A hyperacute immune map of ischaemic stroke patients reveals alterations to circulating innate and adaptive cells

Systemic immune changes following ischaemic stroke are associated with increased susceptibility to infection and poor patient outcome due to their role in exacerbating the ischaemic injury and long-term disability. Alterations to the abundance or function of almost all components of the immune system post-stroke have been identified, including lymphocytes, monocytes and granulocytes. However, subsequent infections have often confounded the identification of stroke-specific effects. Global understanding of very early changes to systemic immunity is critical to identify immune targets to improve clinical outcome. To this end, we performed a small, prospective, observational study in stroke patients with immunophenotyping at a hyperacute time point (< 3 h) to explore early changes to circulating immune cells. We report, for the first time, decreased frequencies of type 1 conventional dendritic cells (cDC1), haematopoietic stem and progenitor cells (HSPCs), unswitched memory B cells and terminally differentiated effector memory T cells re-expressing CD45RA (TEMRA). We also observed concomitant alterations to human leucocyte antigen D-related (HLA-DR), CD64 and CD14 expression in distinct myeloid subsets and a rapid activation of CD4+ T cells based on CD69 expression. The CD69+ CD4+ T cell phenotype inversely correlated with stroke severity and was associated with naive and central memory T (TCM) cells. Our findings highlight early changes in both the innate and adaptive immune compartments for further investigation as they could have implications the development of post-stroke infection and poorer patient outcomes.

Systemic inflammation affects reperfusion following transient cerebral ischaemia

Reperfusion after stroke is critical for improved patient survival and recovery and can be achieved clinically through pharmacological (recombinant tissue plasminogen activator) or physical (endovascular intervention) means. Yet these approaches remain confined to a small percentage of stroke patients, often with incomplete reperfusion, and therefore there is an urgent need to learn more about the mechanisms underlying the no-reflow phenomenon that prevents restoration of adequate microvascular perfusion. Recent evidence suggests systemic inflammation as an important contributor to no-reflow and to further investigate this here we inject interleukin 1 (IL-1) i.p. 30 min prior to an ischaemic challenge using a remote filament to occlude the middle cerebral artery (MCA) in mice. Before, during and after the injection of IL-1 and occlusion we use two-dimensional optical imaging spectroscopy to record the spatial and temporal dynamics of oxyhaemoglobin concentration in the cortical areas supplied by the MCA. Our results reveal that systemic inflammation significantly reduces oxyhaemoglobin reperfusion as early as 3h after filament removal compared to vehicle injected animals. CD41 immunohistochemistry shows a significant increase of hyper-coagulated platelets within the microvessels in the stroked cortex of the IL-1 group compared to vehicle. We also observed an increase of pathophysiological biomarkers of ischaemic damage including elevated microglial activation co-localized with interleukin 1α (IL-1α), increased blood brain barrier breakdown as shown by IgG infiltration and increased pyknotic morphological changes of cresyl violet stained neurons. These data confirm systemic inflammation as an underlying cause of no-reflow in the post-ischaemic brain and that appropriate anti-inflammatory approaches could be beneficial in treating ischaemic stroke.

Zinc depletion regulates the processing and secretion of IL-1β

Sterile inflammation contributes to many common and serious human diseases. The pro-inflammatory cytokine interleukin-1β (IL-1β) drives sterile inflammatory responses and is thus a very attractive therapeutic target. Activation of IL-1β in sterile diseases commonly requires an intracellular multi-protein complex called the NLRP3 (NACHT, LRR, and PYD domains-containing protein 3) inflammasome. A number of disease-associated danger molecules are known to activate the NLRP3 inflammasome. We show here that depletion of zinc from macrophages, a paradigm for zinc deficiency, also activates the NLRP3 inflammasome and induces IL-1β secretion. Our data suggest that zinc depletion damages the integrity of lysosomes and that this event is important for NLRP3 activation. These data provide new mechanistic insight to how zinc deficiency contributes to inflammation and further unravel the mechanisms of NLRP3 inflammasome activation.

Analysis of global gene expression changes in human bronchial epithelial cells exposed to spores of the allergenic fungus, Alternaria alternata

Exposure and sensitivity to ubiquitous airborne fungi such as Alternaria alternata have long been implicated in the development, onset, and exacerbation of chronic allergic airway disorders. This present study is the first to investigate global changes in host gene expression during the interaction of cultured human bronchial epithelial cells and live Alternaria spores. In in vitro experiments human bronchial epithelial cells (BEAS-2B) were exposed to spores or media alone for 24 h. RNA was collected from three biological replicates per treatment and was used to assess changes in gene expression patterns using Affymetrix Human Genome U133 Plus 2.0 Arrays. In cells treated with Alternaria spores compared to controls, 613 probe sets representing 460 individual genes were found differentially expressed (p ≤ 0.05). In this set of 460 statistically significant, differentially expressed genes, 397 genes were found to be up-regulated and 63 were down-regulated. Of these 397 up-regulated genes, 156 genes were found to be up-regulated ≥2 fold. Interestingly, none of the 63 down-regulated genes were found differentially expressed at ≤−2 fold. Differentially expressed genes were identified following statistical analysis and subsequently used for pathway and network evaluation. Interestingly, many cytokine and chemokine immune response genes were up-regulated with a particular emphasis on interferon-inducible genes. Genes involved in cell death, retinoic acid signaling, and TLR3 response pathways were also significantly up-regulated. Many of the differentially up-regulated genes have been shown in other systems to be associated with innate immunity, inflammation and/or allergic airway diseases. This study now provides substantial information for further investigating specific genes and innate immune system pathways activated by Alternaria in the context of allergic airway diseases.

Centrally administered galanin-like peptide modifies food intake in the rat: a comparison with galanin

Galanin-like peptide (GALP) is a recently identified neuropeptide that shares sequence homology with the orexigenic neuropeptide, galanin. In contrast to galanin, GALP is reported to bind preferentially to the galanin receptor 2 subtype (GalR2) compared to GalR1. The aim of this study was to determine the effect of GALP on feeding, body weight and core body temperature after central administration in rats compared to the effects of galanin. Intracerebroventricular (i.c.v.) injection of GALP (1 micro g-10 micro g) significantly stimulated feeding at 1 h in both satiated and fasted Sprague-Dawley rats. However, 24 h after GALP injection, body weight gain was significantly reduced and food intake was also usually decreased. In addition, i.c.v. GALP caused a dose-related increase in core body temperature, which lasted until 6-8 h after injection, and was reduced by peripheral administration of the cyclooxygenase inhibitor, flurbiprofen (1 mg/kg). Similar to GALP, i.c.v. injection of galanin (5 micro g) significantly increased feeding at 1 h in satiated rats. However, there was no difference in food intake and body weight at 24 h, and galanin only caused a transient rise in body temperature. Thus, similar to galanin, GALP has an acute orexigenic effect on feeding. However, GALP also has an anorectic action, which is apparent at a later time. Therefore, GALP has complex opposing actions on energy homeostasis.

Anorexic but not pyrogenic actions of interleukin-1 are modulated by central melanocortin-3/4 receptors in the rat

The cytokine interleukin-1 (IL-1), which mediates many responses to infection and injury, induces anorexia and fever through direct actions in the central nervous system. The melanocortin neuropeptides, such as alpha melanocyte-stimulating hormone (alpha-MSH), reportedly antagonize many actions of IL-1, including fever and anorexia. However, it is unknown whether endogenous melanocortins modulate anorexia induced by IL-1. The objective of the present study was to establish the effect of endogenous melanocortins on IL-1-induced anorexia and fever in the rat. Intracerebroventricular (i.c.v.) injection of IL-1beta caused a significant reduction in food intake and body weight gain, and a rise in core body temperature in conscious rats. Coadministration of the melanocortin-3/4 receptor (MC3/4-R) antagonist, SHU9119, reversed IL-1beta-induced reductions in food intake and body weight, but did not affect the febrile response to IL-1beta. These data suggest IL-1beta may elicit its effects on food intake through the melanocortin system, predominantly via the MC3-R or MC4-R. In contrast, IL-1beta-induced fever does not appear to be mediated or modulated by MC3-R or MC4-R activity.

Enhanced disease resistance conferred by expression of an antimicrobial magainin analog in transgenic tobacco

Magainins are a group of short peptides originally isolated from frog skin and thought to function as a natural defense mechanism against infection due to their antimicrobial properties. The engineered magainin analog peptide Myp30 was found to inhibit spore germination of the oomycete, Peronospora tabacina (Adam) in vitro, and the growth of a bacterial pathogen Erwinia carotovora subsp. carotovora (Jones). Transgenic tobacco (Nicotiana tabacum L.) plants expressing Myp30 were evaluated for resistance to these pathogens. The expression of the peptide only to an extracellular location resulted in significant reduction in sporulation and lesion size due to P. tabacina infection. A significant increase in resistance to the bacterial pathogen was also observed regardless of the targeting location of the peptide.

Alternative role for prolactin-releasing peptide in the regulation of food intake

Prolactin-releasing peptide (PrRP) is a peptide ligand for the human orphan G-protein-coupled receptor hGR3/GPR10 and causes the secretion of prolactin from anterior pituitary cells. However, the lack of immunoreactive staining for PrRP in the external layer of the median eminence seems to rule out this peptide as a classical hypophysiotropic hormone and, furthermore, PrRP is less effective than another inducer of prolactin secretion, thyrotropin-releasing hormone, both in vitro and in vivo. Here we show a reduction in the expression of PrRP mRNA during lactation and fasting and an acute effect of PrRP on food intake and body weight, supporting the hypothesis of an alternative role for the peptide.

The yeast polyadenylate-binding protein (PAB1) gene acts as a disease lesion mimic gene when expressed in plants

We have expressed the gene (PAB1) encoding the yeast polyadenylate-binding protein (Pab1p) in tobacco. Plants that accumulate the Pab1p display a range of abnormalities, ranging from a characteristic chlorosis in leaves to a necrosis and large inhibition of growth. The severity of these abnormalities reflects the levels of yeast Pab1p expression in the transgenic plants. In contrast, no obvious differences could be seen in callus cultures between the transgene and vector control. Plants that display PAB-associated abnormalities were resistant to a range of plant pathogens, and had elevated levels of expression of a pathogenesis-related gene. These two properties--impairment of growth and induction of defense responses--indicate that the yeast PAB1 gene can act as a disease lesion mimic gene in plants.

Hypothalamic control of feeding

Our understanding of the hypothalamic control of energy homeostasis has increased greatly since the discovery of leptin, the adipose cell derived protein. Recent studies have identified several new hypothalamic neuropeptides that affect food intake and energy balance. By studying these molecules and their neuronal systems, receptors and interactions, we are beginning to unravel the circuitry between peripheral adipogenic signals and hypothalamic effector pathways.

Genes from mycoparasitic fungi as a source for improving plant resistance to fungal pathogens

Disease resistance in transgenic plants has been improved, for the first time, by the insertion of a gene from a biocontrol fungus. The gene encoding a strongly antifungal endochitinase from the mycoparasitic fungus Trichoderma harzianum was transferred to tobacco and potato. High expression levels of the fungal gene were obtained in different plant tissues, which had no visible effect on plant growth and development. Substantial differences in endochitinase activity were detected among transformants. Selected transgenic lines were highly tolerant or completely resistant to the foliar pathogens Alternaria alternata, A. solani, Botrytis cinerea, and the soilborne pathogen Rhizoctonia solani. The high level and the broad spectrum of resistance obtained with a single chitinase gene from Trichoderma overcome the limited efficacy of transgenic expression in plants of chitinase genes from plants and bacteria. These results demonstrate a rich source of genes from biocontrol fungi that can be used to control diseases in plants.

Interleukin-1beta and the interleukin-1 receptor antagonist act in the striatum to modify excitotoxic brain damage in the rat

The cytokine interleukin-1 (IL-1) has been implicated in ischaemic, traumatic and excitotoxic brain damage. The results presented here reveal novel actions of IL-1 in the striatum which markedly exacerbate cortical neuronal damage elicited by local excitotoxins in the striatum or cortex. Intrastriatal infusion of IL-1 receptor antagonist, IL-1ra, markedly inhibited striatal neuronal damage caused by N-methyl-D-aspartate (NMDA) or alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptor activation in the rat. In contrast, intracortical infusion of IL-1ra failed to inhibit NMDA or AMPA receptor-induced damage in the cortex. Intrastriatal co-infusion of IL-1 with the NMDA or AMPA receptor agonist did not affect local striatal damage induced by activation of either glutamate receptor subtype, but caused extensive cortical damage when administered into the striatum with AMPA. This secondary damage was significantly reduced by pretreatment with the NMDA receptor antagonist (MK-801), which did not affect local (striatal) damage caused by AMPA. Infusion of IL-1beta into the striatum (but not the cortex) markedly enhanced cortical damage caused by infusion of an NMDA or AMPA receptor agonist into the cortex. These data reveal selective actions of IL-1 and IL-1ra in the striatum, which influence cortical neuronal loss and suggest that IL-1 selectively enhances damage caused by AMPA receptor activation.

Interleukin-1 beta and interleukin-1 receptor antagonist do not affect glutamate release or calcium entry in rat striatal synaptosomes

The cytokine interleukin-1 beta (IL-1 beta) has been implicated in various forms of neurodegeneration, and several lines of evidence indicate that it also modulates synaptic transmission in the central nervous system. Excessive release of the excitatory neurotransmitter L-glutamate results in cell death and probably mediates many neurodegenerative conditions. We set out to test the hypothesis that involvement of IL-1 beta in neurodegeneration results in some interaction with excitatory amino acid-mediated synaptic transmission in the rat striatum, either by modifying glutamate release or actions. Presynaptic effects of IL-1 beta and the IL-1 receptor antagonist (IL-1ra) on glutamate release and calcium entry were investigated in isolated nerve terminals (synaptosomes) prepared from the striatum. In order to evaluate the involvement of IL-1 in neuronal damage caused by glutamate receptor over-activation, the effect of IL-1ra was studied on N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptor-mediated brain damage in the rat striatum and cortex in vivo. Neither rat recombinant IL-1 beta (rrIL-1 beta: 0.01-2 nM) or human recombinant IL-1ra (hrIL-1ra: 0.2 microM) had any significant effect on the KCl-evoked glutamate efflux or calcium entry in striatal synaptosomes, indicating that their actions are unlikely to be presynaptic. In contrast, intrastriatal infusion of hrIL-1ra markedly inhibited (by 43-46%, P < 0.05) neuronal damage caused by striatal NMDA or AMPA receptor activation in the rat in vivo, whereas no effect was seen on damage induced in the cortex. Thus, our data suggest that IL-1 beta and IL-1ra influence neuronal damage in the striatum by acting to modify events that occur after excitatory amino acid receptor activation.

Short-day weight loss and effect of food deprivation on hypothalamic NPY and CRF mRNA in Djungarian hamsters

The effect of food deprivation on hypothalamic neuropeptide Y (NPY) and corticotropin-releasing factor (CRF) gene expression in the Djungarian hamster was quantified by in situ hybridization. Hamsters housed in short days (SD) for 18 wk decreased body weight by 40% and exhibited 200% increases in both NPY and CRF mRNA when deprived of food for 24 h. Prior gonadectomy in long days (LD) affected neither basal gene expression nor the induction of gene expression by food deprivation. Gene expression in juvenile LD hamsters similar in body weight to SD animals was relatively insensitive to food deprivation of either 24- or 48-h duration or to subsequent refeeding. In juvenile hamsters, food deprivation for 24 but not 48 h decreased ob (obese) gene expression in inguinal but not epididymal white adipose tissue; ob mRNA levels were restored by refeeding. All food-deprived hamsters had reduced plasma insulin concentrations, but plasma cortisol was only elevated in SD food-deprived animals. NPY gene expression was also increased after daily dexamethasone injections in adult LD hamsters. These results suggest that the neuroendocrine consequences of food deprivation in SD Djungarian hamsters are determined by some factor other than absolute body mass such as the size of adipose tissue reserves.

Regulation of galanin gene expression in the hypothalamic paraventricular nucleus of the obese Zucker rat by manipulation of dietary macronutrients

Lean and obese male Zucker rats were fed high fat (72% of energy as fat), high carbohydrate (66% of energy as carbohydrate) or intermediate diets for 4 weeks commencing 1 week after weaning. We examined the effects of these diets on growth rates, plasma insulin and corticosterone titres, and hypothalamic gene expression of 3 appetite-related neuropeptides. Messenger RNA levels for neuropeptide Y (NPY), galanin (GAL) and corticotropin-releasing factor (CRF) in critical hypothalamic locations were measured by in situ hybridization in each brain. Obese rats grew more rapidly and had elevated plasma insulin and corticosterone concentrations relative to their lean littermates. The obese phenotype was also associated with elevated NPY gene expression in the arcuate nucleus of the hypothalamus and increased GAL gene expression in the hypothalamic paraventricular nucleus. There was no effect of diet on NPY or CRF gene expression in either lean or obese rats. However, maintenance on the high fat diet had a significant effect on GAL gene expression in obese but not lean rats: high fat diet significantly reduced mRNA levels in the obese rats. This reduction in GAL mRNA was accompanied by attenuation of the hyperinsulinemia that is characteristic of this genetic obesity.

Coexpression of leptin receptor and preproneuropeptide Y mRNA in arcuate nucleus of mouse hypothalamus

Leptin, the protein product of the adipose tissue-specific ob (obese) gene (1), reduces the body weight, adiposity and food intake of obese ob/ob mice on peripheral or central injection (2, 3, 4). [125I]leptin binding has been detected in mouse choroid plexus (5), from which a leptin receptor gene was expression cloned (5). The gene has at least 6 splice variants (6, 7). Leptin receptor mRNA was localized in the hypothalamus by in situ hybridization being particularly abundantly expressed in the arcuate nucleus (8). There is evidence linking the physiological effects of injected leptin with hypothalamic neuropeptide Y (9, 10) (NPY), which has potent central effects on food intake and energy balance (11), and is also expressed in the arcuate nucleus. Here we report dual in situ hybridization studies for leptin receptor and NPY gene expression in the mouse arcuate nucleus, where the majority of cells examined expressed both genes. This provides the first direct evidence that leptin acts on cells that express NPY mRNA.

Hypothalamic NPY and CRF gene expression in the food-deprived Syrian hamster

Because the Syrian hamster, Mesocricetus auratus, does not increase food intake in response to food deprivation, we investigated whether hypothalamic NPY gene expression in this species was sensitive to this imposed state of negative energy balance. In the rat, food deprivation for 48 h resulted in a 150% increase in total preproNPY gene expression in the arcuate nucleus of the hypothalamus (ARC). NPY gene expression in food-deprived Syrian hamsters did not differ significantly from that of ad lib-fed controls, although there was a trend towards increased mRNA levels in the fasted animals. However, food deprivation for 48 h was associated with a rise in preproCRF mRNA in the paraventricular nucleus of the hypothalamus (PVN) of 80-g, but not 150-g, hamsters. The expected reductions in plasma insulin accompanied food deprivation in the Syrian hamster, but cortisol titre was only elevated in the lower body weight group. NPY gene expression in the Syrian hamster appeared, however, to be sensitive to glucocorticoids; daily administration for 28 days of the synthetic glucocorticoid, dexamethasone, increased ARC NPY mRNA levels by 43%. The response of NPYergic and other hypothalamic neuropeptide systems to food deprivation, and the involvement of neuroendocrine substrates in energy homeostasis, may vary between species.

Localization of leptin receptor mRNA and the long form splice variant (Ob-Rb) in mouse hypothalamus and adjacent brain regions by in situ hybridization

Expression of the leptin receptor gene has been examined in mouse hypothalamus and other brain regions by in situ hybridization. With a probe recognizing all the known splice variants, receptor mRNA was evident in several brain regions (cortex, hippocampus, thalamus), with strong expression in the hypothalamus (arcuate, ventromedial, paraventricular and ventral premammillary nuclei), choroid plexus and leptomeninges. A probe specific to the long splice variant of the leptin receptor (Ob-Rb), containing the putative intracellular signaling domain, again revealed strong expression in the hypothalamus; there was, however, minimal hybridization to choroid plexus and leptomeninges. These results indicate that the hypothalamus is a key site of leptin action, although other brain regions are also targeted.

A graph conceptual model for developing Human Genome Center databases

We have developed a representation of genome data which has proven itself useful for describing data at a Human Genome Center. Genomic data have a graph-like structure and representing the concepts and relationships of genetics as a graph simplifies the development of databases for genome laboratories. Graphs are a comfortable communication medium for biologists and computer scientists and graph diagrams assist in the development of databases by facilitating the exchange of expertise. We have tailored a graph language for modeling genomic data and describe our process of using graphs to develop genome databases.

Hypothalamic NPY and prepro-NPY mRNA in Djungarian hamsters: effects of food deprivation and photoperiod

Two catabolic states leading to loss of body weight were compared in the Djungarian hamster (Phodopus sungorus campbelli). Hypothalamic neuropeptide Y (NPY) and gene expression for NPY and corticotropin-releasing factor (CRF) were examined after withdrawal of food for 48 h or exposure to short photoperiod for 10 or 20 wk. Food deprivation was accompanied by increases in both NPY and prepro-NPY mRNA in the hypothalamic arcuate nucleus (ARC). Increases in gene expression were limited compared with published data from the rat and were inversely related to predeprivation body weight. Exposure to short photoperiod for 20 wk reduced body weight by 39%, but the activity of the NPY-ergic system was not affected; peptide concentration and gene expression were similar in short photoperiod hamsters and long photoperiod controls. The hypothalamic NPY-ergic system of the Djungarian hamster is sensitive to weight loss due to imposed manipulations of energy balance, but the catabolism observed in short photoperiod gives rise to a body weight that is appropriate to the season encoded by the photoperiod. CRF gene expression was not affected by food deprivation or short photoperiod.

Fat mobilisation in short days is not associated with altered noradrenergic sensitivity of adipocytes in Djungarian hamsters

One of the primary physiological responses of the Djungarian hamster to short photoperiods is a reduction in body weight with fat mobilisation. The depletion of fat to a minimum level may be regulated either in the periphery, through the sensitivity of adipocytes to hormonal stimulation, or centrally, via adjustments in efferent activity. To investigate this, we examined the lipolytic pathway in fat cells from animals at various stages of entrainment to long or short photoperiod. Short photoperiod exposure of up to a 10-week duration was without effect on basal glycerol release by unstimulated cells or on the ability of norepinephrine or an adenosine analogue to stimulate or inhibit lipolysis, respectively. Prolonged exposure to short photoperiod reduced basal glycerol release, but adipocytes retained their sensitivity to hormonal stimulation. Short photoperiod had no effect on the density or affinity of membrane-bound beta-adrenergic or adenosine receptors, or upon the ability of isoproterenol or forskolin to stimulate adenylate cyclase in adipocyte membranes. This suggests that the regulation of fat depletion in short photoperiod is determined centrally and does not involve alterations in adipocyte sensitivity and, in particular, the desensitisation of the adipocyte beta-adrenergic receptor-linked adenylate cyclase pathway.

Identification of human gene structure using linear discriminant functions and dynamic programming

Development of advanced technique to identify gene structure is one of the main challenges of the Human Genome Project. Discriminant analysis was applied to the construction of recognition functions for various components of gene structure. Linear discriminant functions for splice sites, 5'-coding, internal exon, and 3'-coding region recognition have been developed. A gene structure prediction system FGENE has been developed based on the exon recognition functions. We compute a graph of mutual compatibility of different exons and present a gene structure models as paths of this directed acyclic graph. For an optimal model selection we apply a variant of dynamic programming algorithm to search for the path in the graph with the maximal value of the corresponding discriminant functions. Prediction by FGENE for 185 complete human gene sequences has 81% exact exon recognition accuracy and 91% accuracy at the level of individual exon nucleotides with the correlation coefficient (C) equals 0.90. Testing FGENE on 35 genes not used in the development of discriminant functions shows 71% accuracy of exact exon prediction and 89% at the nucleotide level (C = 0.86). FGENE compares very favorably with the other programs currently used to predict protein-coding regions. Analysis of uncharacterized human sequences based on our methods for splice site (HSPL, RNASPL), internal exons (HEXON), all type of exons (FEXH) and human (FGENEH) and bacterial (CDSB) gene structure prediction and recognition of human and bacterial sequences (HBR) (to test a library for E. coli contamination) is available through the University of Houston, Weizmann Institute of Science network server and a WWW page of the Human Genome Center at Baylor College of Medicine.

Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions. The accuracy of our splice site recognition function is 97% for donor splice sites and 96% for acceptor splice sites. For exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. This corresponds to a correlation coefficient for exon prediction of 0.87. The precision of this approach is better than other methods and has been tested on a larger data set. We have also developed a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers.

Effect of photoperiod on mitochondrial GDP binding and adenylate cyclase activity in brown adipose tissue of Djungarian hamsters

Experiments were designed to investigate the involvement of brown adipose tissue (BAT) thermogenesis in the weight loss exhibited by Djungarian hamsters (Phodopus sungorus campbelli) in response to a short photoperiod. Significant decreases in body weight preceded reductions in food intake, suggesting a photoperiod-induced change in energy expenditure. Sixteen weeks exposure to short photoperiod resulted in large decreases in body weight and interscapular BAT mass that were accompanied by an increase in the thermogenic activity of BAT (estimated by mitochondrial GDP binding). However, exposure to short photoperiod for 8 weeks, that induced smaller but significant reductions in body weight, was without effect on the BAT parameters measured. This suggests that increased BAT thermogenesis is unlikely to initiate, or contribute to, the early stages of photoperiod-induced weight loss. In addition, short photoperiod failed to induce any change in the specific activity or sensitivity of adenylate cyclase in BAT membranes, in contrast to the downregulation of catecholamine-stimulated cAMP production observed in BAT following cold exposure.

Novel estrogen response elements identified by genetic selection in yeast are differentially responsive to estrogens and antiestrogens in mammalian cells

A powerful and versatile system for the identification of novel response elements for members of the intracellular receptor family is presented as applied to the human estrogen receptor. In the past, a limited number of estrogen response elements (EREs) have been functionally identified in the promoter regions of estrogen-regulated genes. From these a consensus ERE has been defined that is identical to the ERE of the Xenopus laevis vitellogenin gene, i.e., 5'-GGTCA NNN TGACC-3'. In order to investigate without bias the range of sequences that could function as EREs in vivo, we have developed a genetic selection in yeast expressing the human estrogen receptor (hER) and transformed with a random oligonucleotide library in a vector where expression of a selectable marker requires insertion of an upstream activating sequence. More than 1,000,000 transformants were screened and of 726 clones that contained activating sequences, 65 were found to be hormone-dependent. Sequencing revealed that the majority contained at least one 4/5 match to a canonical ERE half-site, but only one contained a full consensus ERE as previously defined. Some contained half-sites arranged as direct repeats. Twelve elements were further characterized to compare estrogen activation in yeast and mammalian cells and in vitro binding to hER. The results of these studies reveal that sequences that bind weakly to hER in vitro are fully functional as EREs in yeast and are conditionally responsive to estrogen in mammalian cells. In addition, an element was identified that is more sensitive to the partial agonist activities of tamoxifen and nafoxidine than is the consensus ERE, indicating that not only promoter context but the sequence of the binding site itself can allow distinction between receptor activated by agonist and that activated by antagonist.

The genome reconstruction manager: a software environment for supporting high-throughput DNA sequencing

A new software system designed for use in high-throughput DNA sequencing laboratories is described. The Genome Reconstruction Manager (GRM) was developed from requirements derived from ongoing large-scale DNA sequencing projects. Object-oriented principles were followed in designing the system, and tools supporting object-oriented system development were employed for its implementation. GRM provides several advances in software support for high-throughput DNA sequencing: support for random, directed, and mixed sequencing strategies; a novel system for fragment assembly; a commercial object data-base management system for data storage; a client/server architecture for using network computational servers; and an underlying data model that can evolve to support fully automatic sequence reconstruction. GRM is currently being deployed for production use in high-throughput DNA sequencing projects.

Assignment of position-specific error probability to primary DNA sequence data

DNA sequence predicted from polyacrylamide gel-based technologies is inaccurate because of variations in the quality of the primary data due to limitations of the technology, and to sequence-specific variations due to nucleotide interactions within the DNA molecule and with the gel. The ability to recognize the probability of error in the primary data will be useful in reconstructing the target sequence of a DNA sequencing project, and in estimating the accuracy of the final sequence. This paper describes the use of linear discriminant analysis to assign position-specific probabilities of incorrect, over- and under-prediction of nucleotides for each predicted nucleotide position in primary sequence data generated by a gel-based DNA sequencing technology. Using this method, most of the error potential in primary sequence data can be assigned to a limited number of discrete positions. The use of probability values in the sequence reconstruction process, and in estimating the accuracy of consensus sequence determination is described.

Satiety signals in sheep: involvement of CCK, propionate, and vagal CCK binding sites

The satiety effects of the hormone, cholecystokinin (CCK), and propionate, an important gluconeogenic substrate, were studied in ad lib-fed sheep. Hepatic portal infusion of either sodium propionate (1.2 mmol/min) or sulphated CCK-8 (sCCK-8; 18.3 pmol/kg/min) had no effect on food intake. However, together, they decreased intake by 44%; similar to the effect of 2.4 mmol/min propionate alone. CCK infusions reduced the frequency of reticular contractions in the presence or absence of propionate. The effects of infusions on motility and food intake were, therefore, dissociated. Further studies demonstrated axonal transport of CCK binding sites in the ovine vagus. Binding sites accumulated to a similar extent on both sides of a ligature indicating the existence of both anterograde and retrograde transport which was limited to a small proportion of fibres. Binding incubations carried out in the presence of the CCK receptor antagonists, MK-329 and L-365,260, indicated that the majority of binding sites, if not the total population, possessed pharmacology typical of type B CCK receptors.

G-protein coupling of vagal CCK binding sites and comparisons of transport rates

The ability of nanomolar concentrations of guanine, but not adenine, nucleotides to inhibit specific 125I-Bolton-Hunter CCK binding to ligated rat vagus nerve demonstrated that vagal CCK binding sites were linked to G-proteins during axonal transport. The GTP analogue, GTP[S], reduced specific binding to both anterogradely and retrogradely transported binding sites by more than 90% at 1 microM. Transport of these putative receptor-G-protein complexes was examined under conditions of food deprivation or physiological hyperphagia induced by either lactation or genetic obesity. None of the physiological or imposed manipulations of food intake had any effect on the axonal transport of CCK binding sites. Transection of the cervical vagus resulted in an accumulation of binding sites at the lesion site that was indistinguishable from that seen following ligation for the same period.

Corticotropin-releasing factor binding sites undergo axonal transport in the rat vagus nerve

Corticotropin-releasing factor (CRF) binding sites were found to be present in the rat vagus nerve and underwent axonal transport. Binding sites accumulated on both sides of ligatures placed on the nerve and at similar rates following ligation of right or left cervical vagal trunks of either male or female rats. CRF binding sites also accumulated proximal and distal to ligatures on subdiaphragmatic vagal trunks. Binding was specific, reversible and inhibited by the CRF receptor antagonist α-helical-CRF(9-41). [(125) l]Tyr(0) -ovine-CRF binding to rat vagus nerve was not guanine nucleotide-sensitive. CRF and cholecystokinin binding sites were transported at a similar rate in the cervical vagus, although turnover of CRF binding sites was more rapid. No differences in CRF binding site transport were observed between Zucker rats of lean or obese genotype.

Selectivity of cholecystokinin (CCK) receptor antagonists, MK-329 and L-365,260, for axonally-transported CCK binding sites on the rat vagus nerve

The ability of the cholecystokinin (CCK) receptor antagonists, MK-329 and L-365,260, to selectively inhibit 125I-Bolton-Hunter-CCK8 binding to ligated rat vagus nerve in vitro was examined at concentrations ranging from 10(-10) M to 10(-6) M. Both antagonists inhibited binding to CCK binding sites accumulating proximal to ligatures on the cervical vagus. Incubation of nerve sections in the presence of both antagonists produced an additive effect, indicating that both CCK-A and CCK-B binding sites are transported towards the periphery. In contrast, CCK binding sites accumulating distal to the ligature possessed the pharmacological characteristics of the CCK-B receptor sub-type only.

Effect of neonatal capsaicin treatment on cholecystokinin-(CCK8) satiety and axonal transport of CCK binding sites in the rat vagus nerve

Cholecystokinin (CCK) binding sites which accumulate at ligatures placed on the rat vagus nerve may mediate the satiety actions of CCK. Treatment of neonatal rats with capsaicin attenuated the satiety effect of injected CCK in adult life. Capsaicin pretreatment also reduced, but did not eliminate, the accumulation of CCK binding sites proximal and distal to ligatures on either cervical trunk. A similar effect was observed following ligation of subdiaphragmatic vagal trunks. The CCK receptor antagonists, MK-329 and L-365,260, inhibited binding to capsaicin- and vehicle-treated nerves to a similar degree. Densities of CCK binding sites in the nucleus tractus solitarius and area postrema were also markedly affected by neonatal capsaicin treatment.

RNA secondary structure analysis of the packaging signal for Moloney murine leukemia virus

We have examined the cis-acting RNA packaging signal (psi) from Moloney murine leukemia virus using a combination of chemical and primary sequence analysis techniques. For our chemical analyses, we used dimethyl sulfate, kethoxal, and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluene sulfonate as probes for RNA secondary structure. The structural information obtained from these studies was used to constrain computer algorithms for prediction of RNA secondary structure. In addition, we generated and analyzed a phylogenetic comparison of homologous sequences from related retroviruses. From these data, we have developed two models for the RNA secondary structure of the packaging signal psi. Both of these models suggest the presence of secondary structure elements in a region of the psi RNA known to be required for function.

Use of homology domains in sequence similarity detection

We have found the detection of homology domains using a nonlinear similarity score and the DD algorithm to be a useful approach for identifying similarity between sequences and evaluating potential homology. There are several reasons for the success of the method. (i) Homology domains are identified by a rigorous method that guarantees they will be locally optimal. (ii) The relative significance of different homology domains can be directly compared using the nonlinear similarity score. (iii) Different cost matrices can be used in the calculation of the similarity score. (iv) Relatively long sequences can be compared in a single pass as storage requirements are proportional to the shorter of the two sequences being compared. (v) The method has proved to be very sensitive in practice. (vi) The boundaries of authentic regions of homology are accurately identified. (vii) The information required to define a homology domain (its location, size, similarity score, etc.) can be stored in a compact data structure, facilitating the sharing of homology domain data among different software tools. (viii) The method can be applied to similarity searches of the nucleotide and protein sequence data banks. These properties make the identification of homology domains for studying sequence similarity a useful companion to other accepted methods, such as dynamic programming based analyses.

A retrovirus vector which transduces a functional estrogen receptor gene at high efficiency

A high titer retroviral vector containing the cDNA of human estrogen receptor (hER) was generated and used to transfer the hER gene into the rat 208F cell line. Southern blot analysis showed the integration of the provirus to be at a unique site and that the provirus was intact in the genome of recipient cells. The expression of the integrated hER gene in the infected rat cells was detected by Northern blot analysis and by a functional assay in which the hER gene product stimulated the production of a chloramphenicol acetyl transferase gene under the control of an estrogen-responsive element. These experiments demonstrate the feasibility of using a retroviral vector system to introduce a functional ER gene into cultured cells lacking this receptor.

Two new members of the OmpR superfamily detected by homology to a sensor-binding core domain

The OmpR superfamily includes proteins that act as transcriptional regulators of operons that respond to environmental stimuli. A homologous domain near the N-terminus, termed a sensor-binding core domain, is thought to play a role in recognition of a signal transduction protein. We have identified two previously unrecognized members of this regulator family of proteins: a 23.8-kd protein transcribed from the uvrC transcription unit and the PgtA gene product, which is a phosphoglycerate transport regulatory protein. The sensor-binding core domain is also present in four proteins that regulate bacterial sporulation and chemotaxis. The 23.8-kd protein also has sequence similarity to elongation factor Tu and two regulatory proteins: HtpR, the heat-shock regulatory protein, and TraJ, a regulator of expression of genes involved in conjugation. There is a 77-amino acid region near the C-terminus of the 23.8-kd protein that has 30% similarity with a 28.1-kd protein coded for by an open reading frame 5' to the reading frame of the 23.8-kd protein in the uvrC transcription unit. Genetic distance analysis of amino acid sequences of proteins with a sensor-binding core domain suggests that the 23.8-kd protein and the chemotaxis regulatory proteins are distantly related to the other regulatory proteins in the OmpR superfamily.

Infection of bovine cells of embryonic origin by amphotropic retroviral vectors

Two amphotropic-based mouse retroviral vectors carrying the neomycin-resistance gene were used to infect four bovine cell lines. Two cell lines, bovine kidney and spleen cells, were refractory to the infection while two independent bovine cells of apparent embryonic origin were infected by the amphotropic retroviral vectors at a measurable titer. Southern blot analysis reveals the presence of neomycin-resistance gene in the G418-resistant bovine cells. The results demonstrate the successful transfer of a gene to bovine cells of embryonic origin using a murine retroviral vector system.

The effects of reserpine upon the cardiac enlargement of copper deficiency

Copper (Cu) deficiency, induced in rats by suckling from Cu-deficient dams and by offering a semisynthetic low-Cu diet from weaning, resulted in cardiac enlargement. This enlargement was not due to accumulation of excess fluid in the heart but was characterized by mitochondrial hypertrophy as demonstrated by electron microscopy and biochemical studies. Administration of reserpine limited the extent of cardiac enlargement; however, heart total noradrenaline (NA), unchanged by Cu deficiency, was significantly reduced by reserpine. It was concluded that cardiac enlargement in Cu deficiency was not directly related to NA concentration. An alteration in cardiac energy status, however, was suggested by reduction in activity of the nonheme iron-dependent enzyme, succinic dehydrogenase.

Definition and identification of homology domains

A method is described for identifying and evaluating regions of significant similarity between two sequences. The notion of a 'homology domain' is employed which defines the boundaries of a region of sequence homology containing no insertions or deletions. The relative significance of different potential homology domains is evaluated using a non-linear similarity score related to the probability of finding the observed level of similarity in the region by chance. The sensitivity of the method is demonstrated by simulating the evolution of homology domains and applying the method to their detection. Several examples of the use of homology domain identification are given.

Chemical modification as a tool for analysis of messenger RNA secondary structure in ribonucleoprotein particles

Chemical modification of unpaired bases is demonstrated in this study to be a reliable method for determining the conformation of nucleotides in mRNA. The modified nucleotides are identified by primer extension using reverse transcriptase. We have used this procedure to compare the structure of limited regions of SV40 T-antigen mRNA in solution, in nonpolysome-bound cytoplasmic messenger ribonucleoprotein particles, and in nuclear ribonucleoprotein complexes. The results indicate that SV40 T-antigen mRNA adopts a specific structure both in solution and when complexed with cellular proteins. The structures adopted by the mRNA in solution and in native cellular protein particles are very similar.

Genetic relatedness of human DNA polymerase beta and terminal deoxynucleotidyltransferase

The Protein Identification Resource (PIR) protein sequence data bank was searched for sequence similarity between known proteins and human DNA polymerase beta (Pol beta) or human terminal deoxynucleotidyltransferase (TdT). Pol beta and TdT were found to exhibit amino acid sequence similarity only with each other and not with any other of the 4750 entries in release 12.0 of the PIR data bank. Optimal amino acid sequence alignment of the entire 39-kDa Pol beta polypeptide with the C-terminal two thirds of TdT revealed 24% identical aa residues and 21% conservative aa substitutions. The Monte Carlo score of 12.6 for the entire aligned sequences indicates highly significant aa sequence homology. The hydropathicity profiles of the aligned aa sequences were remarkably similar throughout, suggesting structural similarity of the polypeptides. The most significant regions of homology are aa residues 39-224 and 311-333 of Pol beta vs. aa residues 191-374 and 484-506 of TdT. In addition, weaker homology was seen between a large portion of the 'nonessential' N-terminal end of TdT (aa residues 33-130) and the first region of strong homology between the two proteins (aa residues 31-128 of Pol beta and aa residues 183-280 of TdT), suggestive of genetic duplication within the ancestral gene. On the basis of nucleotide differences between conserved regions of Pol beta and TdT genes (aligned according to optimally aligned aa sequences) it was estimated that Pol beta and TdT diverged on the order of 250 million years ago, corresponding roughly to a time before radiation of mammals and birds.

Studies on the effect of copper deficiency on rat liver mitochondria. III. Effects on adenine nucleotide translocase

Liver mitochondria from Cu-deficient rats exhibit impaired State 3 respiration (oxygen consumption in the presence of exogenous ADP) compared with Cu-adequate controls, whereas State 4 respiration (oxygen consumption after depletion of exogenous ADP) and ADP/O are unaffected. In view of previous observations (Davies, N.T., Lawrence, C.B., Mills, C.F. and Nicol, F. (1985) Biochim. Biophys. Acta 809, 351-361) it seemed that a decline in cytochrome c oxidase activity (EC 1.9.3.1) could not fully account for these findings. Cu deficiency resulted in a significant decline (40%, P less than 0.01) in [14C]ADP uptake by liver mitochondria which suggests there is a reduced activity of the adenine nucleotide translocase. The reduced translocase activity was not associated with any marked change in fatty-acid composition of either intact mitochondria or inner mitochondrial membranes. Inhibitor titrations with the irreversible inhibitor carboxyatractyloside showed that 'Cu-deficient' mitochondria required the same concentration of inhibitor to produce 100% inhibition of State 3 respiration as control mitochondria, suggesting that the amount of functional translocase enzyme present is unaffected. When the translocase assay was allowed to proceed until equilibrium was established between external and internal nucleotides, it was apparent that the exchangeable adenine nucleotide pool of Cu-deficient mitochondria was 36% lower than in controls. Analysis of mitochondria for their ATP, ADP and AMP contents showed that, whereas the AMP content was unaffected, ATP and ADP contents were 39 and 40% lower, respectively, which resulted in a significantly reduced pool of total adenine nucleotides (ATP + ADP + AMP) and a reduced 'energy charge' [(ATP + 0.5 ADP)/(ATP + ADP + AMP)]. These results are discussed in relation to current concepts of the regulation and control of mitochondrial respiration.

A novel, simple and rapid method for the isolation of mitochondria which exhibit respiratory control, from rat small intestinal mucosa

A method is described for the isolation of functional mitochondria from rat intestinal mucosa. Its novel feature is the removal of mucus from the initial homogenate by treatment with DEAE-cellulose. The preparations exhibited acceptable ADP:O ratios, high State-3 respiration rates, and respiratory control ratios in excess of 3 when succinate, beta-hydroxybutyrate, glutamate/malate and glutamine were test substrates.

Data structures for DNA sequence manipulation

Two data structures designated Fragment and Construct are described. The Fragment data structure defines a continuous nucleic acid sequence from a unique genetic origin. The Construct defines a continuous sequence composed of sequences from multiple genetic origins. These data structures are manipulated by a set of software tools to simulate the construction of mosaic recombinant DNA molecules. They are also used as an interface between sequence data banks and analytical programs.

Comparative sequence analysis as a tool for studying the secondary structure of mRNAs

Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNAs and mRNA precursors. We observed many conserved helices in all mRNA groups analyzed. Three criteria were used to identify potential helices which were not conserved solely because of coding sequence constraints, and may therefore be important for the structure and function of the RNA. These results suggest that this approach will be useful in deriving secondary structure models for informational RNAs when used in conjunction with other complementary techniques, and in designing experiments to determine the functional significance of conserved base pairing interactions.

Studies on the effects of copper deficiency on rat liver mitochondria. II. Effects on oxidative phosphorylation

Effects of dietary copper deficiency in rats on respiratory enzymes of isolated rat liver mitochondria have been studied. After 2 weeks of Cu-depletion, cytochrome c oxidase (EC 1.9.3.1) activity had declined by 42% and between 4 and 8 weeks exhibited between 20 and 25% of the activity of control mitochondria. Activities of NADH cytochrome c reductase (EC 1.6.99.3) and succinate cytochrome c reductase (EC 1.3.99.1), were unaffected initially but declined by 32 and 46%, respectively, after 8 weeks of Cu-depletion. After 4 weeks there was a significant (34%) decline in succinate supported state 3 respiration with only a modest (18%) decline in state 4 respiration. The ADP:O ratio was unaffected by Cu-depletion after 6 and 8 weeks of dietary Cu-restriction. State 3 respiration was significantly reduced after 6 weeks when glutamate/malate or beta-hydroxybutyrate were used as substrates, whereas state 4 respiration and ADP:O ratios were unaffected. The fall in state 3 respiration was of sufficient magnitude at 8 weeks to cause a significant decline in the respiratory control ratio with all substrates. Comparisons between the relative activities of cytochrome c oxidase and reductase activities in Cu-deficient preparations, the relatively specific effect of the deficiency on state 3 respiration with all substrates tested and the ability to increase significantly oxygen consumption in excess of maximal state 3 respiration by the uncoupler 2,4-dinitrophenol suggest that the defect in Cu-deficient mitochondria cannot be attributed solely to the decreased activity of cytochrome c oxidase.

Studies on the effects of copper deficiency on rat liver mitochondria. I. Changes in mitochondrial composition

As part of an investigation of the lesions of copper (Cu) deficiency a study was undertaken of the copper, iron, cytochrome and fatty acid composition of liver mitochondria from Cu deficient and Cu-adequate control rats. Cu concentrations were significantly decreased in whole liver, liver mitochondria and in blood plasma. Total iron was significantly increased in whole liver but remained at the normal level in mitochondria. Cytochrome c oxidase (EC 1.9.3.1) and its component cytochromes a and a3 were significantly reduced in liver mitochondria from Cu-deficient rats, whereas there was no effect on the concentration of cytochromes b, c1 and c. Evidence from comparisons between cytochrome c oxidase activity and the amount of enzyme present, as assessed from the mitochondrial cytochrome a and a3 content, suggests that in addition to an absolute loss of enzyme, Cu-deficiency adversely affects the efficiency of the residual enzyme. Severe Cu deficiency had no effect on 'ageing' or 'swelling' properties of liver mitochondria, indicating no marked effects on fatty acid composition. Fatty acid analyses demonstrated a slight but significant increase in docosapentenoic acid (22:5) of Cu-deficient mitochondria, but since this represents a minor component there was no change observed in the 'unsaturation index'. It was concluded that, in contrast to previous reports, Cu deficiency of the severity reported did not have a deleterious effect on the integrity and permeability of the inner mitochondrial membrane as exemplified by any qualitative modification of fatty acid constitution per se.

Analysis of repetitive sequence elements containing tRNA-like sequences

Several repetitive sequence elements from diverse species share extensive sequence homology with tRNA molecules. Analysis of the tRNA-like sequences within these elements suggest that they have originated from authentic tRNA sequences. Elements containing tRNA-like sequences can be divided into three distinct groups whose members share extensive sequence homology, have similar sequence organization and have unique species distribution. We suggest that these three groups represent independent examples of retroposon families that have originated from tRNAs.