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Neotropical shade-grown coffee systems are renowned for their potential to conserve avian biodiversity. Yet, little is known about food resources consumed by insectivorous birds in these systems, the extent of resource competition between resident and migratory birds, or how management of shade trees might influence diet selection. We identified arthropods in stomach contents from obligate and generalist insectivorous birds captured in mist-nets at five coffee farms in Chiapas, Mexico between 2001-2003. Overall stomach contents from 938 individuals revealed dietary differences resulting from changes in seasons, years, and foraging guilds. Of four species sampled across all management systems, Yellow-green Vireo (Vireo flavoviridis) prey differed depending on coffee shade management, consuming more ants in shaded monoculture than polyculture systems. Diets of obligate and generalist resident insectivores were 72% dissimilar with obligate insectivores consuming more Coleoptera and Araneae, and generalist insectivores consuming more Formicidae and other Hymenoptera. This suggests that obligate insectivores target more specialized prey whereas generalist insectivores rely on less favorable, chemically-defended prey found in clumped distributions. Our dataset provides important natural history data for many Nearctic-Neotropical migrants such as Tennessee Warbler (Leiothlypis peregrina; N = 163), Nashville Warbler (Leiothlypis ruficapilla; N = 69), and Swainson's Thrush (Catharus ustulatus; N = 68) and tropical residents including Red-legged Honeycreepers (Cyanerpes cyaneus; N = 70) and Rufous-capped Warblers (Basileuterus rufifrons; N = 56). With declining arthropod populations worldwide, understanding the ecological interactions between obligate and generalist avian insectivores gives researchers the tools to evaluate community stability and inform conservation efforts.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Artificial Spin Ice (ASI), consisting of a two dimensional array of nanoscale magnetic elements, provides a fascinating opportunity to observe the physics of out-of-equilibrium systems. Initial studies concentrated on the static, frozen state, whilst more recent studies have accessed the out-of-equilibrium dynamic, fluctuating state. This opens up exciting possibilities such as the observation of systems exploring their energy landscape through monopole quasiparticle creation, potentially leading to ASI magnetricity, and to directly observe unconventional phase transitions. In this work we have measured and analysed the magnetic relaxation of thermally active ASI systems by means of SQUID magnetometry. We have investigated the effect of the interaction strength on the magnetization dynamics at different temperatures in the range where the nanomagnets are thermally active. We have observed that they follow an Arrhenius-type Néel-Brown behaviour. An unexpected negative correlation of the average blocking temperature with the interaction strength is also observed, which is supported by Monte Carlo simulations. The magnetization relaxation measurements show faster relaxation for more strongly coupled nanoelements with similar dimensions. The analysis of the stretching exponents obtained from the measurements suggest 1-D chain-like magnetization dynamics. This indicates that the nature of the interactions between nanoelements lowers the dimensionality of the ASI from 2-D to 1-D. Finally, we present a way to quantify the effective interaction energy of a square ASI system, and compare it to the interaction energy computed with micromagnetic simulations.

Designing and constructing model systems that embody the statistical mechanics of frustration is now possible using nanotechnology. We have arranged nanomagnets on a two-dimensional square lattice to form an artificial spin ice, and studied its fractional excitations, emergent magnetic monopoles, and how they respond to a driving field using X-ray magnetic microscopy. We observe a regime in which the monopole drift velocity is linear in field above a critical field for the onset of motion. The temperature dependence of the critical field can be described by introducing an interaction term into the Bean-Livingston model of field-assisted barrier hopping. By analogy with electrical charge drift motion, we define and measure a monopole mobility that is larger both for higher temperatures and stronger interactions between nanomagnets. The mobility in this linear regime is described by a creep model of zero-dimensional charges moving within a network of quasi-one-dimensional objects.

Designing and constructing model systems that embody the statistical mechanics of frustration is now possible using nanotechnology. We have arranged nanomagnets on a two-dimensional square lattice to form an artificial spin ice, and studied its fractional excitations, emergent magnetic monopoles, and how they respond to a driving field using X-ray magnetic microscopy. We observe a regime in which the monopole drift velocity is linear in field above a critical field for the onset of motion. The temperature dependence of the critical field can be described by introducing an interaction term into the Bean-Livingston model of field-assisted barrier hopping. By analogy with electrical charge drift motion, we define and measure a monopole mobility that is larger both for higher temperatures and stronger interactions between nanomagnets. The mobility in this linear regime is described by a creep model of zero-dimensional charges moving within a network of quasi-one-dimensional objects.

Artificial Spin Ice (ASI), consisting of a two dimensional array of nanoscale magnetic elements, provides a fascinating opportunity to observe the physics of out-of-equilibrium systems. Initial studies concentrated on the static, frozen state, whilst more recent studies have accessed the out-of-equilibrium dynamic, fluctuating state. This opens up exciting possibilities such as the observation of systems exploring their energy landscape through monopole quasiparticle creation, potentially leading to ASI magnetricity, and to directly observe unconventional phase transitions. In this work we have measured and analysed the magnetic relaxation of thermally active ASI systems by means of SQUID magnetometry. We have investigated the effect of the interaction strength on the magnetization dynamics at different temperatures in the range where the nanomagnets are thermally active. We have observed that they follow an Arrhenius-type Néel-Brown behaviour. An unexpected negative correlation of the average blocking temperature with the interaction strength is also observed, which is supported by Monte Carlo simulations. The magnetization relaxation measurements show faster relaxation for more strongly coupled nanoelements with similar dimensions. The analysis of the stretching exponents obtained from the measurements suggest 1-D chain-like magnetization dynamics. This indicates that the nature of the interactions between nanoelements lowers the dimensionality of the ASI from 2-D to 1-D. Finally, we present a way to quantify the effective interaction energy of a square ASI system, and compare it to the interaction energy computed with micromagnetic simulations.

ABSTRACTClimate change projections are for higher temperatures and extreme droughts by the end of the 21st century. This will alter the natural recharge of groundwater, including decreased inflow from runoff, increased evaporative losses, and warmer and shorter winter seasons, impacts that are likely to exacerbate already existing groundwater overdraft in many basins. Additionally, the imported surface water that can be delivered from the Central Valley Project (CVP) and State Water Project (SWP) to areas reliant on this water for groundwater recharge and consumptive use is projected to be less reliable and more expensive. Yet groundwater is a critical water supply source during drought when it compensates for reduced surface water supplies. The need for proactive adaptation strategies to address the extreme droughts projected under climate change are frequently discussed, yet there are limited examples of such groundwater management strategies. This paper therefore explores: 1) How groundwater management agencies are planning for drought 2) What new approaches are currently being used that show promise for addressing the more extreme droughts projected under climate change? First, the paper provides a review of the research on drought and groundwater management including strategies currently used to address drought. Second, case studies illustrate newer and varied approaches being used to reduce drought impacts. Highlighted are the different approaches used by groundwater managers to both increase storage and develop drought reserves. These strategies can help to reduce vulnerability to the extreme droughts projected under climate change. Two additional case studies discuss the limits of a drought reserve strategy and indicate that more is needed under climate change to address the range of basin conditions and the varied needs of communities reliant on groundwater.Several overall groundwater management trends are noted:A shift from voluntary to mandatory requirements for the sustainable management of groundwater after the 2014 passage of SGMA; An increase in the use of recycled water from 190,000 AF in 1976 to 714,000 AF in 2016 that can be used for groundwater recharge to enhance storage; An increase in the development of groundwater drought reserves;Suggested future research projects include:Benefits and challenges of long-term strategies to manage groundwater under climate change and extreme droughts; Practices implemented during past droughts that were effective in reducing drought vulnerability in subsequent droughtsThe different approaches presented in this paper to increase groundwater storage specifically for use during drought are important first steps to proactively manage groundwater to adapt to the higher temperatures and future extreme droughts projected under climate change.Keywords: drought, climate change, groundwater management strategies, drought reserves

Artificial spin ices (ASI) are arrays of single domain nano-magnetic islands, arranged in geometries that give rise to frustrated magnetostatic interactions. It is possible to reach their ground state via thermal annealing. We have made square ASI using different FePd alloys to vary the magnetization via co-sputtering. From a polarized state the samples were incrementally heated and we measured the vertex population as a function of temperature using magnetic force microscopy. For the higher magnetization FePd sample, we report an onset of dynamics at T = 493 K, with a rapid collapse into >90% ground state vertices. In contrast, the low magnetization sample started to fluctuate at lower temperatures, T = 393 K and over a wider temperature range but only reached a maximum of 25% of ground state vertices. These results indicate that the interaction strength, dynamic temperature range and pathways can be finely tuned using a simple co-sputtering process. In addition we have compared our experimental values of the blocking temperature to those predicted using the simple Néel-Brown two-state model and find a large discrepancy which we attribute to activation volumes much smaller than the island volume.

Artificial spin ices (ASI) are arrays of single domain nano-magnetic islands, arranged in geometries that give rise to frustrated magnetostatic interactions. It is possible to reach their ground state via thermal annealing. We have made square ASI using different FePd alloys to vary the magnetization via co-sputtering. From a polarized state the samples were incrementally heated and we measured the vertex population as a function of temperature using magnetic force microscopy. For the higher magnetization FePd sample, we report an onset of dynamics at T = 493 K, with a rapid collapse into >90% ground state vertices. In contrast, the low magnetization sample started to fluctuate at lower temperatures, T = 393 K and over a wider temperature range but only reached a maximum of 25% of ground state vertices. These results indicate that the interaction strength, dynamic temperature range and pathways can be finely tuned using a simple co-sputtering process. In addition we have compared our experimental values of the blocking temperature to those predicted using the simple Néel-Brown two-state model and find a large discrepancy which we attribute to activation volumes much smaller than the island volume.

Temperature and fluid pressure conditions control rock deformation and mineralization on geological faults, and hence the distribution of earthquakes. Typical intraplate continental crust has hydrostatic fluid pressure and a near-surface thermal gradient of 31 ± 15 degrees Celsius per kilometre. At temperatures above 300-450 degrees Celsius, usually found at depths greater than 10-15 kilometres, the intra-crystalline plasticity of quartz and feldspar relieves stress by aseismic creep and earthquakes are infrequent. Hydrothermal conditions control the stability of mineral phases and hence frictional-mechanical processes associated with earthquake rupture cycles, but there are few temperature and fluid pressure data from active plate-bounding faults. Here we report results from a borehole drilled into the upper part of the Alpine Fault, which is late in its cycle of stress accumulation and expected to rupture in a magnitude 8 earthquake in the coming decades. The borehole (depth 893 metres) revealed a pore fluid pressure gradient exceeding 9 ± 1 per cent above hydrostatic levels and an average geothermal gradient of 125 ± 55 degrees Celsius per kilometre within the hanging wall of the fault. These extreme hydrothermal conditions result from rapid fault movement, which transports rock and heat from depth, and topographically driven fluid movement that concentrates heat into valleys. Shear heating may occur within the fault but is not required to explain our observations. Our data and models show that highly anomalous fluid pressure and temperature gradients in the upper part of the seismogenic zone can be created by positive feedbacks between processes of fault slip, rock fracturing and alteration, and landscape development at plate-bounding faults.

Temperature and fluid pressure conditions control rock deformation and mineralization on geological faults, and hence the distribution of earthquakes. Typical intraplate continental crust has hydrostatic fluid pressure and a near-surface thermal gradient of 31 ± 15 degrees Celsius per kilometre. At temperatures above 300-450 degrees Celsius, usually found at depths greater than 10-15 kilometres, the intra-crystalline plasticity of quartz and feldspar relieves stress by aseismic creep and earthquakes are infrequent. Hydrothermal conditions control the stability of mineral phases and hence frictional-mechanical processes associated with earthquake rupture cycles, but there are few temperature and fluid pressure data from active plate-bounding faults. Here we report results from a borehole drilled into the upper part of the Alpine Fault, which is late in its cycle of stress accumulation and expected to rupture in a magnitude 8 earthquake in the coming decades. The borehole (depth 893 metres) revealed a pore fluid pressure gradient exceeding 9 ± 1 per cent above hydrostatic levels and an average geothermal gradient of 125 ± 55 degrees Celsius per kilometre within the hanging wall of the fault. These extreme hydrothermal conditions result from rapid fault movement, which transports rock and heat from depth, and topographically driven fluid movement that concentrates heat into valleys. Shear heating may occur within the fault but is not required to explain our observations. Our data and models show that highly anomalous fluid pressure and temperature gradients in the upper part of the seismogenic zone can be created by positive feedbacks between processes of fault slip, rock fracturing and alteration, and landscape development at plate-bounding faults.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

drought, climate change, sustainable groundwater management

We report on the crossover from the thermal to the athermal regime of an artificial spin ice formed from a square array of magnetic islands whose lateral size, 30 nm × 70 nm, is small enough that they are dynamic at room temperature. We used resonant magnetic soft x-ray photon correlation spectroscopy as a method to observe the time-time correlations of the fluctuating magnetic configurations of spin ice during cooling, which are found to slow abruptly as a freezing temperature of T0=178±5 K is approached. This slowing is well described by a Vogel-Fulcher-Tammann law, implying that the frozen state is glassy, with the freezing temperature being commensurate with the strength of magnetostatic interaction energies in the array. The activation temperature, TA=40±10 K, is much less than that expected from a Stoner-Wohlfarth coherent rotation model. Zero-field-cooled/field-cooled magnetometry reveals a freeing up of fluctuations of states within islands above this temperature, caused by variation in the local anisotropy axes at the oxidised edges. This Vogel-Fulcher-Tammann behavior implies that the system enters a glassy state upon freezing, which is unexpected for a system with a well-defined ground state.

We report on the crossover from the thermal to the athermal regime of an artificial spin ice formed from a square array of magnetic islands whose lateral size, 30 nm × 70 nm, is small enough that they are dynamic at room temperature. We used resonant magnetic soft x-ray photon correlation spectroscopy as a method to observe the time-time correlations of the fluctuating magnetic configurations of spin ice during cooling, which are found to slow abruptly as a freezing temperature of T0=178±5 K is approached. This slowing is well described by a Vogel-Fulcher-Tammann law, implying that the frozen state is glassy, with the freezing temperature being commensurate with the strength of magnetostatic interaction energies in the array. The activation temperature, TA=40±10 K, is much less than that expected from a Stoner-Wohlfarth coherent rotation model. Zero-field-cooled/field-cooled magnetometry reveals a freeing up of fluctuations of states within islands above this temperature, caused by variation in the local anisotropy axes at the oxidised edges. This Vogel-Fulcher-Tammann behavior implies that the system enters a glassy state upon freezing, which is unexpected for a system with a well-defined ground state.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.

An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.

Sézary syndrome is a rare leukemic form of cutaneous T cell lymphoma characterized by generalized redness, scaling, itching and increased numbers of circulating atypical T lymphocytes. It is rarely curable, with poor prognosis. Here we present a multiplatform genomic analysis of 37 patients with Sézary syndrome that implicates dysregulation of cell cycle checkpoint and T cell signaling. Frequent somatic alterations were identified in TP53, CARD11, CCR4, PLCG1, CDKN2A, ARID1A, RPS6KA1 and ZEB1. Activating CCR4 and CARD11 mutations were detected in nearly one-third of patients. ZEB1, encoding a transcription repressor essential for T cell differentiation, was deleted in over one-half of patients. IL32 and IL2RG were overexpressed in nearly all cases. Our results demonstrate profound disruption of key signaling pathways in Sézary syndrome and suggest potential targets for new therapies.

Despite recent advances in analytical and computational chemistry, lipid identification remains a significant challenge in lipidomics. Ion-mobility spectrometry provides an accurate measure of the molecules' rotationally averaged collision cross-section (CCS) in the gas phase and is thus related to ionic shape. Here, we investigate the use of CCS as a highly specific molecular descriptor for identifying lipids in biological samples. Using traveling wave ion mobility mass spectrometry (MS), we measured the CCS values of over 200 lipids within multiple chemical classes. CCS values derived from ion mobility were not affected by instrument settings or chromatographic conditions, and they were highly reproducible on instruments located in independent laboratories (interlaboratory RSD < 3% for 98% of molecules). CCS values were used as additional molecular descriptors to identify brain lipids using a variety of traditional lipidomic approaches. The addition of CCS improved the reproducibility of analysis in a liquid chromatography-MS workflow and maximized the separation of isobaric species and the signal-to-noise ratio in direct-MS analyses (e.g., "shotgun" lipidomics and MS imaging). These results indicate that adding CCS to databases and lipidomics workflows increases the specificity and selectivity of analysis, thus improving the confidence in lipid identification compared to traditional analytical approaches. The CCS/accurate-mass database described here is made publicly available.

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Despite recent advances in analytical and computational chemistry, lipid identification remains a significant challenge in lipidomics. Ion-mobility spectrometry provides an accurate measure of the molecules' rotationally averaged collision cross-section (CCS) in the gas phase and is thus related to ionic shape. Here, we investigate the use of CCS as a highly specific molecular descriptor for identifying lipids in biological samples. Using traveling wave ion mobility mass spectrometry (MS), we measured the CCS values of over 200 lipids within multiple chemical classes. CCS values derived from ion mobility were not affected by instrument settings or chromatographic conditions, and they were highly reproducible on instruments located in independent laboratories (interlaboratory RSD < 3% for 98% of molecules). CCS values were used as additional molecular descriptors to identify brain lipids using a variety of traditional lipidomic approaches. The addition of CCS improved the reproducibility of analysis in a liquid chromatography-MS workflow and maximized the separation of isobaric species and the signal-to-noise ratio in direct-MS analyses (e.g., "shotgun" lipidomics and MS imaging). These results indicate that adding CCS to databases and lipidomics workflows increases the specificity and selectivity of analysis, thus improving the confidence in lipid identification compared to traditional analytical approaches. The CCS/accurate-mass database described here is made publicly available.

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Metabolomics is a rapidly evolving analytical approach in life and health sciences. The structural elucidation of the metabolites of interest remains a major analytical challenge in the metabolomics workflow. Here, we investigate the use of ion mobility as a tool to aid metabolite identification. Ion mobility allows for the measurement of the rotationally averaged collision cross-section (CCS), which gives information about the ionic shape of a molecule in the gas phase. We measured the CCSs of 125 common metabolites using traveling-wave ion mobility-mass spectrometry (TW-IM-MS). CCS measurements were highly reproducible on instruments located in three independent laboratories (RSD < 5% for 99%). We also determined the reproducibility of CCS measurements in various biological matrixes including urine, plasma, platelets, and red blood cells using ultra performance liquid chromatography (UPLC) coupled with TW-IM-MS. The mean RSD was < 2% for 97% of the CCS values, compared to 80% of retention times. Finally, as proof of concept, we used UPLC-TW-IM-MS to compare the cellular metabolome of epithelial and mesenchymal cells, an in vitro model used to study cancer development. Experimentally determined and computationally derived CCS values were used as orthogonal analytical parameters in combination with retention time and accurate mass information to confirm the identity of key metabolites potentially involved in cancer. Thus, our results indicate that adding CCS data to searchable databases and to routine metabolomics workflows will increase the identification confidence compared to traditional analytical approaches.

Metabolomics is a rapidly evolving analytical approach in life and health sciences. The structural elucidation of the metabolites of interest remains a major analytical challenge in the metabolomics workflow. Here, we investigate the use of ion mobility as a tool to aid metabolite identification. Ion mobility allows for the measurement of the rotationally averaged collision cross-section (CCS), which gives information about the ionic shape of a molecule in the gas phase. We measured the CCSs of 125 common metabolites using traveling-wave ion mobility-mass spectrometry (TW-IM-MS). CCS measurements were highly reproducible on instruments located in three independent laboratories (RSD < 5% for 99%). We also determined the reproducibility of CCS measurements in various biological matrixes including urine, plasma, platelets, and red blood cells using ultra performance liquid chromatography (UPLC) coupled with TW-IM-MS. The mean RSD was < 2% for 97% of the CCS values, compared to 80% of retention times. Finally, as proof of concept, we used UPLC-TW-IM-MS to compare the cellular metabolome of epithelial and mesenchymal cells, an in vitro model used to study cancer development. Experimentally determined and computationally derived CCS values were used as orthogonal analytical parameters in combination with retention time and accurate mass information to confirm the identity of key metabolites potentially involved in cancer. Thus, our results indicate that adding CCS data to searchable databases and to routine metabolomics workflows will increase the identification confidence compared to traditional analytical approaches.

Groundwater, sustainable yield

Periodic droughts, projected to become more frequent and severe with climate change, present a significant planning challenge for California’s water agencies. This research examined approaches to reducing drought vulnerability, focusing on five water agencies on California’s north and central coast that rely on local and regional sources of water. Curtailing water use is the principal response to drought. In contrast, this project highlights an important but underutilized proactive adaptation to improve water supply security during drought: the development of locally based groundwater drought reserves. While this approach represents an obvious solution in principle, it is uncommon to find it in practice, and this research provides insight into (1) motivating factors, (2) legal barriers and opportunities, (3) tools, and (4) policy options to support increased drought resilience and the development of drought reserves.

The Nature Conservancy and U.S. Fish and Wildlife Service are leading efforts to restore an ecologically viable 100-mile stretch of the Sacramento River, between Red Bluff and Colusa. Within the Sacramento River Conservation Area, the river will be allowed to do what rivers normally do – meander, flood, erode and deposit sediment. Native vegetation will also be re-planted to help create much needed habitat (indeed refuge) for some of the region’s more than 250 indigenous animal species, including yellow-billed cuckoos, river otters, Chinook salmon and green sturgeon, as well as threatened bat and insect species. The restored wildlife area will also provide valuable educational and recreational opportunities for school-age children and the general public.

Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC) clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum), Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete Triticeae genome. This study demonstrates that global fingerprinting of the large plant genomes is a viable strategy for generating physical maps. Physical maps allow the description of the co-linearity between wheat and grass genomes and provide a powerful tool for positional cloning of new genes.

More than half the world’s population is at moderate to high risk of zinc (Zn) deficiency, and biofortification has become an important strategy to alleviate the problem. Grain loading is likely to be a major bottleneck in cereal biofortification. However, very little is known about the transporters involved in this process. We have used barley as a model system to study the transporter genes which are potentially important in grain Zn loading. Here we report effect of over-expressing a barley ZIP gene in barley on grain Zn content. Our results showed that when the transgenic plants were grown at low Zn supply, grain Zn concentrations of transgenic lines were not different from those of the null lines, but with a low dose of Zn supplement during anthesis grain Zn content in transgenic lines increased by 50%. When plants were grown at a high Zn supply, grain Zn concentration of the transgenic lines was doubled relative to the null lines and wildtype. The enhanced concentration of Zn in the grain of the transgenic plants did not alter concentrations of other micronutrients. These results indicate that the constitutive expression of HvZIP7 could specifically increase grain Zn content.

In California, the control of water has shaped the destiny of the land and its inhabitants. Today, when Californians require that water satisfy an increasing array of diverse values, it is essential to understand how control over water is achieved and maintained, how strategies to manage water become defined, and how these strategies influence water allocations.Despite often held assumptions of local rights to water, a central theme in California since the adoption of the doctrine of prior appropriation has been the diversion of water from its originating watershed to an out-of-origin area. In a state where control over water represents security, power and wealth, inter-basin diversions are highly contested, and there are continuous debates over water rights and the consequences and valuation of different allocation regimes. Exemplifying these ongoing conflicts over water, the Potter Valley Hydropower Project (PVP), diverting Eel River water into the Russian River since 1908, serves as a pivotal point of contention where two associated regions with multiple interests battle over claims to Eel River water.This research utilized an in-depth study of negotiations over the Eel – Russian River inter-basin water diversion to explain why particular groups achieve, maintain and lose control over a region’s water, and how shifting power relations affect water allocation decisions.