An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping

Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has been performed in extracts from wildtype cells which often do not have sufficient flux towards the pathways of interest, which can be enhanced by engineering. Here, to address this gap, we create a set of engineered Escherichia coli and Saccharomyces cerevisiae strains rewired via CRISPR-dCas9 to achieve high-flux toward key metabolic precursors; namely, acetyl-CoA, shikimate, triose-phosphate, oxaloacetate, α-ketoglutarate, and glucose-6-phosphate. Cell-free extracts generated from these strains are used for targeted enzyme screening in vitro. As model systems, we assess in vivo and in vitro production of triacetic acid lactone from acetyl-CoA and muconic acid from the shikimate pathway. The need for these platforms is exemplified by the fact that muconic acid cannot be detected in wildtype extracts provided with the same biosynthetic enzymes. We also perform metabolomic comparison to understand biochemical differences between the cellular and cell-free muconic acid synthesis systems (E. coli and S. cerevisiae cells and cell extracts with and without metabolic rewiring). While any given pathway has different interfaces with metabolism, we anticipate that this set of pre-optimized, flux enhanced cell extracts will enable prototyping efforts for new biosynthetic pathways and the discovery of biochemical functions of enzymes.

Information theory and machine learning illuminate large-scale metabolomic responses of Brachypodium distachyon to environmental change

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio-Analytic Resource for Plant Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.

Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.

Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long-term warming

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils.

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE

Phenazines (Phzs), a family of chemicals with a phenazine backbone, are secondary metabolites with diverse properties such as antibacterial, anti-fungal, or anticancer activity. The core derivatives of phenazine, phenazine-1-carboxylic acid (PCA) and phenazine-1,6-dicarboxylic acid (PDC), are themselves precursors for various other derivatives. Recent advances in genome mining tools have enabled researchers to identify many biosynthetic gene clusters (BGCs) that might produce novel Phzs. To characterize the function of these BGCs efficiently, we performed modular construct assembly and subsequent multi-chassis heterologous expression using chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE allowed rapid integration of a PCA BGC into 23 diverse γ-proteobacteria species and allowed us to identify top PCA producers. We then used the top five chassis hosts to express four partially refactored PDC BGCs. A few of these platforms produced high levels of PDC. Specifically, Xenorhabdus doucetiae and Pseudomonas simiae produced PDC at a titer of 293 mg/L and 373 mg/L, respectively, in minimal media. These titers are significantly higher than those previously reported. Furthermore, selectivity toward PDC production over PCA production was improved by up to 9-fold. The results show that these strains are promising chassis for production of PCA, PDC, and their derivatives, as well as for function characterization of Phz BGCs identified via bioinformatics mining.

CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria

It is generally believed that exchange of secondary metabolite biosynthetic gene clusters (BGCs) among closely related bacteria is an important driver of BGC evolution and diversification. Applying this idea may help researchers efficiently connect many BGCs to their products and characterize the products' roles in various environments. However, existing genetic tools support only a small fraction of these efforts. Here, we present the development of chassis-independent recombinase-assisted genome engineering (CRAGE), which enables single-step integration of large, complex BGC constructs directly into the chromosomes of diverse bacteria with high accuracy and efficiency. To demonstrate the efficacy of CRAGE, we expressed three known and six previously identified but experimentally elusive non-ribosomal peptide synthetase (NRPS) and NRPS-polyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens in 25 diverse γ-Proteobacteria species. Successful activation of six BGCs identified 22 products for which diversity and yield were greater when the BGCs were expressed in strains closely related to the native strain than when they were expressed in either native or more distantly related strains. Activation of these BGCs demonstrates the feasibility of exploiting their underlying catalytic activity and plasticity, and provides evidence that systematic approaches based on CRAGE will be useful for discovering and identifying previously uncharacterized metabolites.

An integrated workflow for phenazine-modifying enzyme characterization

Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs.

New insight into the role of MMP14 in metabolic balance

Membrane-anchored matrix metalloproteinase 14 (MMP14) is involved broadly in organ development through both its proteolytic and signal-transducing functions. Knockout of Mmp14 (KO) in mice results in a dramatic reduction of body size and wasting followed by premature death, the mechanism of which is poorly understood. Since the mammary gland develops after birth and is thus dependent for its functional progression on systemic and local cues, we chose it as an organ model for understanding why KO mice fail to thrive. A global analysis of the mammary glands' proteome in the wild type (WT) and KO mice provided insight into an unexpected role of MMP14 in maintaining metabolism and homeostasis. We performed mass spectrometry and quantitative proteomics to determine the protein signatures of mammary glands from 7 to 11 days old WT and KO mice and found that KO rudiments had a significantly higher level of rate-limiting enzymes involved in catabolic pathways. Glycogen and lipid levels in KO rudiments were reduced, and the circulating levels of triglycerides and glucose were lower. Analysis of the ultrastructure of mammary glands imaged by electron microscopy revealed a significant increase in autophagy signatures in KO mice. Finally, Mmp14 silenced mammary epithelial cells displayed enhanced autophagy. Applied to a systemic level, these findings indicate that MMP14 is a crucial regulator of tissue homeostasis. If operative on a systemic level, these findings could explain how Mmp14KO litter fail to thrive due to disorder in metabolism.

Evaluation of DNA methylation at imprinted DMRs in the spermatozoa of oligozoospermic men in association with MTHFR C677T genotype

Altered DNA methylation has been previously identified in the spermatozoa of infertile men; however, the origins of these errors are poorly understood. DNA methylation is an epigenetic modification which is thought to play a fundamental role in male germline development. DNA methylation reactions rely on the cellular availability of methyl donors, which are primarily products of folate metabolism, where a key enzyme is methylenetetrahydrofolate reductase (MTHFR). The MTHFR C677T single nucleotide polymorphism (SNP) reduces enzyme activity and may potentially alter DNA methylation processes during germline development. The objective of this study was to determine whether altered DNA methylation in spermatozoa is associated with the MTHFR C677T SNP. DNA methylation was evaluated at the H19, IG-GTL2, and MEST imprinted differentially methylated regions in the spermatozoa of 53 men - 44 oligozoospermic men and nine fertile men with normal sperm parameters via bisulfite sequencing of sperm clones. The 44 infertile men were stratified by severity of oligozoospermia - three normal (>15 million spermatozoa/mL), eight moderate (5-15 million spermatozoa/mL), 23 severe (1-5 million spermatozoa/mL), and 10 very severe (<1 million spermatozoa/mL). MTHFR C677T SNP genotyping was conducted in a subset of 44 peripheral blood samples via restriction fragment length polymorphism. A total of three men - severe oligozoospermic and CT genotype - were found to be altered, which is defined as having ≥50% of their clones altered, where an altered clone was in turn defined as ≥50% of CpGs with incorrect DNA methylation patterns. The incidence of three altered men within the CT subgroup, however, was not significantly higher than the incidence in the CC subgroup. Taken together, altered DNA methylation in spermatozoa was not significantly associated with the MTHFR C677T SNP; however, there was a trend for higher incidence of alterations among severe oligozoospermic infertile men with CT genotypes.

Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify transcriptional regulators of lipid accumulation, we performed an integrative chromatin signature and transcriptomic analysis to decipher the regulation of lipid biosynthesis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between the algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor, PSR1, as a pivotal switch that triggers cytosolic lipid accumulation. Dissection of the PSR1-induced lipid profiles corroborates its role in coordinating multiple lipid-inducing stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a transcriptional regulator of algal lipid metabolism will facilitate targeted engineering strategies to mediate high lipid production in microalgae.

Recurrent triploidy due to a failure to complete maternal meiosis II: whole-exome sequencing reveals candidate variants

Triploidy is a relatively common cause of miscarriage; however, recurrent triploidy has rarely been reported. A healthy 34-year-old woman was ascertained because of 18 consecutive miscarriages with triploidy found in all 5 karyotyped losses. Molecular results in a sixth loss were also consistent with triploidy. Genotyping of markers near the centromere on multiple chromosomes suggested that all six triploid conceptuses occurred as a result of failure to complete meiosis II (MII). The proband's mother had also experienced recurrent miscarriage, with a total of 18 miscarriages. Based on the hypothesis that an inherited autosomal-dominant maternal predisposition would explain the phenotype, whole-exome sequencing of the proband and her parents was undertaken to identify potential candidate variants. After filtering for quality and rarity, potentially damaging variants shared between the proband and her mother were identified in 47 genes. Variants in genes coding for proteins implicated in oocyte maturation, oocyte activation or polar body extrusion were then prioritized. Eight of the most promising candidate variants were confirmed by Sanger sequencing. These included a novel change in the PLCD4 gene, and a rare variant in the OSBPL5 gene, which have been implicated in oocyte activation upon fertilization and completion of MII. Several variants in genes coding proteins playing a role in oocyte maturation and early embryonic development were also identified. The genes identified may be candidates for the study in other women experiencing recurrent triploidy or recurrent IVF failure.

OpenMSI: a high-performance web-based platform for mass spectrometry imaging

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data access (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.

Resolving brain regions using nanostructure initiator mass spectrometry imaging of phospholipids

In a variety of neurological diseases, pathological progression is cell type and region specific. Previous reports suggest that mass spectrometry imaging has the potential to differentiate between brain regions enriched in specific cell types. Here, we utilized a matrix-free surface mass spectrometry approach, nanostructure initiator mass spectrometry (NIMS), to show that spatial distributions of multiple lipids can be used as a 'fingerprint' to discriminate between neuronal- and glial- enriched brain regions. In addition, glial cells from different brain regions can be distinguished based on unique lipid profiles. NIMS images were generated from sagittal brain sections and were matched with immunostained serial sections to define glial cell enriched areas. Tandem mass spectrometry (LC-MS/MS QTOF) on whole brain extracts was used to identify 18 phospholipids. Multivariate statistical analysis (Nonnegative Matrix Factorization) enhanced differentiation of brain regions and cell populations compared to single ion imaging methods. This analysis resolved brain regions that are difficult to distinguish using conventional stains but are known to have distinct physiological functions. This method accurately distinguished the frontal (or somatomotor) and dorsal (or retrosplenial) regions of the cortex from each other and from the pons region.

Self-degrading, MRI-detectable hydrogel sensors with picomolar target sensitivity

Nanostructured hydrogels have been developed as synthetic tissues and scaffolds for cell and drug delivery, and as guides for tissue regeneration. A fundamental problem in the development of synthetic hydrogels is that implanted gel structure is difficult to monitor noninvasively. This work demonstrates that the aggregation of magnetic nanoparticles, attached to specific macromolecules in biological and synthetic hydrogels, can be controlled to detect changes in gel macromolecular structure with MRI. It is further shown that the gels can be made to self-degrade when they come into contact with a target molecule in as low as pM concentrations. The sensitivity of the gels to the target is finely controlled using an embedded zymogen cascade amplifier. These "MRI reporter gels" may serve as smart, responsive polymer implants, as tissue scaffolds to deliver drugs, or to detect specific pathogens in vivo.

Gastrointestinal nematode parasites of sheep: a dynamic model for their effect on liveweight gain

This paper presents an individual-based model for gastrointestinal nematode parasites of sheep and includes the effect of these parasites on the liveweight performance of young sheep. Parasitism is known to affect the host animal in at least two ways. The first induces a loss of appetite in the host, which reduces pasture consumption compared with the parasite-free animal. This effect is examined in the first part of the study. The second major effect of parasitism is a reduction in the metabolic efficiency of the host which decreases nutrients available for maintenance and growth. The latter part of the paper examines the consequences of incorporating this effect on the liveweight changes in individuals in a group of sheep. Previous models addressing this issue have only given mean liveweight and worm burden changes.

Nematode parasites of sheep: extension of a simple model to include host variability

We use results from a simulation-based model of nematode infection of sheep to refine the parameters in a simpler generic model of host-parasite population dynamics. These parameters describe the following host-parasite traits: probability of establishment of ingested larvae, mortality rate of adult parasites, and fecundity of adult female parasites. This simple model is then extended by allowing those parameters to vary amongst individual hosts. A sensitivity analysis is performed to determine which parameters have most influence on host parasite burden. The establishment parameter has the greatest effect on the peak value of parasite burden whilst the other two parameters have more effect on the duration of the burden. A comparison is made with results from the flock model after discussion of the definition of an average host. By allowing these parameters to vary simultaneously within the individual hosts we are able to reproduce the over-dispersed distribution of adult parasites frequently seen in nematode infections of sheep flocks.

Escherichia coli O157:H7 outbreak linked to salami, British Columbia, Canada, 1999

An outbreak of E. coli O157:H7 infections was identified in November 1999 with a fivefold increase in the occurrence of laboratory-confirmed cases of E. coli O157:H7 infection. A matched case-control study was conducted. Samples of food from cases and from retailers were analysed for the presence of E. coli O157:H7. A total of 143 cases were identified over a 12-week period with the same pulsed-field gel electrophoresis (PFGE) pattern. The case-control study found that Company A salami was significantly associated with illness (Mantel-Haenszel matched odds ratio 10.0%, 95% CI 1.4-434, P=0.01). Company A salami tested positive for E. coli O157:H7 and isolates had the same PFGE pattern as case isolates. An immediate voluntary national recall of Company A dry fermented meat products took place. Findings from the investigation of this outbreak suggest that the hold-and-test option may not be adequate to prevent shiga-toxigenic Escherichia coli (STEC) infection in salami consumers.

Temporally structured replay of awake hippocampal ensemble activity during rapid eye movement sleep

Human dreaming occurs during rapid eye movement (REM) sleep. To investigate the structure of neural activity during REM sleep, we simultaneously recorded the activity of multiple neurons in the rat hippocampus during both sleep and awake behavior. We show that temporally sequenced ensemble firing rate patterns reflecting tens of seconds to minutes of behavioral experience are reproduced during REM episodes at an equivalent timescale. Furthermore, within such REM episodes behavior-dependent modulation of the subcortically driven theta rhythm is also reproduced. These results demonstrate that long temporal sequences of patterned multineuronal activity suggestive of episodic memory traces are reactivated during REM sleep. Such reactivation may be important for memory processing and provides a basis for the electrophysiological examination of the content of dream states.

Metastatic and nonmetastatic models of retinoblastoma

To generate animal models of retinoblastoma that closely resemble metastatic and nonmetastatic human disease for the purposes of examining tumor biology and developing alternate treatments, human retinoblastoma cell lines were injected into the vitreal cavities of immunodeficient mice. Two reproducible animal models with contrasting biological behaviors analogous to human retinoblastoma have been developed. The Y79 retinoblastoma model demonstrated specific tumor evolution similar to that seen in human invasive and metastatic disease. Y79 retinoblastoma cells formed intraocular tumors that were initially confined to the vitreal cavity. Tumors progressively invaded the retina, subretinal space, choroid, optic nerve head, and anterior chamber of the eye. Tumors progressed into the subarachnoid space and focally invaded the brain. Metastases were detected in the contralateral optic nerve. Large tumors developed extraocular extensions. The histology of the tumors showed a poorly differentiated pattern with high mitotic rate, foci of necrosis, and calcification. The WERI-Rb model more closely resembled nonmetastatic human retinoblastoma. WERI- Rb tumors were localized in the eye with only anterior choroidal invasion at late stages. To examine potential biological differences in vitro, the retinoblastoma cell lines were cocultured with adherent choroid cells or adherent glioma cells which represent the targets of invasive retinoblastoma in vivo. Consistent with the in vivo observations, Y79 cells but not WERI-Rb cells adhere specifically to both the choroidal and the glioma cell lines.

Characterization of a cDNA encoding a subtilisin-like serine protease (NC-p65) of Neospora caninum

The NC-p65 cDNA is the first protease sequence cloned and described for Neospora caninum. The full length cDNA was isolated by 5'- and 3'-rapid amplification of cDNA ends (RACE). NC-p65 was composed of 865 amino acids with a predicted signal sequence, a proposed pro-domain, and an internal region of conserved repeats. Analysis of the deduced amino acid sequence revealed that this protein had homology to the serine proteases of the subtilisin-like superfamily (subtilases) and had a predicted active site made up of the catalytic residues, Asp 253, His 309. and Ser 484. Antibodies to recombinant NC-p65 recognized multiple bands on Neospora lysate immunoblots, but most intensely stained a 65 kDa band. When N. caninum proteins were purified with affinity resins specific for NC-p65 and analyzed for enzyme activity, a single specific band of reaction was observed on gelatin-saturated zymograms.

Suicide gene therapy for treatment of retinoblastoma in a murine model

Children presenting with large retinoblastomas are currently treated by enucleation. As most patients are young children, the long-term repercussions of such surgery are often devastating. Subsequent radiation or chemotherapy, although effective in managing residual tumor, greatly increase the probability of the development of second malignancies later in life. Smaller tumors can sometimes be managed with local cryo- or laser surgery, thus saving the eye. The hypothesis that gene therapy could be used to reduce the tumor size sufficiently to allow local control was tested using a murine model of retinoblastoma. Y79Rb human retinoblastoma cells can be killed in vitro when transduced with an adenoviral vector containing the herpes simplex thymidine kinase gene (AdV-TK) followed by treatment with the prodrug ganciclovir. Intravitreal injections of Y79Rb cells in immunodeficient mice produce an aggressive, metastatic murine model of retinoblastoma. When these murine retinoblastomas were transduced in vivo with AdV-TK and the animals treated with intraocular injections of ganciclovir, 70% showed a complete ablation of detectable tumor. Treated animals had a significant prolongation of progression-free survival as compared with untreated controls. Gene therapy effectively reduced the tumor burden in this murine model of retinoblastoma. Thus gene therapy, in conjunction with local surgical control, may provide an effective alternative to enucleation, systemic chemotherapy, or radiotherapy for treatment of large, nonmetastatic retinoblastomas in children.

A continuum mechanics approach to determining the cellular velocity field with a wool follicle

A model, based on the principles of continuum mechanics, is presented for the analysis of cell-velocity fields within wool follicles. The model requires specification of three follicle characteristics in the form of spatially varying fields: viscosity, cell density and cell production rate. The viscosity is introduced as an attempt to model both complex intercellular interactions and individual cell deformation as the cells move. It is demonstrated that the distribution of cell production is more important than axial variation in viscosity in determining the overall flow pattern.

Ascorbate stimulates type I and type III collagen in human Tenon's fibroblasts

PURPOSE

To better understand wound healing after glaucoma filtration surgery by measuring the production of type I and type III collagen in cultured Tenon's fibroblasts and determine the effect of ascorbic acid on collagen subtype production.

METHODS

An ELISA-type dot blot assay was used to directly measure the production of types I and III collagen by subconfluent cultures of fibroblasts from human Tenon's capsule. Because ascorbic acid is both high in aqueous humor and necessary for the production of collagen, we measured the dose response of type I and type III collagen production to ascorbic acid.

RESULTS

Ascorbic acid stimulated an increase in collagen production that reached a maximum level at 100 micrograms/ml. This is approximately half of the ascorbic acid concentration found in human aqueous humor. Unlike previous reports, we found no toxic effects from ascorbic acid at concentrations as high as 250 micrograms/ml over a 24-hour period. The lack of toxicity may result from the use of serum-free media in the assay.

CONCLUSIONS

This culture system will be useful for exploring factors that may alter collagen production and could potentially affect wound healing.

Cloning and characterization of two recombinant Neospora protein fragments and their use in serodiagnosis of bovine neosporosis

Bovine neosporosis causes fetal abortion and/or congenital neurologic disease in cattle. For the serodiagnosis of this parasitic disease, two immunodominant clones from a bovine Neospora lambda gt11 library were identified, characterized, and expressed as recombinant proteins for the development of an enzyme-linked immunosorbent assay (ELISA). These two clones, designated N54 and N57, were 29 and 20 kDa, respectively, when expressed as histidine fusion proteins from the pRSET expression vector. Antibodies to recombinant protein N54 recognized five major bands from a Neospora tachyzoite lysate with molecular masses of 97, 87, 77, 67, and 64 kDa. Antibodies to recombinant protein N57 recognized four primary bands with molecular masses of 34, 31, 30, and 28 kDa. When a defined "gold standard" panel of bovine sera from confirmed Neospora-positive and Neospora-negative cattle were characterized by immunoblotting, 57 of the 60 Neospora-positive serum samples recognized proteins with the molecular masses of the N54 heptuplet. Binding to the N57 quadruplet was more variable. The same gold standard panel was used to evaluate and compare an N54-based ELISA, an N57-based ELISA, and a whole-tachyzoite lysate-based ELISA. The sensitivities and specificities were 95 and 96% (N54 ELISA), 82 and 93% (N57 ELISA), and 74 and 93% (lysate ELISA). Thus, compared to the whole-tachyzoite lysate-based ELISA, both recombinant-protein-based ELISAs had higher sensitivities and higher or the same specificities and can be used to replace the whole-tachyzoite lysate ELISA for the serodiagnosis of bovine neosporosis.

Management of late-onset tibia vara in the obese patient by using circular external fixation

Previously published series of surgery for late-onset tibia vara reported a significant number of complications and fair or poor results. Obesity in many of these patients makes surgical intervention an even more daunting prospect. Circular external fixation is applicable to almost any limb size and allows weight bearing as tolerated, with gradual adjustment of alignment. Twenty-five tibiae in 17 patients who exceeded their ideal body weight by > or =50% underwent correction of late-onset tibia vara with the Ilizarov technique. Average age at surgery was 11 years 7 months (range, 7 years 8 months to 15 years 11 months). Mean varus deformity was 27 degrees (range, 10-55 degrees). Treatment time averaged 12 weeks in patients without lengthening and 16.9 weeks in those requiring lengthening (mean, 3.5 cm). All patients achieved alignment within 5 degrees of normal. Complications included one delayed union, premature consolidation in one, and two residual limb-length inequalities. There were no cases of osteomyelitis, compartment syndrome, or nerve palsy. These results are a significant improvement over reports of traditional methods in these difficult patients.

Effects of excitatory amino acids on phosphoinositide metabolism in frog retina

The effects of excitatory amino acid receptor agonists on the hydrolysis of phosphoinositides were examined using frog retinal membranes prelabeled in vitro with either 32PO4 or [3H]inositol. Glutamate stimulated release of [3H]inositol phosphates (IPs) from the retinas and altered the 32P-labeling pattern of phosphatidylinositol (PI) cycle intermediates. This indicates that glutamate affects not only the hydrolysis of phosphoinositides but possibly other steps involved in the PI cycle. Among glutamate analogs, kainate (KA), quisqualate (QA), and, to a lesser extent, N-methyl-D-aspartate (NMDA) mimicked the glutamate effect, whereas L-2-amino-4-phosphonobutyrate (L-AP4) was not effective in causing either the accumulation of [3H]IPs or the alteration of the 32P-labeling pattern of PI cycle intermediates. Among QA specific agonists, alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA), but not ibotenate (IBO) or trans-1-aminocyclopentane-1,3-dicarboxylate (ACPD) was active in stimulating IPs formation. KA effect on IPs formation may be due to indirect (polysynaptic) activation of receptor(s) other than L-AP4, IBO, or ACPD specific QA receptors. To avoid activating polysynaptic pathways, retinal synaptoneurosomes prelabeled with [3H]inositol were used to examine the hydrolysis of phosphoinositides. As in whole retinas, KA, carbachol (CARB), and NMDA stimulated the release of IPs while L-AP4 had minimal effect. Glycine (GLY) had no effect. Our results show CARB and KA to be the most effective in stimulating the production of IPs. Their effects were exerted directly through separate receptors and not through polysynaptic pathways. ACPD and IBO were the least effective in eliciting the release of IPs. Our studies provide evidence that ionotropic and not metabotropic glutamate receptors are involved in PI metabolism in the retina.

Decreased opioid doses used on a palliative care unit

We have previously published data on our use of opioids in the last week of life. A change in our pattern of opioid use, i.e. switching opioids more frequently and using high-dose methadone suppositories, appears to have resulted in a decrease in the number of patients requiring high-dose opioids. A retrospective chart review of 100 consecutive patients treated on our palliative care unit during 1992 was completed and compared to the original data from 1990. Results confirmed a decrease in the range of opioids used, as well as a statistically significant decrease in the daily opioid dose in the last week of life. We believe that this difference is most likely due to the use of methadone in patients showing either a poor response to other opioids or a rapid development to tolerance, as well as switching opioids more frequently to take advantage of incomplete cross-tolerance.

Simultaneous free-tissue transfer and Ilizarov distraction osteosynthesis in lower extremity salvage: case report and review of the literature

The last decade has witnessed the refinement of microvascular tissue transplantation and its application in treating difficult open wounds. Nonetheless, severe type III tibial injuries continue to challenge reconstructive surgeons. The clinical presentation and surgical treatment of a type IIIB tibial fracture, complicated by long-standing chronic osteomyelitis, angulation deformity, and bone shortening, is presented. This case illustrates the benefit of combining microvascular transplantation of distant tissues with the Ilizarov technique of distraction osteosynthesis in the treatment of complicated lower extremity injuries.

The regulation of an age-structured population by a fatal disease

A model describing the effect of a fatal disease on an age-structured population which would otherwise grow is presented and analysed. If the disease is capable of regulating host numbers, there is an endemic steady age distribution (SAD), for which an analytic expression is obtained under some simplifying assumptions. The ability of the disease to regulate the population depends on a parameter R(alpha), which is defined in terms of the given age-dependent birth and death rates, and where alpha is the age-dependent disease-induced death rate. If R(alpha) < 1 the endemic SAD is attained, while R(alpha) > 1 means the disease cannot control the population's size. The number R(0) is the expected number of offspring produced by each individual in the absence of the disease; for a growing population we require R(0) > 1. A stability analysis is also performed and it is conjectured that the endemic SAD is locally asymptotically stable whenever it is attained. This is demonstrated explicitly for a very simple example where all rates are taken as constant.

Physical interaction of the retinoblastoma protein with human D cyclins

The retinoblastoma protein (pRb) functions as a regulator of cell proliferation and in turn is regulated by cyclin-dependent kinases. Cyclins D1 and D3 can form complexes with pRb that resemble those formed by several viral oncoproteins and are disrupted by the adenovirus E1A oncoprotein and derived peptides. These cyclins contain a sequence motif similar to the pRb-binding conserved region II motif of the viral oncoproteins. Alteration of this motif in cyclin D1 prevents formation of cyclin D1-pRb complexes while enhancing the biological activity of cyclin D1 assayed in vivo. We conclude that cyclins D1 and D3 interact with pRb in a fashion distinct from cyclins A and E, which can induce pRb hyperphosphorylation, and that cyclin D1 activity may be regulated by its association with pRb.

Thresholds and stability analysis of models for the spatial spread of a fatal disease

A simple two-class (susceptibles and infectives) model describing the dynamics of a fatal disease in a variable-size population is presented and analysed. Spatial dependence is introduced into the model by considering two different mechanisms for the geographic spread of the disease: nonlocal interaction between susceptibles and infectives, and migratory spread of the animals. The steady states and their stability for these spatially dependent models are deduced; no spatially heterogeneous steady states were possible. For nonlocal interaction, there were two spatially uniform steady states: the trivial state (no infectives or susceptibles), which was unstable, and the endemic state (constant proportion of the population infected), which was locally asymptotically stable. With migratory spread, the number of spatially uniform steady states was dependent on the boundary conditions imposed. With hostile (Dirichlet) boundary conditions, only the trivial steady state was possible and its local stability found to depend on the rate of diffusion of the total population. With no-flux (Neumann) boundary conditions, the steady states are the trivial and endemic states; these were unstable and locally asymptotically stable, respectively.

Phospholipid molecular species from isolated bovine rod outer segments incorporate exogenous fatty acids at different rates

The incorporation of radiolabeled palmitic (16:0), oleic (18:1), and docosahexaenoic (22:6) acids into different molecular species of membrane phospholipids was investigated in isolated bovine rod outer segments (ROS). Phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) were isolated, and their diacylglyceroacetate and diacylglycerobenzoate derivatives were prepared, separated by HPLC, quantified, and assayed for radioactivity. Maximal incorporation of fatty acids occurred within 15-30 min. The rate of incorporation of the fatty acids into PC was three to six times higher than it was into PS or PE. The rate of incorporation of 22:6 into the molecular species, 22:6-22:6, of PC was ten to 15 times higher than into that of PE or PS, and it was three to four times higher than the incorporation rates of 22:6 into the other 22:6-containing molecular species. Similarly, incorporation of 18:1 into 18:1-22:6 was ten to 30 times more rapid in PC than in PE and PS, but in both PE and PS, 18:1 was incorporated into 18:1-22:6 at a rate of 20 to 25 times higher than the incorporation into the other molecular species analysed. For PC, incorporation of 16:0 was most rapid into 16:0-16:0, but for PE and PS it was most rapid into 16:0-20:4; for all cases, incorporation of 16:0 into these molecular species was four to six times more rapid than into the other 16:0-containing molecular species. These results are further evidence for the presence within a membranous organelle, the ROS, of an active acylation-deacylation system that is selective with regard to phospholipid, molecular species of phospholipid, and fatty acid.

Empathy, anxiety and transcultural nursing

Kem Louie, in a descriptive study, investigates the relationship of empathy and anxiety of nursing students and their attitudes towards patients from ethnic minority groups.

Docosahexaenoate-containing molecular species of glycerophospholipids from frog retinal rod outer segments show different rates of biosynthesis and turnover

We have studied the de novo synthesis and subsequent turnover of major docosahexaenoate-containing molecular species in frog rod outer segment (ROS) phospholipids following intravitreal injection of [2-3H]glycerol. On selected days after injection, ROS were prepared and phospholipids extracted. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) were isolated and converted to diradylglycerols with phospholipase C. Diradylglycerols were derivatized with benzoic anhydride and resolved into diacylglycerobenzoates and ether-linked glycerobenzoates. The diacylglycerobenzoates were fractionated into molecular species by HPLC, quantitated, and counted for radioactivity. Label was incorporated into ROS phospholipids by day 1 and was followed up through the eighth day. The dipolyenoic species 22:6-22:6 from PC showed a 3-5 times higher radiospecific activity than the same species from either PE or PS. In PC, the specific activities of 16:0-22:6 and 18:0-22:6 were 3-5 times lower than the specific activity of 22:6-22:6. In contrast, for PE, the specific activities of 16:0-22:6 and 18:0-22:6 were 2-5 times higher than that of 22:6-22:6. The specific activities of 18:0-22:6 and 22:6-22:6 were similar in PS. Specific activities of the docosahexaenoate-containing species began approximating an exponential decline 6-8 days postinjection and continued through the 31st day. The rate of decline was determined by calculating the half-life of each molecular species, which was used as a measure of the turnover of the species. The species 22:6-22:6-PE and 18:0-22:6-PE showed a 2-3 times slower turnover rate than the corresponding species from either PC or PS.(ABSTRACT TRUNCATED AT 250 WORDS)

Substrate-induced membrane association of phosphatidylserine synthase from Escherichia coli

To better establish the intracellular location of the phosphatidylserine synthase of Escherichia coli and hence better understand how it is regulated in the cell, we compared the size, function, and binding properties of the enzyme made in vitro with the enzyme found in cell lysates and with the purified enzyme. The enzyme made either in vivo or in an active form in vitro was found primarily associated with the ribosomal fraction of the cell and had the same apparent molecular mass as the purified enzyme. These results were unaffected by the presence of protease inhibitors. Addition of unsupplemented E. coli membranes or membranes supplemented with phosphatidylethanolamine did not affect the subcellular distribution of the enzyme in these experiments. However, addition of membranes supplemented with either the lipid substrate, CDP-diacylglycerol, or the lipid product, phosphatidylserine, resulted in membrane association by the enzyme rather than ribosomal association. Addition of membranes supplemented with acidic lipids also brought about membrane association, but this association was primarily ionic since it was disrupted by high salt concentrations. These results strongly suggest that the ribosomal location of this enzyme is not the result of some modification event occurring after cell lysis and that the normal functioning of the enzyme involves membrane association which is primarily induced by the presence of a membrane-associated substrate.