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Abstract For decades, superfluid helium has attracted the interest of the scientific community as an extremely pure realisation of a quantum liquid, only accessible at temperatures close to absolute zero. Previously, helium films have only been observed directly using X-rays. However, this method is limited to temperatures above 1 K due to the high levels of energy deposition, and it also suffers from an inability to distinguish between helium isotopes. Here we show that a 3He layer on top of a phase separated mixture film at 170 mK gradually dissolves into the 4He with increasing temperature. We also observe an anomaly in film behaviour near 300 mK and unexpected restoration of the layered structure at 1.5 K which is consistent with a re-entrant phase transition leading to the suppression of superfluidity in the film near 300 mK. Our successful application of neutron scattering to study helium films at ultra-low temperatures opens up new possibilities for future research.

Abstract Magnetic skyrmions are topologically protected magnetization vortices that form three-dimensional strings in chiral magnets. With the manipulation of skyrmions being key to their application in devices, the focus has been on their dynamics within the vortex plane, while the dynamical control of skyrmion strings remained uncharted territory. Here, we report the effective bending of three-dimensional skyrmion strings in the chiral magnet MnSi in orthogonal thermal gradients using small angle neutron scattering. This dynamical behavior is achieved by exploiting the temperature-dependent skyrmion Hall effect, which is unexpected in the framework of skyrmion dynamics. We thus provide experimental evidence for the existence of magnon friction, which was recently proposed to be a key ingredient for capturing skyrmion dynamics, requiring a modification of Thiele’s equation. Our work therefore suggests the existence of an extra degree of freedom for the manipulation of three-dimensional skyrmions.

Salmonella enterica serovar Agona (S. Agona) has been increasingly recognised as a prominent cause of gastroenteritis. This serovar is a strong biofilm former that can undergo genome rearrangement and enter a viable but non-culturable state whilst remaining metabolically active. Similar strategies are employed by S. Typhi, the cause of typhoid fever, during human infection, which are believed to assist with the transition from acute infection to chronic carriage. Here we report S. Agona's ability to persist in people and examine factors that might be contributing to chronic carriage. A review of 2233 S. Agona isolates from UK infections (2004-2020) and associated carriage was undertaken, in which 1155 had short-read sequencing data available. A subset of 207 isolates was selected from different stages of acute and persistent infections within individual patients. The subset underwent long-read sequencing and genome structure (GS) analysis, as well as phenotyping assays including carbon source utilisation and biofilm formation. Associations between genotypes and phenotypes were investigated to compare acute infections to those which progress to chronic. GS analysis revealed the conserved arrangement GS1.0 in 195 isolates, and 8 additional GSs in 12 isolates. These rearranged isolates were typically associated with early, convalescent carriage (3 weeks- 3 months). We also identified an increase in SNP variation during this period of infection. We believe this increase in genome-scale and SNP variation reflects a population expansion after acute S. Agona infection, potentially reflecting an immune evasion mechanism which enables persistent infection to become established.

Evaluating fault segmentation is important for our understanding of seismic hazard assessment and fault growth. However, it is still unclear what controls if reverse fault earthquakes will rupture across segment boundaries. Here, we combine fault mapping and trench data from the low slip rate (0.04-0.15 mm/yr) multi-segment Nevis-Cardrona Fault (NCF) in the South Island of Aotearoa New Zealand to assess if it has ruptured in single or multi-segment earthquakes during the late Quaternary. Two new trenches on its Nevis segment provide stratigraphic evidence for two surface rupturing earthquakes, which through Optically Stimulated Luminscence dating and OxCal modelling, are constrained to have occurred at 28.9 +12.9 -9.1 ka and 12.8 ± 4.9 ka. The most recent timing is only weakly correlated to surface rupture timings from two trenches along the NCF's NW Cardrona segment. Furthermore, the 2 ± 1 m Nevis segment single event displacements we estimate would be unusually low for a ~85 km long NCF multi-segment rupture. We therefore surmise that late Quaternary NCF surface rupturing earthquakes did not rupture through ~30-50° bends that link these segments. Our trench data and fault mapping also indicate lower slip rates on the Nevis segment than previous studies (0.04-0.1 mm/yr vs 0.4 mm/yr).

ABSTRACT The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the model organism Escherichia coli, as well as major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with the Keio E. coli single-gene deletion library often regarded as a gold standard. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of 13 sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first assess several gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations, we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently acquired essentiality multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival and identifies several instances of essential stress responses masked by redundancy in free-living bacteria.IMPORTANCEThe essential genome, that is the set of genes absolutely required to sustain life, is a core concept in genetics. Essential genes in bacteria serve as drug targets, put constraints on the engineering of biological chassis for technological or industrial purposes, and are key to constructing synthetic life. Despite decades of study, relatively little is known about how gene essentiality varies across related bacteria. In this study, we have collected gene essentiality data for 13 bacteria related to the model organism Escherichia coli, including several human pathogens, and investigated the conservation of essentiality. We find that approximately a third of the genes essential in any particular strain are non-essential in another related strain. Surprisingly, we do not find evidence for essential genes unique to specific genera; rather it appears a substantial fraction of the essential genome rapidly gains or loses essentiality during evolution. This suggests that essentiality is not an immutable characteristic but depends crucially on the genomic context. We illustrate this through a comparison of our essential genes in free-living bacteria to genes conserved in 34 insect endosymbionts with naturally reduced genomes, finding several cases where genes generally regarded as being important for specific stress responses appear to have become essential in endosymbionts due to a loss of functional redundancy in the genome.

Abstract Vulval lichen sclerosus (VLS) is an inflammatory skin disease characterised by itching, apareunia, loss of vulval architecture and scarring. Heterogeneity in outcome reporting precludes comparison between treatments. This study aimed to systematically review outcome measures used to evaluate the efficacy of VLS treatments and present patients' treatment priorities. This review followed the PRISMA guidelines using a registered protocol (PROSPERO: CRD42022356738). Multiple databases were searched, along with grey literature on Clinicaltrials.gov, European Union Clinical Trials and International Standard Randomised controlled trial (RCT) registries. All RCTs assessing any treatment for VLS were eligible for inclusion. A total of 775 patients were assessed across 21 RCTs. The assessment tools reported outcomes in the following domains: patient‐reported symptoms assessed with one validated scale in 12 studies and seven non‐validated scales in nine studies; sexual function with validated female sexual function index and female sexual distress scale in two studies and two non‐validated scales in two studies; quality of life with three validated scales in three studies and clinician‐reported objective outcomes with two validated scales in three studies and six non‐validated scales in fourteen studies. Histological changes were assessed in 10 studies and tissue biomechanics in one study. We also carried out an online survey completed by 809 women with VLS to assess their research and disease treatment priorities and identified validated outcome measures to assess these. There is high variability in assessing treatment outcomes for VLS. We identified validated assessment tools which could be implemented in VLS studies to evaluate the effectiveness of treatments.

Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989–2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.

Around 285 million people worldwide currently have type 2 diabetes and it is projected that this number will be surpassed by 2030. Therefore, it is of the utmost importance to enhance our comprehension of the disease’s development. The regulation of diet, obesity, and inflammation in type 2 diabetes is believed to play a crucial role in enhancing insulin sensitivity and reducing the risk of onset diabetes. Obesity leads to an increase in visceral adipose tissue, which is a prominent site of inflammation in type 2 diabetes. Dyslipidemia, on the other hand, plays a significant role in attracting activated immune cells such as macrophages, dendritic cells, T cells, NK cells, and B cells to visceral adipose tissue. These immune cells are a primary source of pro-inflammatory cytokines that are believed to promote insulin resistance. This review delves into the influence of elevated dietary free saturated fatty acids and examines the cellular and molecular factors associated with insulin resistance in the initiation of inflammation induced by obesity. Furthermore, it explores novel concepts related to diet-induced inflammation and its relationship with type 2 diabetes.

Cellular protein homeostasis (proteostasis) plays an essential role in regulating the folding, sequestration, and turnover of misfolded proteins via a network of chaperones and clearance factors. Previous work has shown that misfolded proteins are spatially sequestered into membrane-less compartments in the cell as part of the proteostasis process. Soluble misfolded proteins in the cytoplasm are trafficked into the juxtanuclear quality control compartment (JUNQ), and nuclear proteins are sequestered into the intranuclear quality control compartment (INQ). However, the mechanisms that control the formation, localization, and degradation of these compartments are unknown. Previously, we showed that the JUNQ migrates to the nuclear membrane adjacent to the INQ at nucleus-vacuole junctions (NVJ), and the INQ moves through the NVJ into the vacuole for clearance in an ESCRT-mediated process. Here we have investigated what mechanisms are involved in the formation, migration, and clearance of the JUNQ. We find Hsp70s Ssa1 and Ssa2 are required for JUNQ localization to the NVJ and degradation of cytoplasmic misfolded proteins. We also confirm that sequestrases Btn2 and Hsp42 sort misfolded proteins to the JUNQ or IPOD, respectively. Interestingly, proteins required for piecemeal microautophagy of the nucleus (PMN) (i.e., Nvj1, Vac8, Atg1, and Atg8) drive the formation and clearance of the JUNQ. This suggests that the JUNQ migrates to the NVJ to be cleared via microautophagy.

Fe-Cr alloys serve as model alloys for the investigation of radiation induced effects in ferritic-martensitic steels which are candidate structural materials for future fusion reactors. In this work the effect of Cr segregation and/or agglomeration in 490 keV Fe+ ion irradiated Fe-10at%Cr alloys in the form of thin films is investigated. The irradiations took place at 300 °C at doses ranging from 0.5 to 20 displacements per atom (dpa). Polarized Neutron Reflectivity (PNR) measurements were used for the determination of the solute Cr concentration in the Fe-Cr matrix. Cr depletion from the Fe-Cr matrix up to 2.4 at% was found. This is related to solute Cr decrement as the accumulated dose increases. After the damage of 4 dpa, solute Cr reaches the asymptotic value of 8.4 at%, close to that of the thermodynamic equilibrium in Fe-Cr. Atom Probe Tomography (APT) measurements showed that after irradiation Cr accumulates into clusters the majority of which is co-located with oxygen.

Abstract Background Despite a low rate of infant mortality, Aotearoa New Zealand has a high rate of Sudden Unexpected Death in Infants (SUDI), with disproportionate impact for Pacific infants. This study explored the infant care practices, factors and relationships associated with increased risk of SUDI amongst Tongan, Samoan, Cook Islands Māori, and Niuean mothers in New Zealand, to inform evidence-based interventions for reducing the incidence of SUDI for Pacific families and their children. Methods Analysis comprised of data collected in 2009–2010 from 1089 Samoan, Tongan, Cook Islands Māori and Niuean mothers enrolled in the Growing Up in New Zealand longitudinal cohort study. The sleeping environment (bed-sharing and sleep position) of the infants was assessed at 6 weeks. Multivariable logistic regression analysis were conducted, controlling for sociodemographic factors to explore the association between selected maternal and pregnancy support and environment factors and the sleeping environment for infants. Results Mothers who converse in languages other than English at home, and mothers who consulted alternative practitioners were less likely to follow guidelines for infant sleeping position. Similarly language, smoking, alcohol, household dwelling, crowding and access to a family doctor or GP were associated with mothers following guidelines for bed-sharing. Conclusion The impact of SUDI on Pacific infants may be lessened or prevented if communication about risk factors is more inclusive of diverse ethnic, cultural worldviews, and languages. Societal structural issues such as access to affordable housing is also important. This research suggests a need for more targeted or tailored interventions which promote safe sleeping and reduce rates of SUDI in a culturally respectful and meaningful way for Pasifika communities in Aotearoa, New Zealand.

The ability of regional air quality models to skilfully represent pollutant distributions throughout the atmospheric column is important to enabling their skilful prediction at the surface. This provides a requirement for model evaluation at elevated altitudes, though observation datasets available for this purpose are limited. This is particularly true of those offering sampling over extended time periods. To address this requirement and support evaluation of regional air quality models such as the UK Met Offices Air Quality in the Unified Model (AQUM), a long-term, quality-assured dataset of the three-dimensional distribution of key pollutants was collected over the southern United Kingdom from July 2019 to April 2022. Measurements were collected using the Met Office Atmospheric Survey Aircraft (MOASA), a Cessna 421 instrumented for this project to measure gaseous nitrogen dioxide, ozone, sulfur dioxide and fine-mode (PM2.5) aerosol. This paper introduces the MOASA measurement platform, flight strategies and instrumentation and is not intended to be an in-depth diagnostic analysis but rather a comprehensive technical reference for future users of these data. The MOASA air quality dataset includes 63 flight sorties (totalling over 150 h of sampling), the data from which are openly available for use. To illustrate potential uses of these upper-air observations for regional-scale model evaluation, example case studies are presented, which include analyses of the spatial scales of measured pollutant variability, a comparison of airborne to ground-based observations over Greater London and initial work to evaluate performance of the AQUM regional air quality model. These case studies show that, for observations of relative humidity, nitrogen dioxide and particle counts, natural pollutant variability is well observed by the aircraft, whereas SO2 variability is limited by instrument precision. Good agreement is seen between observations aloft and those on the ground, particularly for PM2.5. Analysis of odd oxygen suggests titration of ozone is a dominant chemical process throughout the column for the data analysed, although a slight enhancement of ozone aloft is seen. Finally, a preliminary evaluation of AQUM performance for two case studies suggests a large positive model bias for ozone aloft, coincident with a negative model bias for NO2 aloft. In one case, there is evidence that an underprediction in the modelled boundary layer height contributes to the observed biases at elevated altitudes.

Abstract Background The current biodiversity crisis underscores the urgent need for sustainable management of the human uses of nature. In the context of sustainability management, adopting the ecosystem service (ES) concept, i.e., the benefits humans obtain from nature, can support decisions aimed at benefiting both nature and people. However, marine ecosystems in particular endure numerous direct drivers of change (i.e., habitat loss and degradation, overexploitation, pollution, climate change, and introduction of non-indigenous species) all of which threaten ecosystem structure, functioning, and the provision of ES. Marine ecosystems have received less attention than terrestrial ecosystems in ES literature, and knowledge on marine ES is hindered by the highly heterogeneous scientific literature with regard to the different types of marine ecosystem, ES, and their correlates. Here, we constructed a systematic map of the existing literature to highlight knowledge clusters and knowledge gaps on how changes in marine ecosystems influence the provision of marine ES. Method We searched for all evidence documenting how changes in structure and functioning of marine ecosystems affect the delivery of ES in academic and grey literature sources. In addition to Scopus, Web of Science, and Google Scholar, we searched 6 online databases from intergovernmental agencies, supranational or national organizations, and NGOs. We screened English-language documents using predefined inclusion criteria on titles, abstracts, and then full texts, without any geographic or temporal limitations. All qualifying literature was coded and metadata were extracted. No formal validity appraisal was undertaken. We identified knowledge clusters and gaps in terms of which ecosystem types, biodiversity components, or ES types have been studied and how these categories are linked. Review findings Our searches identified 41 884 articles published since 1968 of which 12 140 were duplicates; 25 747 articles were excluded at the title-screening stage, then 2774 at the abstract stage. After full-text screening, a total of 653 articles—having met the eligibility criteria—were included in the final database, spanning from 1977 to July 2021. The number of studies was unevenly distributed across geographic boundaries, ecosystem types, ES, and types of pressure. The most studied ecosystems were pelagic ecosystems on continental shelves and intertidal ecosystems, and deep-sea habitats and ice-associated ecosystems were the least studied. Food provision was the major focus of ES articles across all types of marine ecosystem (67%), followed by climate regulation (28%), and recreation (14%). Biophysical values were assessed in 91% of the analysed articles, 30% assessed economic values, but only 3% assessed socio-cultural values. Regarding the type of impact on ecosystems, management effects were the most studied, followed by overexploitation and climate change (with increase in seawater temperature being the most commonly assessed climate change pressure). Lastly, the introduction of non-indigenous species and deoxygenation were the least studied. Conclusions This systematic map provides, in addition to a database, knowledge gaps and clusters on how marine ecosystem changes impact ES provision. The current lack of knowledge is a threat to the sustainability of human actions and knowledge-based nature conservation. The knowledge gaps and clusters highlighted here could guide future research and impact the beneficial development of policy and management practices.

The 19th century saw the development of vaccines, which were biological preparations designed to enhance immunity against specific diseases. Edible vaccines function by stimulating both systemic and mucosal immune responses against foreign pathogens, and they may potentially protect the host from autoimmunity. The mucosal surfaces provide a convenient and rapid route for delivering therapeutic small molecules. This is due to their large surface areas and easy administration. The effectiveness of mucosal immunization relies on the fact that mucous membranes represent the body’s largest immunogenic organ. Within this interface, there is a well-organized lymphatic structure known as MALT (mucosa-associated lymphoid tissue), which includes both T and B cells and encompasses the adaptive arms of the immune system. Oral vaccines specifically stimulate immune responses in the gut-associated lymphoid tissue (GALT), which consists of lymph nodes, Payer’s patches (where B cells make up about 75% of the population and T cells account for approximately 20%), and isolated lymphoid follicles within the gastrointestinal tract (GIT). However, a significant challenge in developing vaccines is the rapid degradation of antigens within the harsh environment of the digestive tract, which hampers effective protein delivery to the GIT. In light of recent proteomic analysis revealing strong up-regulation of the tryptophan catabolic enzyme indoleamine 2, 3-dioxygenase (IDO1) in DCs inoculated with the Cholera toxin B-subunit-Insulin fusion protein vaccine (CTB-INS), we are interested in investigating the effects of transgene integration into a selected plant cell as an edible vaccine.

Abstract Background Bread wheat is one of the world’s most important food crops and considerable efforts have been made to develop genomic resources for this species. This includes an on-going project by the International Wheat Genome Sequencing Consortium to assemble its large and complex genome, which is hexaploid and contains three closely related ‘homoeologous’ copies for each chromosome. This multi-national effort avoids the complications polyploidy entails for correct assembly of the genome by sequencing flow-sorted chromosome arms one at a time. Here we report on an alternate approach, a direct homoeolog-specific assembly of the expressed portion of the genome, the transcriptome. Results After assessment of the ability of various assemblers to generate homoeolog-specific assemblies, we employed a two-stage assembly process to produce a high-quality assembly of the transcriptome of hexaploid wheat from Roche-454 and Illumina GAIIx paired-end sequence reads. The assembly process made use of a rapid partitioning of expressed sequences into homoeologous clusters, followed by a parallel high-fidelity assembly of each cluster on a 1150-processor compute cloud. We assessed assembly quality through comparison to known wheat gene sequences and found that in ca. 98.5% of cases the assembly was sufficiently accurate for homoeologous triplets to be cleanly separated into either two or three separate contigs. Comparison to publicly available transcript collections suggests that the assembly covers ~75-80% of the complete transcriptome. Conclusions This work therefore describes the first homoeolog-specific sequence assembly of the wheat transcriptome and provides a reference transcriptome for future wheat research. Furthermore, our assembly methodology is transferable to other polyploid organisms.

Background Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with 250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. Conclusion BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.

Abstract Background MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced genomes such as Arabidopsis, rice, poplar and Brachypodium have provided insights into the evolutionary relationships of this class of small RNAs among plants. However, miRNAs from barley, one of the most important cereal crops, remain unknown. Results We performed a large scale study of barley miRNAs through deep sequencing of small RNAs extracted from leaves of two barley cultivars. By using the presence of miRNA precursor sequences in related genomes as one of a number of supporting criteria, we identified up to 100 miRNAs in barley. Of these only 56 have orthologs in wheat, rice or Brachypodium that are known to be expressed, while up to 44 appear to be specifically expressed in barley. Conclusions Our study, the first large scale investigation of small RNAs in barley, has identified up to 100 miRNAs. We demonstrate that reliable identification of miRNAs via deep sequencing in a species whose genome has not been sequenced requires a more careful analysis of sequencing errors than is commonly performed. We devised a read filtering procedure for dealing with errors. In addition, we found that the use of a large dataset of almost 35 million reads permits the use of read abundance distributions along putative precursor sequences as a practical tool for isolating miRNAs in a large background of reads originating from other non-coding and coding RNAs. This study therefore provides a generic approach for discovering novel miRNAs where no genome sequence is available.

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.

Abstract Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring). For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex) using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able to distinguish contributions from individual homoeologs. Furthermore, the comparison between the two species leads us to conclude that the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels, presumably reflecting increased selection pressure on genes coding for proteins present at high levels. In addition, the results indicate the presence of a correlation between sequence and expression conservation within the Triticeae.

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.

Abstract Background Chromosome pairing, recombination and DNA repair are essential processes during meiosis in sexually reproducing organisms. Investigating the bread wheat (Triticum aestivum L.) Ph2 (Pairing homoeologous) locus has identified numerous candidate genes that may have a role in controlling such processes, including TaMSH7, a plant specific member of the DNA mismatch repair family. Results Sequencing of the three MSH7 genes, located on the short arms of wheat chromosomes 3A, 3B and 3D, has revealed no significant sequence divergence at the amino acid level suggesting conservation of function across the homoeogroups. Functional analysis of MSH7 through the use of RNAi loss-of-function transgenics was undertaken in diploid barley (Hordeum vulgare L.). Quantitative real-time PCR revealed several T0 lines with reduced MSH7 expression. Positive segregants from two T1 lines studied in detail showed reduced MSH7 expression when compared to transformed controls and null segregants. Expression of MSH6, another member of the mismatch repair family which is most closely related to the MSH7 gene, was not significantly reduced in these lines. In both T1 lines, reduced seed set in positive segregants was observed. Conclusion Results presented here indicate, for the first time, a distinct functional role for MSH7 in vivo and show that expression of this gene is necessary for wild-type levels of fertility. These observations suggest that MSH7 has an important function during meiosis and as such remains a candidate for Ph2.

A multimodal mass spectrometry imaging (MSI) approach was used to investigate the chemotherapy drug-induced response of a Multicellular Tumour Spheroid (MCTS) 3D cell culture model of osteosarcoma (OS). The work addresses the critical demand for enhanced translatable early drug discovery approaches by demonstrating a robust spatially resolved molecular distribution analysis in tumour models following chemotherapeutic intervention. Advanced high-resolution techniques were employed, including desorption electrospray ionisation (DESI) mass spectrometry imaging (MSI), to assess the interplay between metabolic and cellular pathways in response to chemotherapeutic intervention. Endogenous metabolite distributions of the human OS tumour models were complemented with subcellularly resolved protein localisation by the detection of metal-tagged antibodies using Imaging Mass Cytometry (IMC). The first application of matrix-assisted laser desorption ionization–immunohistochemistry (MALDI-IHC) of 3D cell culture models is reported here. Protein localisation and expression following an acute dosage of the chemotherapy drug doxorubicin demonstrated novel indications for mechanisms of region-specific tumour survival and cell-cycle-specific drug-induced responses. Previously unknown doxorubicin-induced metabolite upregulation was revealed by DESI-MSI of MCTSs, which may be used to inform mechanisms of chemotherapeutic resistance. The demonstration of specific tumour survival mechanisms that are characteristic of those reported for in vivo tumours has underscored the increasing value of this approach as a tool to investigate drug resistance.