High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection

Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974-2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced pluripotent stem cell-derived cardiomyocytes to evaluate the genomic regulatory basis of the non-DNA-binding homeodomain protein HOPX. We show that HOPX interacts with and controls cardiac genes and enhancer networks associated with diverse aspects of heart development. Using perturbation studies in vitro, we define how upstream cell growth and proliferation control HOPX transcription to regulate cardiac gene programs. We then use cell, organoid, and zebrafish regeneration models to demonstrate that HOPX-regulated gene programs control cardiomyocyte function in development and disease. Collectively, this study mechanistically links cell signaling pathways as upstream regulators of HOPX transcription to control gene programs underpinning cardiomyocyte identity and function.

Spatial Transcriptomics in Kidney Tissue

Unlike bulk and single-cell/single-nuclei RNA sequencing methods, spatial transcriptome sequencing (ST-seq) resolves transcriptome expression within the spatial context of intact tissue. This is achieved by integrating histology with RNA sequencing. These methodologies are completed sequentially on the same tissue section placed on a glass slide with printed oligo-dT spots, termed ST-spots. Transcriptomes within the tissue section are captured by the underlying ST-spots and receive a spatial barcode in the process. The sequenced ST-spot transcriptomes are subsequently aligned with the hematoxylin and eosin (H&E) image, giving morphological context to the gene expression signatures within intact tissue. We have successfully employed ST-seq to characterize mouse and human kidney tissue. Here, we describe in detail the application of Visium Spatial Tissue Optimization (TO) and Visium Spatial Gene Expression (GEx) protocols for ST-seq in fresh frozen kidney tissue.

Spatially Resolved Transcriptomes of Mammalian Kidneys Illustrate the Molecular Complexity and Interactions of Functional Nephron Segments

Available transcriptomes of the mammalian kidney provide limited information on the spatial interplay between different functional nephron structures due to the required dissociation of tissue with traditional transcriptome-based methodologies. A deeper understanding of the complexity of functional nephron structures requires a non-dissociative transcriptomics approach, such as spatial transcriptomics sequencing (ST-seq). We hypothesize that the application of ST-seq in normal mammalian kidneys will give transcriptomic insights within and across species of physiology at the functional structure level and cellular communication at the cell level. Here, we applied ST-seq in six mice and four human kidneys that were histologically absent of any overt pathology. We defined the location of specific nephron structures in the captured ST-seq datasets using three lines of evidence: pathologist's annotation, marker gene expression, and integration with public single-cell and/or single-nucleus RNA-sequencing datasets. We compared the mouse and human cortical kidney regions. In the human ST-seq datasets, we further investigated the cellular communication within glomeruli and regions of proximal tubules–peritubular capillaries by screening for co-expression of ligand–receptor gene pairs. Gene expression signatures of distinct nephron structures and microvascular regions were spatially resolved within the mouse and human ST-seq datasets. We identified 7,370 differentially expressed genes (p_adj < 0.05) distinguishing species, suggesting changes in energy production and metabolism in mouse cortical regions relative to human kidneys. Hundreds of potential ligand–receptor interactions were identified within glomeruli and regions of proximal tubules–peritubular capillaries, including known and novel interactions relevant to kidney physiology. Our application of ST-seq to normal human and murine kidneys confirms current knowledge and localization of transcripts within the kidney. Furthermore, the generated ST-seq datasets provide a valuable resource for the kidney community that can be used to inform future research into this complex organ.

Acquisition of murine splenic myeloid cells for protein and gene expression profiling by advanced flow cytometry and CITE-seq

Here, we outline detailed protocols to isolate and profile murine splenic dendritic cells (DCs) through advanced flow cytometry of the myeloid compartment and single-cell transcriptomic profiling with integrated cell surface protein expression through CITE-seq. This protocol provides a general transferrable road map for different tissues and species.

For complete details on the use and execution of this protocol, please refer to Lukowski et al. (2021).

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Protocol to obtain integrated single-cell gene and protein expression data

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Optimized flow cytometry panel for confident delineation of six main myeloid lineages

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Gating strategy identifies large cell state heterogeneity within each lineage

Absence of Batf3 reveals a new dimension of cell state heterogeneity within conventional dendritic cells

Conventional dendritic cells (cDCs) are traditionally subdivided into cDC1 and cDC2 lineages. Batf3 is a cDC1-required transcription factor, and we observed that Batf3−/− mice harbor a population of cDC1-like cells co-expressing cDC2-associated surface molecules. Using single-cell RNA sequencing with integrated cell surface protein expression (CITE-seq), we found that Batf3−/− mitotic immature cDC1-like cells showed reduced expression of cDC1 features and increased levels of cDC2 features. In wild type, we also observed a proportion of mature cDC1 cells expressing surface features characteristic to cDC2 and found that overall cDC cell state heterogeneity was mainly driven by developmental stage, proliferation, and maturity. We detected population diversity within Sirpa+ cDC2 cells, including a Cd33+ cell state expressing high levels of Sox4 and lineage-mixed features characteristic to cDC1, cDC2, pDCs, and monocytes. In conclusion, these data suggest that multiple cDC cell states can co-express lineage-overlapping features, revealing a level of previously unappreciated cDC plasticity.

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Single-cell proteogenomics identifies additional layers of DC heterogeneity

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cDC diversity is driven by proliferation, developmental stage, and maturation

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Lack of Batf3 increases cDCs with lineage-mixed features

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Sox4+ cDCs represent a cell state of lineage-mixed features

Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells

The cellular and molecular profiles that govern the endothelial heterogeneity of the circulatory system have yet to be elucidated. Using a data-driven approach to study the endothelial compartment via single-cell RNA sequencing, we characterized cell subpopulations within and assigned them to a defined endothelial hierarchy. We show that two transcriptionally distinct endothelial populations exist within the aorta and, using two independent trajectory analysis methods, confirm that they represent transitioning cells rather than discrete cell types. Gene co-expression analysis revealed crucial regulatory networks underlying each population, including significant metabolic gene networks in progenitor cells. Using mitochondrial activity assays and phenotyping, we confirm that endovascular progenitors display higher mitochondrial content compared to differentiated endothelial cells. The identities of these populations were further validated against bulk RNA sequencing (RNA-seq) data obtained from normal and tumor-derived vasculature. Our findings validate the heterogeneity of the aortic endothelium and previously suggested hierarchy between progenitor and differentiated cells.

Single-cell transcriptomics of alloreactive CD4+ T cells over time reveals divergent fates during gut graft-versus-host disease

Acute gastrointestinal (GI) graft-versus-host disease (GVHD) is a primary determinant of mortality after allogeneic hematopoietic stem cell transplantation (alloSCT). The condition is mediated by alloreactive donor CD4+ T cells that differentiate into pathogenic subsets expressing IFN-γ, IL-17A, or GM-CSF and is regulated by subsets expressing IL-10 and/or Foxp3. Developmental relationships between Th cell states during priming in mesenteric lymph nodes (mLNs) and effector function in the GI tract remain undefined at genome scale. We applied scRNA-Seq and computational modeling to a mouse model of donor DC-mediated GVHD exacerbation, creating an atlas of putative CD4+ T cell differentiation pathways in vivo. Computational trajectory inference suggested emergence of pathogenic and regulatory states along a single developmental trajectory in mLNs. Importantly, we inferred an unexpected second trajectory, categorized by little proliferation or cytokine expression, reduced glycolysis, and high tcf7 expression. TCF1hi cells upregulated α4β7 before gut migration and failed to express cytokines. These cells exhibited recall potential and plasticity following secondary transplantation, including cytokine or Foxp3 expression, but reduced T cell factor 1 (TCF1). Thus, scRNA-Seq suggested divergence of alloreactive CD4+ T cells into quiescent and effector states during gut GVHD exacerbation by donor DC, reflecting putative heterogeneous priming in vivo. These findings, which are potentially the first at a single-cell level during GVHD over time, may assist in examination of T cell differentiation in patients undergoing alloSCT.

Itch relief in patients with psoriasis: effectiveness of calcipotriol plus betamethasone dipropionate foam

BACKGROUND

Itch is common in psoriasis, adversely affecting health-related quality of life (HRQoL) and sleep.

OBJECTIVE

We evaluated the efficacy of topical fixed-dose combination calcipotriol 50 μg/g plus betamethasone dipropionate 0.5 mg/g cutaneous foam (Cal/BD foam) on itch, itch-related sleep loss and HRQoL vs. foam vehicle.

METHODS

We pooled data from three Phase II/III trials (NCT01536886/NCT01866163/NCT02132936) of Cal/BD foam vs. foam vehicle in adults with mild-severe psoriasis. For itch-related analyses, patients with baseline itch visual analogue scale (VAS) >40 (range 0-100) were analysed. Outcomes included the following: itch VAS reduction >40, ≥70% improvement in itch (Itch70) or itch-related sleep loss, 75% improvement in modified Psoriasis Area and Severity Index (excluding head; mPASI75) and Dermatology Life Quality Index (DLQI) scores 0/1 through 4 weeks.

RESULTS

Of 837 patients, 800 had baseline itch VAS >0 (Cal/BD foam, n = 610; foam vehicle, n = 190); 484 had baseline itch VAS >40. There was no correlation between itch VAS score and mPASI at baseline (R²  = 0.021). In patients with baseline itch VAS >40, more patients achieved itch VAS reduction >40 in the active vs. vehicle group from Day 5 onwards (Day 5: 57.5% vs. 40.2% [P < 0.05]; Week 4: 83.0% vs. 45.8% [P < 0.001]). More Cal/BD-foam-treated patients achieved Itch70 at Day 3 (34.2% vs. 22.5%; P < 0.05) through to Week 4 (79.3% vs. 38.1%; P < 0.001). In patients with baseline itch VAS >40 and sleep loss >20, improvements in itch-related sleep loss occurred at Week 1 and continued through 4 weeks. Itch-related improvements occurred before improvements in mPASI75. There were significant differences in the proportion of Cal/BD-foam- vs. foam-vehicle-treated patients with baseline DLQI >10 (n = 172 vs. n = 50) achieving DLQI ≤1 (25.0% vs. 4.0%; P = 0.001) and DLQI 0 (17.4% vs. 2.0%; P = 0.006) at Week 4.

CONCLUSION

Compared with foam vehicle, Cal/BD foam offers more rapid and effective itch relief, with associated significant improvements in sleep and DLQI.

ascend: R package for analysis of single-cell RNA-seq data

BACKGROUND

Recent developments in single-cell RNA sequencing (scRNA-seq) platforms have vastly increased the number of cells typically assayed in an experiment. Analysis of scRNA-seq data is multidisciplinary in nature, requiring careful consideration of the application of statistical methods with respect to the underlying biology. Few analysis packages exist that are at once robust, are computationally fast, and allow flexible integration with other bioinformatics tools and methods.

FINDINGS

ascend is an R package comprising tools designed to simplify and streamline the preliminary analysis of scRNA-seq data, while addressing the statistical challenges of scRNA-seq analysis and enabling flexible integration with genomics packages and native R functions, including fast parallel computation and efficient memory management. The package incorporates both novel and established methods to provide a framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and a wide range of visualization functions.

CONCLUSIONS

ascend is designed to work with scRNA-seq data generated by any high-throughput platform and includes functions to convert data objects between software packages. The ascend workflow is simple and interactive, as well as suitable for implementation by a broad range of users, including those with little programming experience.

Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media

We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.

Development of a novel cell sorting method that samples population diversity in flow cytometry

Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance.

Genome-wide discovery of human splicing branchpoints

During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.

Abstract P2-04-03: Can the interval cancer ratio diminish the need for background incidence estimates as a mammography screening programme performance indicator?

Background:

Interval cancers (IC) are cancers that are discovered within the interval between two screening examinations, i.e. they present themselves clinically before the next scheduled screening examination.

A mammography screening programme that is run in a population with a high breast cancer incidence can have a high interval cancer rate, and still have as protective an effect as a screening programme with a low IC-rate run in a population with a low breast cancer incidence. The effectiveness of a mammography screening programme is therefore normally evaluated by comparing the IC-rate to the expected breast cancer incidence without screening, i.e. the proportional interval cancer rate. The expected breast cancer incidence in absence of screening, or background incidence is, however, difficult to approximate, as the introduction of a screening program makes it difficult or impossible to find a comparable population group that is not screened.

We propose to use a new measure, the number of interval cancers out of the total number of cancers, called the interval cancer ratio, as an alternative measure for the burden of interval cancers in an organized mammography screening programme. We seek to validate this new measure by comparing it to the old measure, the proportional interval cancer rate.

Method:

We did a systematic review and included studies: 1) covering a service screening programme, 2) with inclusion of women aged 50-69 years, 3) that contained observed data, papers based on modeling only were excluded, 4) that contained data on number of interval cancers and number of women screened, or on interval cancers rate, and 5) that contained information on estimated breast cancer incidence rate of the background population. This resulted in 6 papers describing 12 mammography screening programmes.

Results:

The IC- ratio in studies including only initial screens, varied from 0.13 to 0.32 while the proportional interval cancer rate varied from 0.24 to 0.55 in the same studies. In studies including only subsequent screens the IC-ratio varied from 0.21 to 0.47 with a proportional interval cancer rate of 0.26 to 0.67. One study with mixed initial and subsequent screens with a majority of initial screens had an IC-ratio of 0.18, whereas the proportional interval cancer rate was 0.33. In the study with a majority of subsequent screens had an IC-ratio was 0.32 and the proportional interval cancer rate was 0.67.

There is a strong linear relationship between the interval cancer ratio and the proportional interval cancer rate in initial screens. In subsequent screens the trend is linear but is less obvious.

Conclusion:

Our main aim with this study was to propose and validate the interval cancer ratio as an alternative measure for the burden of interval cancers. The new measure seems to capture the burden of interval cancers just as well or better than the old measure, without the need for increasingly difficult estimations of background incidence, which makes it a more accessible tool when evaluating mammography screening programme performance.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-04-03.

Specificity and stability of the Acromyrmex-Pseudonocardia symbiosis

The stability of mutualistic interactions is likely to be affected by the genetic diversity of symbionts that compete for the same functional niche. Fungus-growing (attine) ants have multiple complex symbioses and thus provide ample opportunities to address questions of symbiont specificity and diversity. Among the partners are Actinobacteria of the genus Pseudonocardia that are maintained on the ant cuticle to produce antibiotics, primarily against a fungal parasite of the mutualistic gardens. The symbiosis has been assumed to be a hallmark of evolutionary stability, but this notion has been challenged by culturing and sequencing data indicating an unpredictably high diversity. We used 454 pyrosequencing of 16S rRNA to estimate the diversity of the cuticular bacterial community of the leaf-cutting ant Acromyrmex echinatior and other fungus-growing ants from Gamboa, Panama. Both field and laboratory samples of the same colonies were collected, the latter after colonies had been kept under laboratory conditions for up to 10 years. We show that bacterial communities are highly colony-specific and stable over time. The majority of colonies (25/26) had a single dominant Pseudonocardia strain, and only two strains were found in the Gamboa population across 17 years, confirming an earlier study. The microbial community on newly hatched ants consisted almost exclusively of a single strain of Pseudonocardia while other Actinobacteria were identified on older, foraging ants in varying but usually much lower abundances. These findings are consistent with recent theory predicting that mixtures of antibiotic-producing bacteria can remain mutualistic when dominated by a single vertically transmitted and resource-demanding strain.

Dynamic Wolbachia prevalence in Acromyrmex leaf-cutting ants: potential for a nutritional symbiosis

Wolbachia are renowned as reproductive parasites, but their phenotypic effects in eusocial insects are not well understood. We used a combination of qrt-PCR, fluorescence in situ hybridization and laser scanning confocal microscopy to evaluate the dynamics of Wolbachia infections in the leaf-cutting ant Acromyrmex octospinosus across developmental stages of sterile workers. We confirm that workers are infected with one or two widespread wsp genotypes of Wolbachia, show that colony prevalence is always 100% and characterize two rare recombinant genotypes. One dominant genotype is always present and most abundant, whereas another only proliferates in adult workers of some colonies and is barely detectable in larvae and pupae. An explanation may be that Wolbachia genotypes compete for host resources in immature stages while adult tissues provide substantially more niche space. Tissue-specific prevalence of the two genotypes differs, with the rarer genotype being over-represented in the adult foregut and thorax muscles. Both genotypes occur extracellularly in the foregut, suggesting an unknown mutualistic function in worker ant nutrition. Both genotypes are also abundant in the faecal fluid of the ants, suggesting that they may have extended functional phenotypes in the fungus garden that the ants manure with their own faeces.

Changes in the epidemiology of acute appendicitis and appendectomy in Danish children 1996-2004

PURPOSE

Aim of the study was to describe changes in the epidemiology of acute appendicitis in Danish children between 0-19 years of age for the period 1996-2004.

METHODS

The study was based on discharge diagnoses taken from the Danish National Patient Registry of all 28 274 patients with a diagnosis of acute uncomplicated or complicated appendicitis, and/or a registered procedure code of appendectomy. These data were computed together with data on the background population, and incidences were calculated.

RESULTS

A significant decrease in the incidence of acute uncomplicated appendicitis was found for all age groups (range, 13-36%). The decrease was present for both sexes, but most prominent in girls. The incidence of complicated acute appendicitis decreased by 10%.

CONCLUSION

The incidence of acute appendicitis is declining. The incidence of uncomplicated appendicitis appears to be declining more rapidly than that of complicated appendicitis. This finding does not necessarily imply poorer management of the disease, but-as suggested by others-could be due to different behaviours of uncomplicated and complicated appendicitis.

Peanut cross-reacting allergens in seeds and sprouts of a range of legumes

BACKGROUND

Recently, peanut-allergic patients have reported symptoms upon ingestion of bean sprouts produced from various legumes.

OBJECTIVE

This study was designed to identify immunoreactivity to seeds and sprouts of legumes other than peanut in sera from peanut-allergic patients.

METHODS

Crude protein extracts of seeds and sprouts (comprising cotelydons and hypocotyls/epicotyls) of peanut, soybean, green pea, blue lupine, mung bean, alfalfa, broad bean, and azuki bean were prepared. The reactivity of sera from 10 peanut-allergic patients to these extracts was analysed by indirect histamine release (HR), enzyme-allergosorbent test (EAST), EAST inhibition, and Western blots. Skin prick tests (SPTs) were performed on the patients with fresh legume seeds as well as four commercial legume sprouts, and food challenges with soybean, pea, and lupine were performed on a subgroup of the patients.

RESULTS

All legume seeds and commercial sprouts induced positive SPTs in some of the patients. Indirect HR experiments indicated an extensive co-reactivity between peanut and the legumes, and cross-reactivity was observed for soybean, pea, and lupine seeds as well as lupine hypocotyls in EAST inhibition experiments. Of the 16 protein extracts, soybean, pea, and lupine seed extracts produced visible bands in Western blots.

CONCLUSION

The symptoms reported by peanut-allergic patients after legume sprout intake might be caused by cross-reactivity of peanut-specific antibodies. The intake of raw legume sprouts might cause symptoms in peanut-allergic patients.

Genetic analysis of resistance to yellow rust in hexaploid wheat using a mixture model for multiple crosses

DNA-based molecular markers have been used in numerous studies for tagging specific genes in wheat for subsequent use in marker-assisted selection. Usually in plant breeding, procedures for mapping genes are based on analysis of a single segregating population. However, breeding programmes routinely evaluate large numbers of progeny derived from multiple-related crosses with some parental lines shared. In most such related crosses, the number of progeny is quite small. Thus, statistical techniques for detecting quantitative trait loci (QTLs) using data from conventional multi-cross breeding programmes are interesting. The objective of this study is to present a mixture model for QTL mapping in crosses of multiple inbred varieties with non-normal phenotype distributions and to use this model to map QTLs for yellow rust resistance in elite wheat breeding material. Three doubled haploid populations consisting of 41, 42 and 55 lines, respectively, originating from four parental varieties were studied. Multi-cross QTL analysis with three specific pathogen isolates of Puccinia striiformis f. sp. tritici and a mixture of the isolates revealed QTLs for resistance at four different genomic locations. These QTLs were found on chromosome 2AL, 2AS, 2BL and 6BL and explained between 21 and 41% of the phenotypic variation. Two of these QTLs, one on the long arm of chromosome 2A and one on the short arm of chromosome 2A were identical to the known yellow rust resistance genes Yr32 and Yr17, respectively, whereas the QTLs located on the long arms of chromosomes 2B and 6B may reflect types of resistance to yellow rust, which have not previously been mapped.

Cross-reactivity to eel, eelpout and ocean pout in codfish-allergic patients

Fish allergy is one of the most common food allergies in both children and adults and patients with allergic reactions to one fish species have in many cases been given the advice to avoid all fish, without further evaluation. The possible common reactivity between different fish species is not well studied. Because of this and a possible exploitation of fish species hitherto not much used in the Scandinavian diet ocean pout, eelpout and eel were evaluated. We examined the serological and biological cross-reactivity of these species in double-blind challenged-confirmed codfish-allergic patients using CAP, Maxisorp-radio allergosorbent test (RAST) inhibition, western blot, skin prick test (SPT) and histamine release (HR). All 18 codfish allergic patients had specific IgE to ocean pout, eelpout and eel determined by Maxisorp-RAST. All four fish species could induce basophil HR using blood from 16 of 18 patients and all patients tested reacted in SPT. This study demonstrates that patients with a verified clinical allergy to codfish in a high frequency express biological cross-reactivity to other fish species. By RAST inhibition this common reactivity was shown to be a true cross-reactivity.

Field evaluation of emmer wheat-derived synthetic hexaploid wheat for resistance to Russian wheat aphid (Homoptera: Aphididae)

Broadening the genetic base for resistance to Russian wheat aphid, Diuraphis noxia (Mordvilko) (Homoptera: Aphididae), in bread wheat, Triticum aestivum L., is desirable. To date, identified Russian wheat aphid resistance genes are either located to the D chromosomes or to rye translocation of wheat, and resistance derived from the A or B genomes of tetraploid Triticum spp. would therefore be highly beneficial. Fifty-eight synthetic hexaploid wheat, derived from interspecific crosses of Triticum dicoccum Schrank. and Aegilops tauschii (Coss.) Schmal. and their parents were evaluated for resistance to Russian wheat aphid under field conditions. Plots infested with aphids were compared with plots protected with insecticides. The T. dicoccum parents were highly resistant to Russian wheat aphids, whereas the Ae. tauschii parents were susceptible. Resistance levels observed in the synthetic hexaploids were slightly below the levels of their T. dicoccum parents when a visual damage scale was used. but no major resistance suppression was observed among the synthetics. Russian wheat aphid infestation on average reduced plant height and kernel weight at harvest in the synthetic hexaploids and the T. dicoccum parents by 3-4%, whereas the susceptible control 'Seri M82' suffered losses of above 20%. Because resistance in the synthetic hexaploid wheat is derived from their T. dicoccum parent, resistance gene(s) must be located on the A and/or B genomes. They must therefore be different from previously identified Russian wheat aphid resistance genes, which have all been located on the D genome of wheat or on translocated segments.

Field evaluation of emmer wheat-derived synthetic hexaploid wheat for resistance to Russian wheat aphid (Homoptera: Aphididae)

Broadening the genetic base for resistance to Russian wheat aphid, Diuraphis noxia (Mordvilko) (Homoptera: Aphididae), in bread wheat, Triticum aestivum L., is desirable. To date, identified Russian wheat aphid resistance genes are either located to the D chromosomes or to rye translocation of wheat, and resistance derived from the A or B genomes of tetraploid Triticum spp. would therefore be highly beneficial. Fifty-eight synthetic hexaploid wheat, derived from interspecific crosses of Triticum dicoccum Schrank. and Aegilops tauschii (Coss.) Schmal. and their parents were evaluated for resistance to Russian wheat aphid under field conditions. Plots infested with aphids were compared with plots protected with insecticides. The T. dicoccum parents were highly resistant to Russian wheat aphids, whereas the Ae. tauschii parents were susceptible. Resistance levels observed in the synthetic hexaploids were slightly below the levels of their T. dicoccum parents when a visual damage scale was used. but no major resistance suppression was observed among the synthetics. Russian wheat aphid infestation on average reduced plant height and kernel weight at harvest in the synthetic hexaploids and the T. dicoccum parents by 3-4%, whereas the susceptible control 'Seri M82' suffered losses of above 20%. Because resistance in the synthetic hexaploid wheat is derived from their T. dicoccum parent, resistance gene(s) must be located on the A and/or B genomes. They must therefore be different from previously identified Russian wheat aphid resistance genes, which have all been located on the D genome of wheat or on translocated segments.

Quantitative trait loci affecting plant regeneration from protoplasts of Brassica oleracea

Quantitative trait loci (QTLs) controlling the plant-regeneration ability of Brassica oleracea protoplasts were mapped in a population of 128 F(2) plants derived from a cross between the high-responding, rapid-cycling line and a low-responding, broccoli breeding line of B. oleracea. A modified bulked segregant analysis with AFLP markers identified two QTLs for plant regeneration. In a multiple regression analysis, the two QTLs explained 83% of the total genetic variation for regeneration recorded 15 weeks after initial transfer of microcalli to regeneration medium. Both QTLs showed additive effects, and the alleles contributing to the high regeneration frequencies were derived from the high-responding, rapid-cycling line. Using microsatellites with known location, the two QTLs were mapped to linkage groups O2 and O9 on the map published by Sebastian et al. [(2000) Theor Appl Genet 100:75-81] or to chromosomes C8 and C7 on the map published by Saal et al. [(2001) Theor Appl Genet 102:695-699]. QTLs for the early flowering trait of the rapid-cycling parent have previously been mapped to the same two linkage groups. Association between flowering time and regeneration ability was, however, not found in the present material, indicating that plant-regeneration ability can be transferred between cultivars independently of the early flowering trait. The detection of two major QTLs for plant regeneration in B. oleracea may provide the initial step towards the identification of markers suitable for marker-assisted selection of regeneration ability.

Characterization of greenbug (Homoptera: Aphididae) resistance in synthetic hexaploid wheats

Twelve greenbug (Schizaphis graminum (Rondani)) biotype E-resistant synthetic hexaploid wheats synthesized by crossing Triticum dicoccum Schrank. and Aegilops tauschii (Coss.) Schmal. were evaluated for the three known insect resistance categories, including antibiosis, anti-xenosis, and tolerance. Different methods were evaluated for calculating antibiosis and tolerance. Calculating intrinsic rate of population increase and measuring leaf chlorophyll content with a SPAD chlorophyll meter proved to be time- and labor-efficient for antibiosis and tolerance determination, respectively. The resistance in all synthetic hexaploids proved to be the result of a combination of antibiosis, antixenosis, and tolerance, which makes them valuable sources of greenbug resistance. To assist plant breeders in selecting the best germplasm for greenbug resistance, a plant resistance index was created that revealed differences among the synthetic hexaploid wheats.

Analysis of potential duplicates in barley gene bank collections using re-sampling of microsatellite data

Redundant duplication among putative Nordic spring barley material held at 12 gene banks worldwide was studied using 35 microsatellite primer pairs covering the entire barley genome. These microsatellite markers revealed an average of 7.1 alleles per locus, and a range of 1 to 17 different alleles per locus. Similarity of accession name was initially used to partition the 174 repatriated accessions into 36 potential duplicate groups, and one group containing 36 apparently unique or unrelated accessions. This partitioning was efficient to produce a distribution of mainly small average genetic distances within potential duplicate groups compared to distances from the group of unique accessions. However, comparisons within potential duplicate groups still contained large genetic distances of the same size as distances between unique accessions indicating classification errors. A bootstrap approach based on re-sampling of both microsatellite markers and alleles within marker loci was used to test for homogeneity within potential duplicate groups. The test was used in each group for sequential elimination of accessions with a significantly large average genetic distance to identify a homogeneous group. Such genetically homogeneous groups of two or more accessions were identified in 22 among the 36 potential duplicate groups studied. Results from the genetic analysis of some potential duplicate groups supported previous conclusions based on passport data through inclusion of the historically most-original accession in the genetically homogeneous group. In other potential duplicate groups the apparently most-original accession according to passport data was not included in the homogeneous set of accessions, indicating that this most-original accession does not have duplicate accessions in the group. During the present study the largest average genetic distance accepted in any homogeneous group was smaller than the smallest distance declared significant in any group, with a threshold average genetic distance of approximately 0.14. The results are discussed with respect to the identification of duplicate accessions within potential duplicate groups, as well as the elimination of genetic off types in such groups. Furthermore, large barley gene bank collections may be screened for potential duplicates with genetic distances below the suggested threshold of 0.14.

Expression and suppression of resistance to greenbug (Homoptera: Aphididae) in synthetic hexaploid wheats derived from Triticum dicoccum x Aegilops tauschii crosses

Fifty-eight synthetic hexaploid wheats, developed by crossing Triticum dicoccum Schrank. and Aegilops tauschii (Coss.) Schmal., were evaluated at the seedling stage, together with their parents, for resistance to greenbug (Schizaphis graminum Rondani) under greenhouse conditions. Seedlings of different synthetic hexaploids showed large phenotypic differences for resistance. All the T. dicoccum parents were susceptible, while high levels of resistance were observed in some of the Ae. tauschii parents. Of the synthetic hexaploids derived from resistant Ae. tauschii parents, a high proportion (76%) showed levels of resistance to the greenbug biotype used that were comparable to those of the resistant parent. While there were clear indications of the presence of suppressor genes for greenbug resistance in the A and/or B genomes of T. dicoccum in some synthetics, positive epistatic interaction was also found in synthetic hexaploids with higher levels of resistance than that of either parent. Resistance from different Ae. tauschii accessions was expressed differently when crossed with the same T. dicoccum, indicating diversity among the resistance genes present in the test synthetic hexaploid wheats. Based on resistance reactions, the genes conferring greenbug resistance in these synthetic hexaploids are probably different from resistance genes previously transferred to wheat from Ae. tauschii.

Expression and suppression of resistance to greenbug (Homoptera: Aphididae) in synthetic hexaploid wheats derived from Triticum dicoccum x Aegilops tauschii crosses

Fifty-eight synthetic hexaploid wheats, developed by crossing Triticum dicoccum Schrank. and Aegilops tauschii (Coss.) Schmal., were evaluated at the seedling stage, together with their parents, for resistance to greenbug (Schizaphis graminum Rondani) under greenhouse conditions. Seedlings of different synthetic hexaploids showed large phenotypic differences for resistance. All the T. dicoccum parents were susceptible, while high levels of resistance were observed in some of the Ae. tauschii parents. Of the synthetic hexaploids derived from resistant Ae. tauschii parents, a high proportion (76%) showed levels of resistance to the greenbug biotype used that were comparable to those of the resistant parent. While there were clear indications of the presence of suppressor genes for greenbug resistance in the A and/or B genomes of T. dicoccum in some synthetics, positive epistatic interaction was also found in synthetic hexaploids with higher levels of resistance than that of either parent. Resistance from different Ae. tauschii accessions was expressed differently when crossed with the same T. dicoccum, indicating diversity among the resistance genes present in the test synthetic hexaploid wheats. Based on resistance reactions, the genes conferring greenbug resistance in these synthetic hexaploids are probably different from resistance genes previously transferred to wheat from Ae. tauschii.

Allergenic components of a novel food, Micronesian nut Nangai (Canarium indicum), shows IgE cross-reactivity in pollen allergic patients

BACKGROUND

New foods may present a risk for food hypersensitive patients. Several examples exist of allergic reactions caused by cross-reactive plant-derived foods, and new foods should be scrutinised before introducing them to the market. We have evaluated the clinical and serological relevance of cross-reactivity between Nangai and pollen allergens.

METHODS

Cross-reactivity was examined with Maxisorp RAST (radioallergosorbent test), RAST inhibition and Western blot, using sera from patients allergic to grass, birch and mugwort pollen. None of the patients reported having seen or eaten Nangai previously. To determine the biological and clinical relevance of the cross-reactivity, histamine release (HR) test, skin prick test (SPT) and food challenge were used.

RESULTS

There was prevalence for reactivity against Nangai in the group of pollen allergic patients. This cross-reactivity seems to be related--at least in part--to carbohydrate epitopes. Three out of 12 patients tested with Nangai were positive upon open challenge, but using double blind placebo controlled food challenge (DBPCFC) this could not be confirmed in two patients. The biological effects of Nangai on allergic patients were confirmed using HR and SPT.

CONCLUSION

The Nangai specific IgE found among pollen allergic patients addresses the need for control of new or changed foods before introduction to the market.

Geophysics. Longitudinal variation in springtime ozone trends

Satellite measurements indicate that mid-latitude ozone depletion in the Northern Hemisphere spring during 1979-97 was worst over Europe and Russia. Here we show that these longitudinal differences in ozone trends are due to a combination of decadal variations in the circulation and transport of ozone-depleted air from the polar vortex. Any increase in ozone depletion in the polar vortex as a result of future cooling of the stratosphere would therefore be particularly bad over Europe and Russia.

Cytodifferentiation and transformation of embryogenic callus lines derived from anther culture of wheat

Three types of callus tissues established from anther culture of eleven doubled haploid (DH) lines of wheat (Triticum aestivum L.) were evaluated for their ability in enhancing friable embryogenic (Type II) culture differentiation and genetic transformation. Differences between types of callus inocula were highly significant (P < 0.001), suggesting that the quality of the initial callus explant is of profound importance in encouraging the proliferation of Type II cultures. Other factors found to be crucial included weekly subculture of friable embryogenic callus tissues on a maintenance medium containing 30 microM dicamba and a predominance of amino-acid nitrogen supplement. Transfer and integration of the beta-glucuronidase gene was also affected by the type of inoculum when suitable embryogenic cell cultures were transformed using silicon carbide whiskers and high velocity microprojectiles. Expression of the hygromycin phosphotransferase selectable marker gene sequence was confirmed in all the stably transformed cell lines maintained on selection media containing lethal levels of hygromycin. Comparatively, there were differences in the frequency of regenerable, transgenic clonal segments between whisker-treated and microprojectile bombarded tissues mainly as a result of the fact that cultures vortexed with whiskers were more capable of post-treatment cell proliferation and embryo differentiation than those bombarded with cDNA-coated microprojectiles. Conditions for obtaining these results are outlined and discussed in relation to the suitability of the two transformation strategies for producing transgenic cell aggregates of wheat.

[Chlamydia pneumoniae]

Chlamydia are obligate intracellular bacteria with a biphasic life cycle. In 1986 a new species of Chlamydiae, Chlamydia psittaci TWAR was discovered, later named Chlamydia pneumoniae. C. pneumoniae is probably an important pathogen causing respiratory tract infections in man, ranging from subclinical infection to life threatening pneumonia. Infections can occur in epidemics. Furthermore, associations between C. pneumoniae infection and coronary artery disease, lethal myocarditis and sarcoidosis have been suggested. The current diagnostic method is based on detection of specific antibodies against C. pneumoniae in blood. Macrolides or tetracyclines are the drugs of choice for treatment of C. pneumoniae infection.

Nuclear genes affecting percentage of green plants in barley (Hordeum vulgare L.) anther culture

The genetics behind response in barley anther culture was studied with 22 reciprocal and one single: cross between three varieties with high and four varieties with low capacity for green plant formation. Effects of genotypes dominated embryo formation and percentages of green plants, accounting for 62 and 76% of total variation, respectively, with almost no genetic effect on the ability to regenerate plants from pollen embryos. Nuclear genes could explain all genotype effects in this plant material, since no reciprocal effects were indicated. The three parents with high and the four parents with low capacity for green plant formation formed two phenotypically homogeneous groups, producing 27-52% and 0-7% green plants, respectively. Genetic variation within hybrids for both embryo and green plant formation could be explained completely by general combining ability (GCA). The results are discussed with respect to a previous similar study in hexaploid wheat and the reported existence of DNA deletions in the plastid genomes in albino plants from anther culture of wheat and barley.

[The polymerase chain reaction used in microbiologic diagnosis]

Among the new DNA technological methods for microbiological diagnosis, the most promising seems to be the polymerase chain reaction (PCR). The sensitivity of the method is approximately 100% and the specificity is between 90% and 100%, depending on the availability of an already existing test sufficient for comparison. The PCR is able to detect only one microorganism in clinical samples. Because of this high sensitivity, contamination of samples is one of the major problems. After certain preparation procedures, the method can be used on different kinds of human sample material. The PCR could be used for detection of a microorganism, for detection of a single gene (toxin gene) or for typing of microorganisms. It is expected that, in the immediate future PCR will be a prominent part of the methods used in microbiological diagnosis.

Nuclear genes affecting albinism in wheat (Triticum aestivum L.) anther culture

Inheritance of the ability to respond in wheat anther culture was studied from 6×2 reciprocal crosses between six varieties with high and two varieties with low capacity for green plant formation and their parents, replicated in two environments. Effects of genotypes dominated embryo formation and percentages of green plants, accounting for 78.4% and 85.4% of total variation, respectively, while smaller genetic effects were indicated for regeneration. Nuclear genes could explain almost all the genotype effects in this material. Embryo formation showed heterosis over high parent for 5 of the 12 hybrids, while percentages of green plants from the hybrids were intermediate to the parents. General Combining Ability (GCA) could explain 78.8% of the variation for embryo formation among the hybrids, whereas differences in percentage of green plants were dominated by Specific Combining Ability (SCA), accounting for 67.9% of hybrid variation. A positive correlation (r=0.81(**)) was observed between the genetic capacity for regeneration and green plant formation. Analysis of covariance indicated that effects causing GCA for green plant formation were mainly responsible for this correlation. A regression model with two parallel lines divided the six parent lines with high green plant formation into three groups with respect to their reactions with the two testers. The results are discussed with regard to possible involvement of two sets of nuclear genes affecting the percentage of green plants obtained in wheat anther culture: one set consisting of mainly additive effects affecting green plant percentage through an initial effect on regeneration ability, and another set of two or a few more major genes with dominance or epistatic effects uncorrelated with regeneration.

Lateral and anterior instability in acute ankle distortion. A radiologic investigation

In a prospective consecutive investigation radiologic tests for lateral and anterior instability in acute ankle distortion were found to be reliable indications of lateral ligament ruptures. Arthrography of the ankle joint was used as reference. Absence of instability, however, gives little information as to the ligamental status. The size of this group constitutes a clinical problem. Better results are achieved by combining lateral and anterior instability tests. If only one test is used, the anterior instability test should be preferred. The results of the two tests bare no relation to the degree of ligament ruptures found at operation.

Ruptures of the lateral ligaments of the ankle. Clinical diagnosis

During the 11-month period 1 October 1977 to 31 August 1978 a total of 44 patients with acute supination trauma of the ankle were examined. The clinical findings were compared with the results of arthrography. This revealed that direct and indirect tenderness of the anterior talofibular ligament and calcaneofibular ligament respectively, combined with a greater than or equal to 4 cm swelling anteriorly and over the lateral malleolus, indicated a ligament injury with great likelihood. If some of the diagnostic signs are absent, most emphasis should be laid on the swelling over the lateral malleolus and on the direct and indirect tenderness of the calcaneofibular ligament. The talar-tilt test and examination for the drawer sign were of limited diagnostic value.

Rupture of the lateral ligaments of the ankle: operation or plaster cast? A propective study

The material comprises 444 patients, aged 12-50 years, with acute sprain of the ankle, seen over an 11-month period (1.10. 1977 to 31.8. 1978). Clinical examination showed no rupture of the ligaments in 53. Arthrography in the remaining patients revealed rupture of the lateral ligaments in 209 (in two-thirds of the anterior talofibular ligament and in one-third of the anterior talofibular as well as calcaneofibular ligament). Conservative treatment with a below-knee plaster cast for 5 weeks was employed in 107 patients, while 102 were treated surgically by suture of the ruptured ligament(s) and subsequently wore a below-knee plaster cast for 5 weeks. The follow-up 1 year after the accident was attended by 63 per cent of the patients. Good results were found in 76 per cent of those treated by plaster cast only and in 81 per cent of those treated by surgery. The difference is not statistically significant.