Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

Background: Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. Results: The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. Conclusions: It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.

Long-term fluid circulation in extensional faults in the central Catalan Coastal Ranges: P-T constraints from neoformed chlorite and K-white mica

The neoformation of chlorite and K-white mica in fault rocks from two main faults of the central Catalan Coastal Ranges, the Vallès and the Hospital faults, has allowed us to constrain the P–T conditions during fault evolution using thermodynamic modeling. Crystallization of M1 and M2 muscovite and microcline occured as result of deuteric alteration during the exhumation of the pluton (290 °C > T > 370 °C) in the Permian. After that, three tectonic events have been distinguished. The first tectonic event, attributed to the Mesozoic rifting, is characterized by precipitation of M3 and M4 phengite together with chlorite and calcite C1 at temperatures between 190 and 310 °C. The second tectonic event attributed to the Paleogene compression has only been identified in the Hospital fault with precipitation of low-temperature calcite C2. The shortcut produced during inversion of the Vallès fault was probably the responsible for the lack of neoformed minerals within this fault. Finally, the third tectonic event, which is related to the Neogene extension, is characterized in the Vallès fault by a new generation of chlorite, associated with calcite C4 and laumontite, formed at temperatures between 125 and 190 °C in the absence of K-white mica. Differently, the Hospital fault is characterized by the precipitation of calcite C3 during the syn-rift stage at temperatures around 150 °C and by low-temperature fluids precipitating calcites C5, C6 and PC1 during the post-rift stage. During the two extensional events (Mesozoic and Neogene), faults acted as conduits for hot fluids producing anomalous high geothermal gradients (50 °C/km minimum).

Lithium isotope constraints on crust–mantle interactions and surface processes on Mars

Lithium abundances and isotope compositions are reported for a suite of martian meteorites that span the range of petrological and geochemical types recognized to date for Mars. Samples include twenty-one bulk-rock enriched, intermediate and depleted shergottites, six nakhlites, two chassignites, the orthopyroxenite Allan Hills (ALH) 84001 and the polymict breccia Northwest Africa (NWA) 7034. Shergottites unaffected by terrestrial weathering exhibit a range in δ7Li from 2.1 to 6.2‰, similar to that reported for pristine terrestrial peridotites and unaltered mid-ocean ridge and ocean island basalts. Two chassignites have δ7Li values (4.0‰) intermediate to the shergottite range, and combined, these meteorites provide the most robust current constraints on δ7Li of the martian mantle. The polymict breccia NWA 7034 has the lowest δ7Li (−0.2‰) of all terrestrially unaltered martian meteorites measured to date and may represent an isotopically light surface end-member. The new data for NWA 7034 imply that martian crustal surface materials had both a lighter Li isotope composition and elevated Li abundance compared with their associated mantle. These findings are supported by Li data for olivine-phyric shergotitte NWA 1068, a black glass phase isolated from the Tissint meteorite fall, and some nakhlites, which all show evidence for assimilation of a low-δ7Li crustal component. The range in δ7Li for nakhlites (1.8 to 5.2‰), and co-variations with chlorine abundance, suggests crustal contamination by Cl-rich brines. The differences in Li isotope composition and abundance between the martian mantle and estimated crust are not as large as the fractionations observed for terrestrial continental crust and mantle, suggesting a difference in the styles of alteration and weathering between water-dominated processes on Earth versus possibly Cl–S-rich brines on Mars. Using high-MgO shergottites (>15 wt.% MgO) it is possible to estimate the δ7Li of Bulk Silicate Mars (BSM) to be 4.2 ± 0.9‰ (2σ). This value is at the higher end of estimates for the Bulk Silicate Earth (BSE; 3.5 ± 1.0‰, 2σ), but overlaps within uncertainty.

The Basement of the Deccan Traps and Its Madagascar Connection: Constraints from Xenoliths

Paleogeographic reconstructions of India and Madagascar before their late Cretaceous rifting juxtapose the Antongil Block of Madagascar against the Deccan Traps of India, indicating that the Western Dharwar Craton extends below the Deccan lavas. Some recent studies have suggested that the South Maharashtra Shear Zone along the northern Konkan coast of India limits the northern extent of the Western Dharwar Craton, implying that the craton does not extend below the Deccan Traps, raising a question mark on paleogeographic reconstructions of India and Madagascar. The continuity of the Western Dharwar Craton north of the South Maharashtra Shear Zone below the Deccan Traps—or its lack thereof—is critical for validating tectonic models correlating Madagascar with India. In this study, zircons in tonalitic basement xenoliths hosted in Deccan Trap dykes were dated in situ, using the U-Pb isotope system. The data furnish U-Pb ages that define three populations at 2527 ± 6, 2456 ± 6, and 2379 ± 9 Ma. The 2527 ± 6 Ma ages correspond to the igneous crystallization of the tonalites, whereas the 2456 ± 6 and 2379 ± 9 Ma ages date metamorphic overprints. The results help to establish for the first time that the basement is a part of the Neoarchean granitoid suite of the Western Dharwar Craton, which extends northward up to at least Talvade in central and Kihim beach in the western Deccan. By implication, the South Maharashtra Shear Zone cannot be the northern limit of the Western Dharwar Craton. The granitoids are correlated with the Neoarchean felsic intrusions (2.57–2.49) of the Masaola suite in the Antongil Block of Madagascar, supporting the existence of a Neoarchean Greater Dharwar Craton comprising the Western Dharwar Craton and the Antongil-Masora Block.

A consistent combination of GNSS and SLR with minimum constraints

In this article, the realization of a global terrestrial reference system (TRS) based on a consistent combination of Global Navigation Satellite System (GNSS) and Satellite Laser Ranging (SLR) is studied. Our input data consists of normal equation systems from 17 years (1994– 2010) of homogeneously reprocessed GPS, GLONASS and SLR data. This effort used common state of the art reduction models and the same processing software (Bernese GNSS Software) to ensure the highest consistency when combining GNSS and SLR. Residual surface load deformations are modeled with a spherical harmonic approach. The estimated degree-1 surface load coefficients have a strong annual signal for which the GNSS- and SLR-only solutions show very similar results. A combination including these coefficients reduces systematic uncertainties in comparison to the singletechnique solution. In particular, uncertainties due to solar radiation pressure modeling in the coefficient time series can be reduced up to 50 % in the GNSS+SLR solution compared to the GNSS-only solution. In contrast to the ITRF2008 realization, no local ties are used to combine the different geodetic techniques.We combine the pole coordinates as global ties and apply minimum constraints to define the geodetic datum. We show that a common origin, scale and orientation can be reliably realized from our combination strategy in comparison to the ITRF2008.

The Resource-Constrained Project Scheduling Problem with Work-Content Constraints

For executing the activities of a project, one or several resources are required, which are in general scarce. Many resource-allocation methods assume that the usage of these resources by an activity is constant during execution; in practice, however, the project manager may vary resource usage by individual activities over time within prescribed bounds. This variation gives rise to the project scheduling problem which consists in allocating the scarce resources to the project activities over time such that the project duration is minimized, the total number of resource units allocated equals the prescribed work content of each activity, and precedence and various work-content-related constraints are met.

Irrigation development in Eritrea: potentials and constraints: Proceedings of the workshop of AEAS and SLM Programme Eritrea

Development of irrigation, which is of crucial importance in Eritrea, is perceived by many as the main technique for improving the precarious food security situation in this Sahelian country in the Horn of Africa. The present publication presents the outcome of a nationwide workshop held in 2003, which brought together administrators, scientists, and members of public development agencies and NGOs. These workshop participants presented experiences, lessons learnt, and ideas about how to move forward in relation to development of irrigation in Eritrea. Specifically, the publication deals with the following broad themes, lessons learnt, and experiences in Eritrea: · spate irrigation systems and measurement of performance, as well as experience with modernisation of spate irrigation systems in Eritrea · small-scale irrigation systems and their potentials and pitfalls, including development of low-cost micro irrigation · climate and irrigation, including rainfall forecasts · socio-economic aspects of irrigation, including gender questions, institutional requirements, and irrigation and livelihoods The publication contains an extensive summary in the Tigrinya language, in order to facilitate access to the key findings by local non-English-speaking stakeholders in irrigation development.

Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls

Here we discuss proteomic analyses of whole cell preparations of the mosquito stages of malaria parasite development (i.e. gametocytes, microgamete, ookinete, oocyst and sporozoite) of Plasmodium berghei. We also include critiques of the proteomes of two cell fractions from the purified ookinete, namely the micronemes and cell surface. Whereas we summarise key biological interpretations of the data, we also try to identify key methodological constraints we have met, only some of which we were able to resolve. Recognising the need to translate the potential of current genome sequencing into functional understanding, we report our efforts to develop more powerful combinations of methods for the in silico prediction of protein function and location. We have applied this analysis to the proteome of the male gamete, a cell whose very simple structural organisation facilitated interpretation of data. Some of the in silico predictions made have now been supported by ongoing protein tagging and genetic knockout studies. We hope this discussion may assist future studies.

Whole-Genome Sequencing of a Canine Family Trio Reveals a FAM83G Variant Associated with Hereditary Footpad Hyperkeratosis

Over 250 Mendelian traits and disorders, caused by rare alleles have been mapped in the canine genome. Although each disease is rare in the dog as a species, they are collectively common and have major impact on canine health. With SNP-based genotyping arrays, genome-wide association studies (GWAS) have proven to be a powerful method to map the genomic region of interest when 10-20 cases and 10-20 controls are available. However, to identify the genetic variant in associated regions, fine-mapping and targeted re-sequencing is required. Here we present a new approach using whole-genome sequencing (WGS) of a family trio without prior GWAS. As a proof-of-concept, we chose an autosomal recessive disease known as hereditary footpad hyperkeratosis (HFH) in Kromfohrl änder dogs. To our knowledge, this is the first time this family trio WGS-approach, has successfully been used to identify a genetic variant that perfectly segregates with a canine disorder. The sequencing of three Kromfohrl änder dogs from a family trio (an affected offspring and both its healthy parents) resulted in an average genome coverage of 9.2X per individual. After applying stringent filtering criteria for candidate causative coding variants, 527 single nucleotide variants (SNVs) and 15 indels were found to be homozygous in the affected offspring and heterozygous in the parents. Using the computer software packages ANNOVAR and SIFT to functionally annotate coding sequence differences and to predict their functional effect, resulted in seven candidate variants located in six different genes. Of these, only FAM83G:c155G>C (p.R52P) was found to be concordant in eight additional cases and 16 healthy Kromfohrl änder dogs.

Constraints on barium isotope fractionation during aragonite precipitation by corals

We present a barium (Ba) isotope fractionation study of marine biogenic carbonates (aragonitic corals). The major aim is to provide first constraints on the Ba isotope fractionation between modern surface sea water and coral skele- ton. Mediterranean surface sea water was found to be enriched in the heavy Ba isotopes compared to previously reported values for marine open ocean authi- genic and terrestrial minerals. In aquarium experiments with a continuous sup- ply of Mediterranean surface water, the Ba isotopic composition of the bulk sample originating from cultured, aragonitic scleractinian corals (d137/134Ba between +0.16 +/- 0.12permil and +0.41 +/-0.12permil) were isotopically identical or lighter than that of the ambient Mediterranean surface sea water (d137/134Ba = +0.42 +/- 0.07permil, 2SD), which corresponds to an empirical maximum value of Ba isotope fractionation of D137/134Bacoral-seawater = -0.26 +/- 0.14permil at 25°C. This maximum Ba isotope fractionation is close and identical in direction to previous results from inorganic precipitation experiments with aragonite- structured pure BaCO3 (witherite). The variability in measured Ba concentrations of the cultured corals is at odds with a uniform distribution coefficient, DBa/Ca, thus indicating stronger vital effects on isotope than element discrimination. This observation supports the hypothesis that the Ba isotopic compositions of these corals do not result from simple equilibrium between the skeleton and the bulk sea water. Complementary coral samples from natural settings (tropical shallow-water corals from the Bahamas and Florida and cold- water corals from the Norwegian continental shelf) show an even wider range in d137/134Ba values (+0.14 +/- 0.08permil and +0.77 +/- 0.11permil), most probably due to additional spatial and/or temporal sea water heterogeneity, as indicated by recent publications.