These invade red blood cells where they multiply before bursting out and infecting more red blood cells, which can cause fever and damage vital organs. Some merozoites develop into gametocytes, which infect mosquitos when they take a blood meal. In the mosquito, the gametocytes give rise to sporozoites, thus completing the parasite's life cycle. Because malaria parasites are now resistant to many antimalarial drugs, the preferred first-line treatment for P. falciparum malaria in most countries is artemisinin combination therapy (ACT). Artemisinin derivatives are fast-acting antimalarial agents that, unlike previous first-line treatments, reduce the number of gametocytes in patients' blood, making them less infectious to mosquitos, and therefore have more potential to reduce malaria transmission. These compounds are used in combination with another antimalarial drug to reduce the chances of P. falciparum becoming resistant to either drug.Because malaria poses such a large global public-health burden, there is considerable national and international interest in eliminating it or at least minimizing its transmission. Malaria control agencies need to know how to choose between available types of ACT as well as other antimalarials so as to not only cure malaria illness but also prevent transmission as much as possible. The financial resources available to control malaria are limited, so for planning integrated transmission reduction programs it is important for policy makers to know what contribution their treatment policy could make in addition to other control strategies  to reducing transmission. Furthermore, in areas with high levels of malaria, it is uncertain to what extent treatment can reduce transmission since many infected people are immune and do not suffer symptoms or seek health care, but continue to transmit to others. In this study, the researchers develop a mathematical model to predict the impact on malaria transmission of the introduction of ACT and alternative first-line treatments for malaria in six regions of Tanzania with different levels of malaria transmission.The researchers developed a “deterministic compartmental” model of malaria transmission in human and mosquito populations and included numerous variables likely to affect malaria transmission (variables were based on data collected in Tanzania just before the introduction of ACT). They then used the model to estimate the impact on malaria transmission of introducing ACT or other antimalarial drugs with different properties. The model predicted that the percentage reduction in the prevalence of infection  and the incidence of infection (the number of new cases in the population per year) associated with a 100% switch to ACT would be greater in areas with low initial transmission rates than in areas with high transmission rates. For example, in the area with the lowest initial transmission rates, the model predicted that the prevalence of infection would drop by 53%, but in the area with the highest initial transmission rate, the drop would be only 11%. However, because more people get malaria in high-transmission areas, the total number of malaria illness episodes prevented would be ten times higher in the area with highest transmission than in the area with lowest transmission. The model also predicted that, in areas with high transmission, long-acting treatments which protect patients from reinfection would reduce transmission more effectively than some common currently used ACT regimens which are gametocyte-killing but short-acting. Treatments which were both long-acting and gametocyte-killing were predicted to have the biggest impact across all settings.As with all mathematical models, the accuracy of the predictions made by this model depend on the many assumptions incorporated into the model. In addition, because data from Tanzania were fed into the model, its predictions are to some extent specific to the area. Nevertheless the Tanzanian setting is typical of sub-Saharan malaria-affected areas, and the authors show that varying their assumptions and the data fed into the model within realistic ranges in most cases does not substantially change their overall conclusions. The findings in this study suggest that in low-transmission areas, provided ACT is widely used, ACT may reduce malaria transmission as effectively as the widespread use of insecticide-treated bed nets. The findings also suggest that the use of longer-acting regimens with or without artemisinin components might be a good way to reduce transmission in high-transmission areas, provided the development of parasite resistance can be avoided. More generally, these findings suggest that public-health officials need to take the properties of antimalarial drugs into account together with the levels of transmission in the area when designing policies in order to achieve the highest impact on malaria transmission.http://dx.doi.org/10.1371/journal.pmed.0050226.Please access these Web sites via the online version of this summary at PLoS MedicinePerspective by Maciej Boni and colleaguesThis study is further discussed in a MedlinePlus encyclopedia contains a page on malaria (in English and Spanish)The malaria Information is available from the World Health Organization on malaria (in English and Spanish)The US Centers for Disease Control and Prevention provides information on Roll Back Malaria Partnership on its approach to the global control of malaria, on artemisinin-based combination therapies, and on malaria in TanzaniaInformation is available from the  P. falciparum malaria in many endemic countries in response to parasite resistance that rendered previous first line treatments ineffective [Since 2000, artemisinin combination therapies (ACTs) have become widely adopted as first-line treatment policy for uncomplicated ffective ,2. A secffective –6, whichffective . With thffective , it is iP. falciparum prevalence or disease incidence after ACT became the main treatment for clinical malaria in the area. Since then, data from a number of settings including Zanzibar [Evidence for transmission or disease reductions following ACT deployment initially came from studies in South East Asia –12 and SZanzibar  and RwanZanzibar ,13, chanZanzibar , and chaZanzibar ,16.A previous mathematical model of symptomatic case management predicted moderate to substantial impact of the nonartemisinin-based antimalarials sulfadoxine-pyrimethamine (SP) and amodiaquine (AQ) on age-prevalence patterns of infection and rates of severe disease and mortality under scenarios of 40% or 100% coverage . Rates oWith increasing investment in research, the range of drugs in development for treatment of malaria is widening and a greater number are also becoming available in combination with artemisinins as ACT . The strP. falciparum malaria transmission intensity. We use data from a survey prior to ACT introduction covering six different transmission settings in Tanzania typical of malaria-endemic Africa, in order to characterise rates of infection, symptomatic episodes, and antimalarial use. We then estimate potential transmission reduction following introduction of ACT as a first-line treatment and examine how the size of the reduction depends on coverage, use of diagnostic testing, and how it compares to the impact of alternative drugs with different pharmacodynamics. In this way we aim to elucidate potential goals for ACT policy implementation and inform future choices of first-line treatment.Here we develop a mathematical model to describe the impact of ACTs and other antimalarials on P. falciparum dhfr and dhfs genes, respectively, would cause parasitological failure, i.e., parasites would not be fully cleared by SP treatment and the infection would persist, while the double-mutant dhfr would be sufficient to reduce the effective prophylactic time of SP [We use data from a cross-sectional malariometric survey of 5,667 residents of Tanzania undertaken during the rainy season (March–June) of 2002 prior to the introduction of ACT in treatment policy or their licensure and wider availability in the private market. Details of the methodology and results of this survey are described in detail elsewhere . For ourme of SP . We alsoIncidence rates of symptomatic malaria were calculated from the observed prevalence of symptomatic cases by region, altitude and age as prevalence/duration, using estimates of duration of symptoms from the literature . ParasitS; latent, E; infectious and untreated, I; infectious and treated, T; or protected, P, where the latter state is included to model prophylaxis from treatment. Susceptible individuals become infected at a rate dependent on the density of mosquitoes, the human biting rate, the prevalence of infection in the mosquito, and the probability of developing blood stage infection following an infectious bite. The latent period is divided into two stages; during the first the parasites are liver- and early blood-stage and are subpatent , and during the second stage the infection becomes patent. The infection then develops to the infectious, untreated state I, which is divided into four stages with infectiousness greatest in the first two stages and lower in subsequent stages to replicate patterns observed in longitudinal human-to-mosquito transmission experiments  occur independently of the initial infection at the same rate as in susceptible, uninfected individuals and upon superinfection individuals return to the first stage of the infectious period, extending the overall duration of parasitaemia. A proportion of infections and superinfections are symptomatic and we assume that symptoms occur at the beginning of an infection and are followed by a longer period of asymptomatic parasitaemia , individuals enter the protected state P before returning to the susceptible state S. Treatment clears infection with a certain percentage efficacy determined by the prevalence of infections consisting of parasites susceptible to the drug. Treated patients with resistant parasites experience parasitological treatment failure and enter the first stage of the untreated state I. Clinical failure, i.e. parasitological failure accompanied by symptoms, is not explicitly incorporated in the model. In our data from the Tanzania survey, individuals were asked if they had used antimalarials within the previous 14 d. Clinical failure usually occurs on average around 5 d after treatment [Nonartemisinin treatment with a given rate of parasitological failure representing widely used antimalarials at the time of the Tanzania survey  is introreatment , so we aThe effects of nonartemisinin and ACT antimalarials on the infectiousness of patients to mosquitoes were estimated from antimalarial trial data, which measured human-to-mosquito transmission, taking into account subpatent gametocytaemia ,40. ThesFollowing introduction of failing nonartemisinin treatment into the model, the product of the mosquito density and age-specific probability of mosquito-to-human transmission for each age group was varied so that at the subsequent second equilibrium the age prevalence of patent infection fitted the observed values for a given area in the survey data. The proportion of infections that developed symptoms was set for each age group so as to reproduce the observed symptomatic malaria age prevalence for a given area at the second equilibrium. These parameters, used in fitting prevalence in the model output at the second equilibrium, are known to have a wide range of possible values across different settings and age groups . We assumed conservatively that any remaining treatment episodes were presumptive and were equally distributed within each age group regardless of infection state. The rate of presumptive treatment was calculated as the total age-specific rate of treatment per person-year in the population estimated directly from the data minus the age-specific rate of treatment of symptomatic cases . We assumed that after introducing a new antimalarial there was negligible short-term change in presumptive treatment rates, but the rate of symptomatic malaria was allowed to change after introduction of a new treatment. We also explored the impact of introducing diagnostic testing (microscopy or antibody-based rapid diagnostic tests) together with ACT by removing presumptive treatment of those without a patent infection.The rates of infection, clinical episodes, and treatment in each transmission setting estimated from the survey prior to ACT introduction are shown in The time taken to achieve the reduction in infection incidence becomes longer as pre-ACT transmission intensity decreases . With anThe importance of presumptive treatment to overall ACT impact was explored by modelling a scenario in which additional testing for the presence of parasites is incorporated into an ACT treatment programme. Under such a programme, individuals without detectable infection who seek treatment are no longer prescribed antimalarials; however, those with asymptomatic infection who have patent parasitaemia  continue to be treated. In the two lowest-transmission settings in Tanzania, reported rates of treatment per person-year in the cross-sectional survey were higher than the estimated rates of clinical episodes , suggestIn addition to investigating ACT impact on transmission, and thus the impact of a gametocytocidal drug, we used the model to examine the importance of the efficacy and prophylactic effects of antimalarials in reducing transmission . We consReplacing 100% of the failing treatments with a theoretical, 100% efficacious nongametocytocidal antimalarial with a prophylactic time of 10 d (as assumed for a short-acting ACT) is estimated to reduce the rate of clinical episodes by 2.5%–12.6% A. Again Gametocytocidal drug action was less effective in reducing transmission from an initially high than from a low level because following clearance of gametocytes individuals were more quickly reinfected. By contrast, prophylactic effects were more important for reducing new inoculations and clinical episodes in high- than in low-transmission settings, because there was a greater chance of receiving an infectious challenge during the prophylactic period. Prophylactic and, to some extent, gametocytocidal drugs are predicted to have less effect on infection prevalence than on the incidence of clinical episodes in higher-transmission settings B. A simiModel results were relatively robust to variations in the majority of key parameters  in trial settings  and, as Our analysis finds that gametocytocidal properties of antimalarials have the most relative impact in lower-transmission settings, while prophylactic effects have more impact in areas with high transmission. An ACT with the gametocytocidal effects of the artemisinin derivative and the prophylactic effect of a longer-acting partner drug is predicted to have the greatest impact on transmission across all areas in the short-term time scale of our model. ACT with long-acting partner drugs are currently in use in some areas; for example, artesunate-mefloquine is recommended by WHO. The more recently formulated dihydroartemisinin-piperaquine is also likely to become used more widely . If usedEstimated treatment impact did not vary evenly with baseline slide-prevalence of infection, particularly in the medium-transmission settings A, and 5.Our model predictions are roughly compatible with some of the trends from observational studies in areas where ACT was introduced, although it is uncertain to what extent these trends were attributable to ACT. In studies where transmission was similar to our lowest transmission setting  or lower, around 50% ,12 to 75With the current interest in reducing malaria transmission with a view to elimination of the parasite , our resText S1(866 KB DOC)Click here for additional data file.


Sudden arrhythmic death as a result of a blunt chest wall blow has been termed Commotio Cordis (CC). CC is being reported with increasing frequency with more than 180 cases now described in the United States Commotio Cordis Registry. The clinical spectrum is diverse; however young athletes tend to be most at risk, with victims commonly being struck by projectiles regarded as standard implements of the sport. Sudden death is instantaneous and victims are most often found in ventricular fibrillation (VF). Chest blows are not of sufficient magnitude to cause any significant damage to overlying thoracic structures and autopsy is notable for the absence of any structural cardiac injury. Development of an experimental model has allowed for substantial insights into the underlying mechanisms of sudden death. In anesthetized juvenile swine, induction of VF is instantaneous following chest impacts that occur during a vulnerable window before the T wave peak. Other critical variables, including the impact velocity and location, and the hardness of the impact object have also been identified. Rapid left ventricular pressure rise following chest impact likely results in activation of ion channels via mechano-electric coupling. The generation of inward current through mechano-sensitive ion channels results in augmentation of repolarization and non-uniform myocardial activation, and is the cause of premature ventricular depolarizations that are triggers of VF in CC. Currently available chest protectors commonly used in sport are not adequately designed to prevent CC. The development of more effective chest protectors and the widespread availability of automated external defibrillators at youth sporting events could improve the safety of young athletes. Although the clinical context has proven diverse, many instances of CC occur as a result of chest impact with projectiles used in organized sports, such as baseball, hockey, and lacrosse3. In the United States, CC has now been recognized as a leading cause of sudden death in youth athletics and is being reported with increasing frequency. Over the last decade, CC has achieved broader visibility through a series of reports detailing its clinical spectrum [Sudden cardiac death as a result of a blunt and often innocent-appearing chest wall blow has been termed commotio cordis (CC). Derived from Latin and meaning he heart ,2. This spectrum . At the spectrum . This arSince being initiated in 1996, the United States Commotio Cordis Registry  has now accrued more than 180 cases -5. As awAlthough commonly associated with sport, CC has now been reported in a diverse spectrum of non-sports related activities . Many ofThe overall survival rate in known victims of CC is only 15%, with successful resuscitation often quite difficult ,8. InitiIt is now apparent that CC is a primary electrical event, with sudden death resulting from the instantaneous induction of VF initiated by a chest wall blow. Autopsy data generally has not revealed any underlying congential or acquired heart disease in victims. Available evidence suggests that the pathophysiology of impact-induced VF is multi-factorial and requires the precise confluence of several variables. Development of an experimental animal model has allowed for a deeper understanding of the underlying mechanisms. This model attempts to mimic the clinical profile of CC, and entails propelling projectiles commonly used in sport  at the chest wall of anesthetized juvenile swine . ReleaseSeveral other factors have also been identified as crucial to the development of VF in this model of CC. Using echocardiographic guidance, the importance of impact location directly over the anatomic position of the heart was revealed . VF occuThe importance of the location, hardness, and velocity of chest wall impacts in CC relate to the effects of these variables on induction of a critical left ventricular (LV) pressure that is necessary to produce VF. In experiments of impact velocity, higher velocities correlated with the generation of greater peak instantaneous LV pressures. As with impact velocities, the risk of VF correlated with the LV pressure rise created by the chest wall blow in a Gaussian distribution  8,11,12,1211,12.+ATP channel is primarily responsible for ST-segment elevation noted in myocardial infarction, and contributes to the increased risk of VF associated with ischemia. In addition, mechano-sensitivity of the K+ATP channel has been previously demonstrated in a rat model [+ATP channel inhibitor, reduced the magnitude of ST-elevation and the incidence of VF following chest blows [+ATP channel by chest wall impacts is in part responsible for the induction of VF in CC. Other stretch-sensitive ion channels are also likely to be involved. Interestingly, however, blockade of the non-selective cation stretch-activated channel (SAC) with streptomycin did not prevent induction of VF in our model [Mechanical stimulation of the myocardium resulting in electrical events is well-described, occurring in such circumstances as catheter induced ectopic beats and thumping of the chest wall during asystole to produce PVCs ,8. This at model . In our st blows . Our resur model .trigger - premature ventricular depolarization - occurring in the setting of (ii) a susceptible myocardial substrate [In CC, the inward current generated through the opening of mechano-sensitive ion channels results in ventricular depolarizations that in turn, trigger development of VF. However, ventricular depolarization alone is not sufficient to result in reentrant arrhythmia that underlies the mechanism of VF. Thus, initiation of VF in CC appears to require at least two features: (i) a ubstrate . The necubstrate . PVCs we further increase in repolarization dispersion. Thus, it appears that the upstroke of the T wave signifies a window of potential vulnerability for development of VF in CC, due to spontaneous increase in repolarization dispersion. The potential vulnerability for the induction of VF is realized when chest impact results in sudden elevation in LV pressure leading to further increase in repolarization dispersion. Analogous to this hypothesis is the R on T phenomenon. In non-ischemic myocardium, premature ventricular depolarization during the T wave does not normally induce VF. Thus, continuous ventricular pacing (VOO) is generally safe. However, with the increase in repolarization dispersion in the setting of ischemia, the potential for inducing VF can be realized when a PVC falls on the vulnerable portion of the T wave [Interestingly, both trigger for CC and the susceptible myocardial substrate are in part created by a chest wall blow occurring in the vulnerable portion of the cardiac cycle. Susceptibility to development of CC relates to dispersion of repolarization that is present during the vulnerable period of the cardiac cycle when chest impact occurs. Recent data by Bode et al support this hypothesis . Fluid-fe T wave ,18.In addition, the experiments by Bode et al provide further insight into the electrical properties by which increase in repolarization dispersion might produce VF in CC . In thei+ATP channel is shared by both CC and ischemic myocardium, the mechanism of activation is quite different. In our model, angiography performed immediately after impact in animals that developed VF did not reveal any evidence of stenosis or spasm in epicardial coronary arteries [Although activation of the Karteries . Myocardarteries . On patharteries .Deaths of young athletes from CC are tragic and often highly visible events. In the United States, several preventive strategies have been considered, including increasing the use of softer balls and chest wall protectors in organized youth sports. Safety baseballs with soft rubber cores have been designed to reduce the risk of head and other bodily injury from traumatic impacts. In our experimental model, safety baseballs significantly reduced, but did not eliminate, the risk of sudden cardiac death with chest impacts at 48 km/h and 64 km/h (30 and 40 mph) . DespiteIn the United States, chest protectors are marketed with claims of protecting athletes from chest wall trauma. However, in the USCCR, more than 38% of the fatal impacts occurring during organized sport involved individuals who were wearing a chest protector . In seveLikely due to a lack of early recognition and the failure to initiate timely aggressive resuscitation and defibrillation, the survival rate in the USCCR is only about 15% . Surviva+ATP channel, via mechano-electric coupling. Inward current through these mechano-sensitive ion channels results in further augmentation of repolarization and non-uniform myocardial activation, and is the cause of premature ventricular depolarizations that are the triggers of VF. Survival in the USCCR is quite poor and largely dependes on institution of early defibrillation and resuscitation. Increasing the availability of AEDs at organized youth sporting events should enhance the safety of young athletes. In addition, the importance of developing more effective primary prevention strategies for CC - such as effective chest protectors and safety balls - and promoting their widespread use is needed.CC is being reported with increasing frequency and young athletes tend to be most at-risk. Sudden cardiac death results from the instantaneous induction of VF following a precordial chest wall blow. A narrow window of vulnerability corresponding to the time of intrinsic increase in repolarization dispersion, just before the peak of the T wave has been identified. In addition, several other variables, including the impact location and the hardness and velocity of the projectile relate to the production of a critical LV pressure that is necessary to induce VF. Rapid LV pressure rise following chest impact results in myocardial stretch and activation of ion channels, including the K


A 41-year-old white woman was referred to our Department to rule out the presence of a Fuch's corneal dystrophy. On slit-lamp biomicroscopy, small bilateral punctuate opacities appearing mostly in the posterior stroma were observed, suggesting a differential diagnosis of pre-Descemet's dystrophy as opposed to Cornea Farinata.Confocal microscopy in the central cornea of both eyes revealed the normal appearance of superficial and basal epithelial layers. However throughout the full thickness of the cornea fine highly refractive granules, localized both in the keratocytes cytoplasm and in the stroma matrix were noted. In both eyes abnormal polymegatism and pleomorphism was observed. Several corneal dystrophies such as Cornea Farinata, Punctuate Dystrophy, pre-Descement's Dystrophy, Fleck's Dystrophy, Deep Filiform Dystrophy and Posterior Punctiform Dystrophy have the clinical appearance of fine opacities limited to the posterior corneal stroma. These deposits are not associated with ocular or systemic diseases, they often are asymptomatic and only very rarely they interfere with visual acuity .Sometimes the differential diagnosis between these dystrophies may prove challenging . In vivoA 41-year old white woman was referred to us to rule out the presence of a Fuch's corneal dystrophy.Her family history did not reveal the presence of corneal dystrophies; in both eyes her best corrected visual acuity was 20/20, while intraocular pressure was within normal limits, and the findings on external examination and dilated pupil fundus examination were unremarkable. On slit lamp biomicroscopy small bilateral punctuate opacities mostly located in the posterior stroma were observed, suggesting the differential diagnosis between pre-Descemet's dystrophy as against Cornea Farinata Figure .The patient underwent in vivo CM with Confoscan 3  in order to obtain further details of her corneal disorder.2 with abnormal polymegatism (46.1%) and pleomorphism (37.9%), whereas in the left eye the endothelial cell count was 2,984 cell/mm2 with abnormal polymegatism (49.9%) and pleomorphism (26.9%).In both eyes it revealed a normal appearance of the superficial and basal epithelial layers. Nevertheless throughout the full thickness of the corneal stroma fine highly refractive granules, localized both in the keratocytes cytoplasm and in the stromal matrix, were observed Figure , while nCorneal dystrophies affecting the entire corneal stroma, and in particular the posterior stroma, can often show a similar appearance on slit-lamp examination, thus the differential diagnosis may prove challenging and some of these dystrophies may actually be a variation of the same disease .In vivo CM has been used by several authors in an attempt to clarify the diagnosis of several deep stroma corneal dystrophies.Cornea Farinata is an asymptomatic degenerative condition characterized by a myriad of fine, dust-like opacities found bilaterally in the posterior stroma near Descemet's membrane. They are best seen on retro illumination and appear grey-brown to white colour. On CM the superficial (dark and light cells) and the mid stroma layers appear normal; highly reflective small particles can be found in the cytoplasm of some keratocytes only in the deep stroma adjacent to the corneal endothelial layer with no abnormalities of the Descemet's membrane and endothelial cell layers .Pre-Descemet's dystrophy, a condition bearing a close clinical resemblance to Cornea Farinata, on slit-lamp examination shows larger and more polymorphous opacities than those of Cornea Farinata, distributed throughout the cornea but with a predilection for the deep stroma . CM demoFleck's dystrophy is a rare dominant autosomal corneal dystrophy with discrete opacities similar to those of Cornea Farinata and pre-Descemet dystrophy, but the opacities are located not only in the posterior but throughout the entire corneal stroma ; intraceDeep Filiform dystrophy of Maeder and Danis consists of multiple filiform gray opacities in the pre-Descemet area that affect the entire width of the cornea except for the perilimbal region. The original case occurred in a middle-aged woman with keratoconus. This disorder may represent a degeneration rather than a dystrophy .In Posterior Punctiform dystrophy punctiform elements are present in small groups of filament some of which are of a dendritic type, whereas others resemble canes or comas, and are of a bluish-white colour, being visible to direct and indirect illumination with ring or strictly axial distribution of the opacities .According to our findings our case report does not seem to belong to any of the above described corneal dystrophies both on account of the appearance and distribution of the deposits.On the basis of our findings we suggest that the classification of these dystrophies should be revised. The diagnosis of pre-Descemet's dystrophies should be limited to those dystrophies where CM rules out the involvement of the anterior and mid-stroma, whereas those with an involvement of the anterior and mid stroma, should be classified differently.This CM based classification, could be very important for future genetic studies on corneal dystrophies. Clearly, further longitudinal studies on a large number of patients should be performed in order to rule out the possibility that these dystrophies are not evolving pictures of a phenotypic variation of a unique dystrophy, as happened in the so-called Avellino dystrophy case .Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the informed consent is available for review by the Editor-in-Chief of this journal.The authors declare that they have no competing interests.LM has been involved in drafting the manuscript and has given final approval of the version to be published BM. has been involved in drafting the manuscript and has given final approval of the version to be published. BE has made substantial contributions to conception and design, acquisition of data and has given final approval of the version to be published.RN has made substantial contributions to conception and design, acquisition of data and has given final approval of the version to be published


Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers.The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci (1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions.The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available. Sorghum bicolor L.), a major staple food and fodder crop, is among the world's most important cereals, typically ranking fifth globally in terms of annual tonnage [Sorghum . Mole tonnage  fertilit tonnage , ergot r tonnage , midge r tonnage  and phot tonnage ,11.. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the existing genetic linkage maps generated through other marker technologies. Additionally, the majority of sorghum genetic linkage maps published to date are based on crosses wider than most crosses routinely made in sorghum breeding programs. However, for application in molecular breeding strategies, genetic linkage maps based on wide crosses are often of limited utility, as they are not representative of the genome organisation and gene function of the cultivated gene pool [Genetic linkage maps are an essential prerequisite for studying the inheritance of both qualitative and quantitative traits, to develop markers for molecular breeding, for map-based gene cloning and for comparative genomic studies. Molecular breeding is more effective if the molecular map is densely populated with markers, in order to provide more choice in the quality and type of marker and to increase the probability of polymorphic markers in important chromosomal intervals. Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade -28. The ene pool . The conHere, we report on the comparison of the genetic linkage maps obtained from six independent component maps and on the integration of the component maps into a single consensus linkage map of sorghum. One of the component maps used, based on BTx623/IS3620C, developed at Texas A&M University and USDA-ARS scientists , is a reThe parental genotypes of the six component mapping populations varied in their level of polymorphism per cross Table , with thThe component maps constructed using the MultiPoint software contained between 117 (S6) and 807 (CIRAD) loci and between 88 (S5) and 183 (CIRAD) lines Tables . ClusterA total of 498 markers (384 of which were DArTs) were in common, i.e. they were mapped in at least two mapping populations. A total of 1557 markers (816 of which were DArTs) were unique to a particular mapping population, while seven DArT loci were mapped in five or more mapping populations. The order of those markers that segregated in more than one population was highly consistent between the six individual mapping data sets. Fig. As observed previously , markersThe sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci  overall but one of the lowest percentages of DArT markers (49.7%)  to 118.5 cM (SBI-05) Fig. . The 'sPThe approximate locations of the pericentromeric regions of heterochromatin were identified Fig. , based oS. propinquum map consisting of 2512 loci spanning 1059.2 cM [The final consensus map comprised 2029 loci, spanning 1603.5 cM, following the integration of 6 individual maps derived from 6 distinct RIL mapping populations. It has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. Only two other published sorghum genetic linkage maps are of a comparable marker density; the BTx623/IS3620C map consisting of 2926 loci spanning 1713 cM  and the The overall consensus map marker order was in good agreement across the individual maps. Locally, the consensus map resolution was slightly compromised by occasional inconsistencies in groups of markers, commonly covering about 1–6 cM, but also swaps of individual markers over even longer distances. The majority of the 77 observed marker order inconsistencies involved closely-spaced markers. Inversion is a common feature of closely spaced markers and this phenomenon has been observed previously in sorghum when aligning different sorghum maps ,30. Thesde novo from an integrated set of segregation data [Differences of local recombination frequencies (map length) between populations can also effect marker ordering between maps, and the importance of similar recombination frequencies across individual maps when constructing a consensus map has previously been noted . A diffeion data , at leasThe non-random distribution of markers across the consensus map, due to both clusters and gaps of markers across chromosomes, is a feature that has also been observed in previous sorghum maps. Figure In addition to the uneven distribution of recombination events along chromosomes and the potential for the confounding effects of marker redundancy, non-random marker distribution can also be due to the preferential survey of DNA polymorphism that is unevenly distributed along chromosomes. In particular, areas of low marker density may correspond to regions of similar ancestry or identity by descent in the germplasm included in the initial diversity representation for the development of the sorghum DArT markers . In the 2 population structures [Approximately 75% of the consensus map (524 markers spanning 1495 cM) was associated with markers which had skewed segregation in one or more of the six component maps. However, only 407 (19.8% of the markers on the consensus map) of the 524 skewed markers were linked by less than 5 cM to other markers showing distortion. The 117 markers with skewed segregation that were linked by at least 5 cM to markers that weren't distorted could reflect residual levels of heterozygosity in the lines (when scored with dominant markers), due to either natural or artificial selection, sampling bias due to lower numbers of markers in these regions or mis-scoring of the markers. Skewed segregation was observed for both DArT and non-DArT markers; no one marker type showed a particular tendency for skewness. Marked differences were observed, however, for the distribution of markers with skewed segregation across chromosomes, although there was some similarity between the component maps, e.g. the short arm of SBI-01 showed skewed marker segregation in four of the six maps . Highly significant deviation from the expected 1:1 segregation ratio on SBI-01 towards the BTx623 allele was also observed by , which aructures , due to Of the 1997 markers included in the DArT consensus map, 35 mapped to different chromosomes in the component maps. The frequency of multicopy markers detected in this study (1.8%) is much lower than observed by , who fou and probe sequence information for a subset of RFLP markers with the prefixes bcd, bnl, cdo, csu, psb, RG, rz and umc  included on the consensus map already provides immediate opportunities to anchor the presented consensus map to the physical map, hence faciliating sequence mapping of known genes from other species, taking advantage of known syntenic relationships between sorghum, rice, maize and other grasses [) and bin-mapped on the maize genome ; data presented in Additional File ) in the 265,271 bp euchromatic region between the two RFLP markers rz630 and umc90 on the sorghum genome (SBI-01) were made between rice and sorghum. BLAST similarity between the sorghum predicted genes and the rice sequence, requiring hits with E ≤ 1e-10 based on BLASTn, are detailed in Additional File The DArT consensus map presented in this paper will help link information on sorghum diversity and QTLs to the sorghum physical map and to the sorghum genome sequence. The availability of the primer sequence information for the majority of SSRs  grasses ,46, in aAn additional use of the presented DArT consensus map is in whole genome profiling-assisted breeding. The marker density on the consensus map is sufficient to provide a better choice of markers for specific breeding populations to ensure adequate polymorphic marker coverage in regions of interest. Further, the marker density on the consensus map is suitable for whole genome pedigree analysis, and calculating identity-by-descent through generations. The consensus map provides a large number of markers along the length of the chromosome that can be used to genotype individuals for detecting recombinants, fixing loci, restoring a recurrent genetic background, or assembling complex genotypes in complex crosses. The co-location of a range of marker types  on the consensus map will enable sorghum breeders to quickly identify target loci through whole-genome DArT scans and then select markers of interest from the same region for marker-assisted selection.The integration of six distinct genetic maps into a consensus map has made it possible to obtain a general order and distances for a greater number of markers, and to obtain more complete coverage of the sorghum genome. The consensus map presented here is a good estimation of the marker position from the six component maps. The exact fine marker order may differ slightly in other populations, and users should be prepared to establish the order for closely linked markers in their mapping and breeding populations. The obtained consensus map can be used as a reference map to develop genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources.A total of six component mapping populations were used to integrate over 2000 unique loci, including 1182 unique DArT markers, into a single consensus map , following the methodology detailed in [Several sources of markers, including DArTs, RFLPs and SSRs, mapped in the individual component maps were used to prepare the sorghum consensus map. Segregation data from a total of 331 unique SSRs/STSs  aailed in . The CIRailed in  were excailed in . Marker ailed in , howeverDArT marker names are standardised and automatically generated by a DArT-specific Laboratory Information Management System . Different laboratories used slightly different names for the same SSR and RFLP markers. Non-DArT marker names were therefore curated to the extent required to create an unambiguous nomenclature.s value of between 0.1 to 0.40 was used to initially group the markers into a minimum of ten linkage groups. Multipoint linkage analysis of loci within each LG was then performed and marker order was further verified through re-sampling for quality control via jack-knifing [The component genetic linkage maps of the six sorghum mapping populations were constructed using MultiPoint software . The RIL-knifing . Markers-knifing , SSR and-knifing  markers -knifing . The Kos-knifing  mapping -knifing . The obsThe distance measurement of interval variables between 2 individuals, proposed originally by  and modiik is the length (cM) of the kth shared marker interval on the ith chromosome of map A, and Bik is the length (cM) of the kth shared marker interval on the ith chromosome of map B. The Σ|Aik - Bik| is the absolute value of the length difference of each shared marker interval on the ith chromosome between maps A and B, and Ai + Bi is an additive value of all shared intervals for the ith chromosome of maps A and B which is used to normalise the difference value, Σ|Aik - Bik| [where Ak - Bik| .The locus positions from the six component maps were merged to build a 'synthetic' map using basic Microsoft Excel functionalities. This strategy differs from the alternative approach of constructing a consensus map using the segregation data from different mapping populations to compute the optimum order of loci . The TAMESM carried out the mapping analyses and drafted the manuscript; JFR was involved in the development of the CIRAD population, contributed to the mapping analyses, and editing of the manuscript; SB was involved in the generation of DArT data for the CIRAD mapping population and participated in the mapping analysis; PEK was involved in the development of the TAMU-ARS mapping population, generation of non-DArT marker data for the TAMU-ARS population and editing of the manuscript; RRK was also involved in the development of the TAMU-ARS mapping population, generation of non-DArT marker data for the TAMU-ARS population and editing of the manuscript; AK supervised the generation of DArT data for all mapping populations, participated in the study's design and helped to draft the manuscript; PW contributed to quality assessment of sorghum clones and data generated for this study and editing of the manuscript; LX was involved in the generation of DArT data for all mapping populations; KH was involved in the generation of marker data for the DPI&F mapping populations; DRJ conceived of the study, participated in its design and coordination, mapping analyses and helped to draft the manuscript.Locus positions in the component maps. Excel spreadsheet containing a list of all component map loci, the chromosome and position of each locus.Click here for fileMulticopy marker summary. Excel spreadsheet containing details of the total numbers of multicopy markers identified per chromosome on the sorghum DArT consensus mapClick here for fileLocus positions in the consensus map. Excel spreadsheet containing a list of all consensus map loci and their features; data include the chromosome and position of each locus, details of which component map each locus was mapped in, and multicopy marker details.Click here for fileComparison of 42 RFLP markers across sorghum, rice and maize. Excel spreadsheet containing a list of 42 RFLP markers, and their physical location on both the sorghum and rice genome and chromosome and bin identity in maize.Click here for fileSorghum/rice gene microcolinearity across a 0.26 MB region of SBI-01 between rz630 and umc90. Excel spreadsheet containing a list of 15 predicted sorghum genes on SBI-01, between rz630 and umc90, their physical location and predicted function, and the homologous rice gene ID, physical location and predicted function of the best hit based on BLASTn and the total number of hits at E = 1e-10.Click here for file


The Guyon's canal syndrome is a well known clinical entity and may have significant impact on patient's quality of life. We report a case of 43-year-old male who presented with complaints of pain and numbness in right hand and difficulty in writing for past one month. On imaging diagnosis of Guyon's canal syndrome because of tortuous ulnar artery was made with additional findings of DeQuervain's stenosing tenosynovitis and dorsal intercalated segmental instability syndrome with ligamentous injury and subsequently these were confirmed on surgery.Although it is a rare syndrome, early diagnosis and treatment prevents permanent neurological deficits and improve patient's quality of life. The Guyon's canal is a fibro-osseous tunnel situated along the anteromedial aspect of wrist joint. It contains the ulnar nerve, ulnar artery and veins . Its maiIt can be caused by a number of causes like trauma , lipoma Rare causes due to arterial compression include posttraumatic pseudoaneurysm, true aneurysm of distal ulnar artery or tortuous ulnar artery ,7.Only two case reports of tortuous ulnar artery leading to compression of ulnar nerve in Guyon's canal yet have been published in the literature while no one associated with other incidental findings as seen in our case.A 43-year-old male Asian, Pakistani presented in our outpatient department with complaints of pain and numbness in right hand and difficulty in writing, for past one month. On further questioning, there was a remote history of fall while playing hockey. On examination, the bulk and tone of right hand was normal, however, the power was decreased to 3/5.Subsequently, an x-ray of right hand was ordered which was normal. As the signs and symptoms of the patient were not improving on previous medications, MRI of right hand was advised, which revealed tortuous distal ulnar artery just proximal to the wrist joint causing compression of ulnar nerve within Guyon's canal Figure . AbnormaIn addition, there was inflammation of first extensor compartment with thickening of abductor pollicis longus and extensor pollicis brevis, suggestive of De Quervain's stenosing tenosynovitis. The tendon sheath of extensor carpi ulnaris was also inflamed. There was dorsal tilt of lunate bone with angle measuring greater than 30 degrees with associated mild dorsal placement of capitate bone in relation to the radius. Mild increased signal intensity seen within the short radiolunate ligament and deltoid/arcuate ligament with also evidence of laxity seen. Considering these findings, the diagnosis of dorsal intercalated segmental instability syndrome (DISI) with ligamentous injuries were also made Figure .st metacarpal bone.The patient then underwent right ulnar nerve decompression, excision of torn ligaments with arthrodesis and closing wedge osteotomy of 1He was then followed as an outpatient and is doing well, except for mild loss of sensation over the dorsal aspect of skin of right thumb. He regained his power 5/5 in his right hand, with the exception of right little finger, power of which remains 4/5.The medial cord of brachial plexus gives origin to ulnar nerve C8 and T1). The ulnar nerve descends along the axillary and brachial arteries medially and downward up to the mid shaft of humerus. The nerve then courses dorsally, penetrates the medial intermuscular septum and descends along medial head of triceps muscle. It then enters into the cubital tunnel, at the medial condyle of humerus [ and T1. Below the elbow, it descends between two heads of flexor carpi ulnaris muscle and courses distally between the flexor carpi ulnaris and the flexor digitorum profundus muscles. At wrist, the ulnar nerve runs through the Guyon's canal.The neuropathies produced by entrapment of the ulnar nerve include cubital tunnel syndrome and Guyon's canal syndrome. It results from a lesion of the ulnar nerve at the level of the Guyon canal  .The possible causes of ulnar nerve lesions at the Guyon canal include ganglia, lipomas, and other cysts; anomalies of ligaments or muscles; ulnar artery aneurysms; fractures of the radius, pisiform bone, hook of the hamate, or other wrist bones; and chronic repetitive trauma -7.The MRI is the best imaging modality to diagnose and classify these lesions, especially the T1 weighted sequences. On T1-weighted images, the nerve can be seen as a round or ovoid structure with surrounding small amount of fat. The ulnar nerve bifurcation is usual well visualized and can be followed distally .The size and signal intensity of ulnar nerve is an important marker and should be assessed in patients suspected to have ulnar nerve lesions in the Guyon's canal. MR imaging may help to exclude mass lesion and can also demonstrate compression by an anomalous or accessory muscle or fibrous band . In addiThe DeQuervain's tenosynovitis is more common in females and presents with pain and swelling in the first dorsal extensor sheath. The female gender, greater than 40 years of age and black race are the predisposing factors . It is uOn MRI, the most reliable sign to diagnose DeQuervain's synovitis is increased thickness of extensor pollicis brevis and abductor pollicis longus tendons with peritendinous edema. Surrounding subcutaneous edema and increased intratendinous signals may support the diagnosis .Recent advances in MR imaging showed that DISI and VISI can be diagnosed on sagittal images, as on plain x-ray film malposition of wrist can mimic these in certain cases. The capitolunate, radiolunate and scapholunate angles are used to diagnose it .In literature, there are only two cases reported yet and none in any of the radiology journal. In the case, reported by Segal et al . patientIn our case, both sensory and motor symptoms were the presenting complaint and after decompression patient still has some sensory and motor deficits.The tortuous peripheral arteries are very rare causes of peripheral nerve entrapment syndromes. The MRI is an excellent tool of diagnosis in such cases and also delineates other important associated findings. The early diagnosis and subsequent treatment prevent permanent deficits and improve patient's quality of life.The authors declare that they have no competing interests.MZ: participated in literature search, manuscript writing and review of document.FA: was the radiologist involved in diagnosis, contributed in literature search and manuscript review.DK: participated in literature search, reviewing the document and coordination with the patient.QSBK: participated in manuscript review, collecting imaging and surgical data.MNA: was senior radiologist involved in the diagnosis.All authors read the paper and approved the final manuscript.Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.


Throughout the period of one year, approximately 50% of recreational runners will sustain an injury that disrupts their training regimen. Foot orthoses have been shown to be clinically effective in the prevention and treatment of several running-related conditions, yet the physical effect of this intervention during running remains poorly understood. The aim of this literature review was therefore to evaluate the effect of foot orthoses on lower extremity forces and pressure (kinetics) during running.A systematic search of electronic databases including Medline (1966-present), CINAHL, SportDiscus, and The Cochrane Library occurred on 7 May 2008. Eligible articles were selected according to pre-determined criteria. Methodological quality was evaluated by use of the Quality Index as described by Downs & Black, followed by critical analysis according to outcome variables.The most widely reported kinetic outcomes were loading rate and impact force, however the effect of foot orthoses on these variables remains unclear. In contrast, current evidence suggests that a reduction in the rearfoot inversion moment is the most consistent kinetic effect of foot orthoses during running.The findings of this review demonstrate systematic effects that may inform the direction of future research, as further evidence is required to define the mechanism of action of foot orthoses during running. Continuation of research in this field will enable targeting of design parameters towards biomechanical variables that are supported by evidence, and may lead to advancements in clinical efficacy. Throughout the period of one year, approximately 50% of recreational runners will sustain an injury that disrupts their training regimen ,2. IntriPatellofemoral pain syndrome is reported to be the most commonly encountered running-related injury ,31,32, aThe clinical effectiveness of foot orthoses has been demonstrated in clinical trials for either the prevention -37 or trSeveral literature reviews have evaluated the effects of foot orthoses on lower extremity position and movement (kinematics) without a systematic search strategy -47. ThesA systematic search of electronic databases including Medline (1966-present), CINAHL, SportDiscus, and The Cochrane Library occurred on 7 May 2008. The search terms foot orthotic$, foot orthos$s and insole$ were used in conjunction with the terms kinetic$, biomechanic$, running, and force$ in various combinations  studies were also excluded, as they measured biophysical variables that are distinct from kinetics. Furthermore, in accordance with definitions contained in the Australian Podiatry Council's 'Guidelines on Orthotic Therapy' , studiesAll articles accepted for review underwent methodological assessment to evaluate the research quality. This process occurred in accordance with the Quality Index described by Downs & Black , in whicFollowing methodological assessment, articles were grouped and discussed according to kinetic outcome variables. However the evaluation was unable to be conducted as a meta-analysis, due to heterogenicity in experimental designs.The search process generated a total 1801 citations for initial screening Table . All incThe mean Quality Index Score for the articles was 64 % (SD = 10.5), demonstrating limited overall quality Table . The majDespite the limitations described above, all studies provided adequate descriptions of outcome variables and orthosis design parameters, and reported findings with estimates of random variability. Furthermore, all used standardised footwear and running speeds during experimental conditions.The vertical loading rate is the vertical impact force quantified with reference to time, and is normally reported as either the maximum or average in Newtons per second (N/s) . Five arA study of 8 military recruits  found a In addition to investigating loading rates, four of the studies above measured the peak impact force magnitude -55. ThisComparison of the foot orthoses used in these trials fails to demonstrate correlations with orthosis design, as conflicting data was collected by use of orthoses with similar features Table . FurtherAs the trials described above have similar methodological quality and research designs, current evidence suggests that foot orthoses have non-systematic effects on the loading rate and peak impact force during running.A resultant joint moment is the rotational force generated at the joint axis by a force applied to a biomechanical lever-arm, and is calculated by multiplying the applied force (Newtons) by the length (metres) of the lever-arm by which it acts . Three aAll three trials investigating the effect of foot orthoses on rearfoot inversion moments demonstrate a consistent trend. Two of these trials ,57 reporThe findings of these studies are consistent despite differences in subject foot morphology, with two trials only including healthy subjects ,56, and These trials suggest that foot orthoses have a systematic effect on the rearfoot inversion moment of runners with both normal and excessively pronated foot posture, and suggest a linear relationship between degree of rearfoot posting and effect magnitude. Furthermore, the findings of these trials contribute significantly to current understanding of the mechanism of action of foot orthoses during running.Plantar pressure may be described as the quantity of force acting over the plantar surface area of the foot, and is normally reported as Newtons per centimetre squared (N/cm2) . Two artA trial of 22 runners with recurring lower limb injury found medially-posted foot orthoses to have a consistent effect on plantar pressure during running . This trIn addition to variations in orthosis design between these two trials Table , there aThe findings of these trials suggest that plantar pressure beneath the lateral foot may be increased while running in foot orthoses with both medial and lateral posting designs, and that detection of effects may depend on the interface at which pressure is measured. Current evidence therefore suggests that foot orthoses have a variable effect on medio-lateral plantar pressure distribution during running, and that further research into this parameter is required.In addition to reporting the magnitude of peak impact force, one trial  measuredThe force/time integral is also known by the term impulse, and is calculated as the area below the plantar force/time curve . One triThe studies included in this review are of low methodological quality, with the most confounding error being the lack of randomisation to the order of conditions. The most widely reported kinetic outcomes were loading rate and impact force, however the effect of foot orthoses on these variables remains unclear. In contrast, current evidence suggests that a reduction in the rearfoot inversion moment is the most consistent kinetic effect of foot orthoses during running.This systematic review has evaluated the evidence surrounding the effects of foot orthoses on lower extremity kinetics during running. The findings demonstrate systematic effects that may inform the direction of future research in this field, as further evidence is required to define the mechanism of action of foot orthoses during running. Continuation of research in this field will enable targeting of design parameters towards biomechanical variables that are supported by evidence, and may lead to advancements in clinical efficacy.The authors declare that they have no competing interests.AM conceived the study design, conducted the systematic review, interpreted the findings and drafted the manuscript. CP reviewed the manuscript and provided academic support throughout.AM is an Honours student within the Department of Podiatry, La Trobe University. CP is a Senior Lecturer within the Department of Podiatry, La Trobe University.