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The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community.

The Kalkarindji Large Igneous Province (LIP) is a Middle Cambrian (511 Ma) continental flood basalt (CFB) province located in northern and central–west Australia that has been linked to an extinction event at the Early–Middle Cambrian boundary. The extent of this LIP has been estimated at about 2·1 x 106 km2, with exposures in Western Australia, Northern Territory, Queensland and South Australia. Major and trace element datasets reveal geochemical characteristics typical for continental flood basalts (CFBs) including: tholeiitic affinity; an enrichment in incompatible elements, in particular, large-ion lithophile elements (LILE); enrichment of light rare earth elements (LREE) compared to heavy rare earth elements (HREE) relative to N-MORB; negative Nb and Ta anomalies in normalized extended element patterns. Here we present the first comprehensive geochemical investigation of the Kalkarindji CFB province. The Kalkarindji CFBs are geochemically homogeneous, low-Ti basaltic andesites, with a nearly complete lack of basalts as defined using a total-alkalis vs silica diagram. All of the rocks analysed for Sr, Nd, Pb isotopic ratios display enriched initial (t = 511 Ma) isotopic compositions (143Nd/144Ni = 0·511928–0·511981; 87Sr/86Sri = 0·70917–0·71029; 206Pb/204Pbi = 18·105–18·843; 207Pb/204Pbi = 15·726–15·805; 208Pb/204Pbi = 38·374–39·208). Crustal assimilation models are interpreted to suggest that the geochemical characteristics, as well as the homogenous composition across the entire province, cannot be explained by continental crust contamination. Therefore, the enriched isotopic ratios (particularly the extremely high 207Pb/204Pbi and elevated 208Pb/204Pbi for moderate 206Pb/204Pbi), coupled with relative depletions in Nb and Ta concentrations, indicate the involvement of an ancient enriched lithospheric-like component in the genesis of the Kalkarindji CFB. We propose a model in which the source region was affected by an enrichment event at around 2·5 Ga (possibl

A single limestone sample from the Early Triassic (late Dienerian) of the Salt Range in Pakistan has yielded numerous small gastropods (smaller 2 mm), few bivalves and abundant ammonoids. The limestone is interpreted as a tempestite. Many of the gastropods are extremely well-preserved including protoconch preservation and micro-ornaments. Five species of gastropods are present: (1) isolated larval shells representing a neritimorph taxon of the family Trachyspiridae, (2) early juvenile and larval specimens of the caenogastropod Strobeus pakistanensis, (3) the new caenogastropod species Coelostylina hydrobiformis Nützel & Ware, (4) the new heterobranch genus and species Eographis microlineata Nützel & Ware representing the earliest occurrence of the extant family Hyalogyrinidae (Valvatoidea), (5) the heterobranch Sinuarbullina sp., a genus which originates in the Early Triassic and has also been reported from China, Spitsbergen and the US. Three genera (trachyspirid, Strobeus and Coelostylina) represent survivors from the end-Permian mass extinction whereas Eographis and Sinuarbullina have their earliest known occurrence in the Early Triassic. Eographis is the first Early Triassic genus for which coaxial larval heterostrophy is shown. Together with the Devonian genus Palaeocarboninia and the Carboniferous genus Heteroaclisina, it witnesses a high age of Ectobranchia (living families Hyalogyrinidae, Valvatidae, Cornirostridae and Xylodisculidae). This supports the assumption that this group is the first extant offshoot of the Heterobranchia. The studied assemblage is strongly dominated by Strobeus pakistanensis. The small size of the gastropods reflects their ontogenetic stage (early juvenile and larval shells) as well as a small adult size in some of the species. Most of the present gastropods had planktotrophic larval development providing further evidence against the hypothesis that the end-Permian mass extinction event selected against larval planktotrophy. Failure

The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germ-plasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.

IMPORTANCE: Paracentral acute middle maculopathy (PAMM) diagnosed by spectral domain optical coherence tomography (SD-OCT) in patients with poor visual outcome post cataract surgery. BACKGROUND: Case series of severe vision loss due to PAMM after cataract surgery. DESIGN: Retrospective case series. PARTICIPANTS: Cases from five surgical centres in Victoria, Australia. METHODS: Retrospective analysis of cases with unexplained 'patch-off' vision loss post cataract surgery. All patients in our cohort had PAMM and presumed diagnosis of central or transient retinal artery occlusion. MAIN OUTCOME MEASURES: A review of the patient histories focusing on pre-operative ocular and systemic vascular risk factors, anaesthetic and operative factors. RESULTS: Ten cases were included. All patients had 6/72 Snellen visual acuity or worse noted on day one post surgery. Three patients had features of central retinal artery occlusion consisting of retinal pallor with a 'cherry red' macula but absent relative afferent pupillary defect. Seven had no features of retinal pallor or attenuation of retinal arterioles. On SD-OCT, all eyes had evident PAMM. Six patients had a history of cardiovascular disease or blood dyscrasia. CONCLUSIONS AND RELEVANCE: PAMM should be considered in patients with 'patch off' visual loss and absence of other fundal signs. We hypothesise that spasm or transient occlusion of central retinal artery leads to arterial hypoperfusion with subsequent ischaemia or infarction of the retina. Underlying arterial disease may have led to pre-existing hypoperfusion that may have been further compromised by raised intraocular pressure during the procedure itself or via raised orbital pressure from the anaesthesia.

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.

Hypotheses about the Permian–Triassic floral turnover range from a catastrophic extinction of terrestrial plant communities to a gradual change in floral composition punctuated by intervals indicating dramatic changes in the plant communities. The shallow marine Permian–Triassic succession in the Amb Valley, Salt Range, Pakistan, yields palynological suites together with well-preserved cuticle fragments in a stratigraphically well-constrained succession across the Permian–Triassic boundary. Palynology and cuticle analysis indicate a mixed Glossopteris–Dicroidium flora in the Late Permian. For the first time Dicroidium cuticles are documented from age-constrained Upper Permian deposits on the Indian subcontinent. Close to the Permian–Triassic boundary, several sporomorph taxa disappear. However, more than half of these taxa reappear in the overlying Smithian to Spathian succession. The major floral change occurs towards the Dienerian. From the Permian–Triassic boundary up to the middle Dienerian a gradual increase of lycopod spore abundance and a decrease in pteridosperms and conifers are evident. Synchronously, the generic richness of sporomorphs decreases. The middle Dienerian assemblages resemble the previously described spore spikes observed at the end-Permian (Norway) and in the middle Smithian (Pakistan) and might reflect a similar ecological crisis.

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

Funding coastal protection works in Australia has traditionally been achieved through the allocation of public funds by Local and State government alone or in partnership. When protection works provide a benefit to private landowners, the process for reaching agreement to fund such projects is the source of significant tension between State and Local Governments and between foreshore property owners who directly benefit from the project and other rate payers.For Local Government the relatively large cost of coastal protection projects can introduce political risks of accusations of bias towards foreshore property owners by other ratepayers, and places strain on available capital. State Governments are equally reluctant to provide funding due to the perceived risk that it may establish a precedent that could become unmanageable across large stretches of coastline. This tension between parties delays and adds planning costs, compounding the already contested nature of many coastal protection projects.This research is part of an endeavour to understand the potential role of non-government finance for coastal protection projects in Australia. Through the development of a theoretical framework, which includes public goods theory, public private partnerships and ecosystem services, this paper compares a series of case studies within Australia where non-government financing has been used to fund coastal protection works.

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination., Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination., Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

Latest Permian to the Middle Triassic mixed siliciclastic–carbonate shelf deposits of the northern Gondwana margin have been studied in four sections (Nammal, Chhidru, Chitta–Landu, and Narmia) in the Salt Range and Surghar Range of Pakistan. Sedimentological and palynofacies patterns combined with a high resolution ammonoid based age control have been used to assess environmental changes such as sea-level change, distance from the shore, and oxygenation conditions of the sections in the aftermath of the end-Permian mass extinction. The base and the top of the Early Triassic are marked by second order sequence boundaries (SRT1, SRT8). Within the Early Triassic two third order sequence boundaries could be delineated by means of palynofacies analysis and sedimentology, one near the Dienerian–Smithian (SRT2) and the second one near the Smithian–Spathian boundary (SRT5). The extinction event at the Smithian–Spathian boundary seems to be closely associated to the latter globally recorded sea-level low stand. Five additional sequences of undetermined order (SRT3, SRT 4, SRT5/1, SRT6, and SRT7) are reflected in the sedimentological record of the studied sections. The observed changes in the composition of the particulate organic matter (POM) indicate a general shallowing upward trend, which is modulated by smaller transgressive–regressive cycles supporting the sedimentologically defined sequences. The POM is mostly dominated by terrestrial phytoclasts and sporomorphs. The strongest marine signal is reflected by increased abundance of amorphous organic matter (AOM) in the lower part of the Ceratite Marls at Nammal (late Dienerian) and Chhidru (earliest Smithian) and the Lower Ceratite Limestone at Chitta–Landu (late Dienerian). AOM of marine origin is characteristic for deeper, distal basinal settings and is preferentially preserved under dysoxic and anoxic conditions, indicating reduced oxygen conditions during these intervals. Up-section transgressive events are reflected

BACKGROUND: Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR) index can be generated to map repetitive regions in genomic sequences. RESULTS: We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC) clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. CONCLUSION: An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences) regions in uncharacterised genomic sequences. The restriction that a particular MDR index can not be us

Members of the worldwide sorghum (Sorghum spp.) community, including private sector and international scientists as well as community representatives from closely related crops such as sugarcane (Saccharum spp.) and maize (Zea mays), met in St. Louis, Missouri, on November 9, 2004, to lay the groundwork for future advances in sorghum genomics and, in particular, to coordinate plans for sequencing of the sorghum genome. Key developments that made this workshop timely included advances in knowledge of the sorghum genome that provide for the development of a genetically anchored physical map to guide sequence assembly and annotation, the growing role of the sorghum genome as a nucleation point for comparative genomics of diverse tropical grasses including many leading crops, and the need for dramatically increased sorghum production to sustain human populations in many regions where its inherent abiotic stress tolerance makes it an essential staple. This report reviews current knowledge of the sorghum genome, a community-endorsed schema for integrating this knowledge into a finished sequence, and early plans for translating the sequence into sustained advances to benefit a worldwide group of stakeholders.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1969., Bibliography: leaves 36-37., by Ware D. Fuller., M.S.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1969., Bibliography: leaves 36-37., by Ware D. Fuller., M.S.

Members of the worldwide sorghum (Sorghum spp.) community, including private sector and international scientists as well as community representatives from closely related crops such as sugarcane (Saccharum spp.) and maize (Zea mays), met in St. Louis, Missouri, on November 9, 2004, to lay the groundwork for future advances in sorghum genomics and, in particular, to coordinate plans for sequencing of the sorghum genome. Key developments that made this workshop timely included advances in knowledge of the sorghum genome that provide for the development of a genetically anchored physical map to guide sequence assembly and annotation, the growing role of the sorghum genome as a nucleation point for comparative genomics of diverse tropical grasses including many leading crops, and the need for dramatically increased sorghum production to sustain human populations in many regions where its inherent abiotic stress tolerance makes it an essential staple. This report reviews current knowledge of the sorghum genome, a community-endorsed schema for integrating this knowledge into a finished sequence, and early plans for translating the sequence into sustained advances to benefit a worldwide group of stakeholders.

We have developed a mathematical model of the human cardiopulmonary system that is able to simulate the normal functions of the cardiovascular and pulmonary systems, as well as their coupled interactions. Included in the model are descriptions of atrial and ventricular mechanics, the hemodynamics of the systemic and pulmonic circulations, baroreflex control of arterial pressure, airway and lung mechanics, as well as, gas transport at alveolar-capillary membrane. With the suitable parameter set, the integrated cardiopulmonary model yielded pressure, volume and flow waveforms that agree well with published data. In addition, The model demonstrated stability under large amplitude perturbations of the physiological variables, such as Valsalva Maneuver., Proceedings: 23rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 25-28 Oct 2001, Istanbul, Turkey. See also ADM001351 for entire conference on cd-rom.

The AN/ASQ-1 magnetic airborne detection equipment is discussed herein. The equipment is used to locate submerged submarines by detecting the small local changes produced by the submarines in the magnetic fields of the earth. The AN/ASQ-1 was designed on the basis of experience gained in the construction, testing, and operation of a substantial number of the previous models (MAD Mark IV-B2). The new equipment is smaller in size, lighter in weight, and comprises fewer individual units. Also all controls are on one unit, making it more convenient. information pertinent to performance characteristics of the detector system and the stabilizer system is contained in graphic form, and photographs show the location of units In the various types of airplanes.

The purpose of this study was to solve the design and development problems critical to the construction of a spectrally scanning CO2 gas laser for chemical agent detection for airfield defense. The spectrally scanning CO2 gas laser is an active spectrometer that samples the infrared transmission of the atmosphere over a one to ten mile path at several wavelengths in order to detect the presence of chemical agents in that path. A high-speed three-to-eight wavelength computer program was generated. Computer runs were made comparing the sensitivity of the system to various agent interferent combinations for four and more wavelengths. A four wavelengths system was selected to detect the specified agents to the required sensitivity and reject the specified interferents. A four-wavelength scanner and modulator was designed and constructed to generate in rapid sequence the four wavelengths selected under the spectral tuning techniques investigation. Studies were carried out of the cavity optical configuration to optimize stability, higher order mode rejection, diffraction losses, Fabry-Perot interference, gain, and power output while maintaining an effective cavity path length exceeding twenty feet. A ten-pass folded system was designed and fabricated that met the requirements needed to obtain the specified performance. Power output and gain measurements were made on two separate, sealed, isotopic CO2 laser systems.