Endogenous retroviruses (ERVs) most likely are remnants of ancient retroviral infections. ERVs preserve functions of exogenous retroviruses to a varying extent, and can be parasites, symbionts or more or less neutral genetic 'junk'.Their evolution has two facets, pre- and post-endogenization. Although the two are not clearly separated, the first pertains to retroviral evolution in general and the second to the fate of repetitive DNA and the evolution of the host organism and its genome. The study of ERVs provides much material for the understanding of retroviral evolution. This sequence archive reflects the history of successes and shortcomings of antiviral resistance, but also of strategic evolutionary decisions regarding genome organization and new gene acquisition. This review discusses retroviral evolution illustrated through HERVs, bioinformatic prerequisites for ERV studies, the endogenization process and HERV evolution post-endogenization, including relation to disease. (Part of a Multi-author Review).

The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. We screened both the human genome (version hg16) and the chimpanzee genome (version PanTro1) for ERVs and conducted a phylogenetic analysis of recent integrations. We found a number of recent integrations within both genomes. They segregated into four groups. Two larger gammaretrovirus-like groups (PtG1 and PtG2) occurred in chimpanzees but not in humans. The PtG sequences were most similar to two baboon ERVs and a macaque sequence but neither to other chimpanzee ERVs nor to any human gammaretrovirus-like ERVs. The pattern was consistent with cross-species transfer via predation. This appears to be an example of horizontal transfer of retroviruses with occasional fixation in the germ line.

About 8 per cent of the human genome consists of human endogenous retroviral sequences (HERVs), which are remains from ancient infections. The HERVs may give rise to transcripts or affect the expression of human genes. The first step in understanding HERV function is to classify HERVs into families. In this work we study the relationships of existing HERV families and detect potentially new HERV families. A Median Self-Organizing Map (SOM), a SOM for non-vectorial data, is used to group and visualize a collection of 3661 HERVs. The SOM-based analysis is complemented with estimates of the reliability of the results. A novel trustworthiness visualization method is used to estimate which parts of the SOM visualization are reliable and which not. The reliability of extracted interesting HERV groups is verified by a bootstrap procedure suitable for SOM visualization-based analysis. The SOM detects a group of epsilonretroviral sequences and a group of ERV9, HERVW, and HUERSP3 sequences which suggests that ERV9 and HERVW sequences may have a common origin.

ABSTRACT The ERV3 locus at chromosome 7q11 is a much studied human endogenous retroviral (HERV) sequence, owing to an env open reading frame (ORF) and placental RNA and protein expression. An analysis of the human genome demonstrated that ERV3 is one of a group of 41 highly related elements (ERV3-like HERVs) which use proline, isoleucine, or arginine tRNA in their primer binding sites. In addition to elements closely related to ERV3, the group included the previously known retinoic acid-inducible element, RRHERVI, also referred to as HERV15, but was separate from the related HERV-E elements. The ERV3-like elements are defective. The only element with an ORF among gag , pro , pol , and env genes was the env ORF of the original ERV3 locus. A search in dbEST revealed ERV3 RNA expression in placenta, skin, carcinoid tumor, and adrenal glands. Expression was also studied with newly developed real-time quantitative PCRs (QPCR) of ERV3 and HERV-E(4-1) env sequences. Results from a novel histone 3.3 RNA QPCR result served as the expression control. QPCR results for ERV3 were compatible with previously published results, with a stronger expression in adrenal gland and placenta than in 15 other human tissues. The expression of the envelope ( env ) of ERV3 at chromosome 7q11 was also studied by using stringent in situ hybridization. Expression was found in corpus luteum, testis, adrenal gland, Hassal's bodies in thymus, brown fat, pituitary gland, and epithelium of the lung. We conclude that ERV3 env is most strongly expressed in adrenal and sebaceous glands as well as in placenta.

ABSTRACT Recently, we identified and classified 926 human endogenous retrovirus H (HERV-H)-like proviruses in the human genome. In this paper, we used the information to, in silico, reconstruct a putative ancestral HERV-H. A calculated consensus sequence was nearly open in all genes. A few manual adjustments resulted in a putative 9-kb HERV-H provirus with open reading frames (ORFs) in gag, pro, pol, and env. Long terminal repeats (LTRs) differed by 1.1%, indicating proximity to an integration event. The gag ORF was extended upstream of the normal myristylation start site. There was a long leader (including a “pre-gag” ORF) region positioned like the N terminus of murine leukemia virus (MLV) “glyco-Gag,” potentially encoding a proline- and serine-rich domain remotely similar to MLV pp12. Another ORF, starting inside the 5′ LTR, had no obvious similarity to known protein domains. Unlike other hitherto described gammaretroviruses, the reconstructed Gag had two zinc finger motifs. Alternative splicing of sequences related to the HERV-H consensus was confirmed using dbEST data. env transcripts were most prevalent in colon tumors, but also in normal testis. We found no evidence for full length env transcripts in the dbEST. HERV-H had a markedly skewed nucleotide composition, disfavoring guanine and favoring cytidine. We conclude that the HERV-H consensus shared a gene arrangement common to gammaretroviruses with gag separated by stop codon from pro-pol in the same reading frame, while env resides in another reading frame. There was also alternative splicing. HERV-H consensus yielded new insights in gammaretroviral evolution and will be useful as a model in studies on expression and function.

PURPOSE:To investigate the quantitative response of retinal circulation in normal human eyes to oxygen and carbon dioxide provocation and to gain more information about retinal mean transit time (MTT).METHODS:Healthy subjects were studied while breathing: room air (O(2) baseline); pure O(2); room air (CO(2) baseline), and CO(2) in room air. The CO(2) level was brought to 30% above individual baseline level. During each gas exposure, blue field simulation was used to estimate the velocity of macular leucocytes and fluorescein angiography was used to determine MTT, arteriovenous passage time (AVP) and vessel diameters.RESULTS:Breathing pure O(2) caused a reduction in macular leucocyte velocity of about 13%, a non-significant change in MTT and AVP from baseline, and a 10% reduction in the diameter of temporal retinal arteries and veins. Breathing CO(2) caused an increase in macular leucocyte velocity of 21%, a non-significant change in MTT and AVP, and no change in retinal vascular diameters.CONCLUSION:Both O(2) and CO(2) had the expected effects on retinal blood flow, as judged by leucocyte velocity in the macular capillaries, but little effect on retinal MTT, indicating concomitant changes in flow and retinal vascular volume. Measuring the diameter of retinal vessels before and during pure O(2) breathing is a simple and effective way of determining the reactivity of retinal vessels.

This study investigates the effects of cerebral microembolism on motor performance and risk assessment behavior in the rat. Cerebral infarcts were produced in rats by injecting small plastic beads into the left heart ventricle under short-acting anesthesia. The functional outcome was tested 24 h later by subjecting the animals to a series of consecutive behavioral tests. Thereafter, the rats were anesthetized and underwent magnetic resonance imaging. On average about seven infarcts per brain were found. The volume of the individual infarcts was largest in the hippocampus (mean=4.26 mm(3)) and smallest in the white matter (mean=0.83 mm(3)). Embolized animals performed spontaneous and evident locomotion. The activity was, however, significantly decreased compared to rats treated with vehicle. More specific tests for motor ability revealed reduced gait capacity and muscular strength. A significant relationship was found between behaviors reflecting motor ability and the total volume of infarcted tissue in the brain stem, cortex and cerebellum. Also the behavioral profile of risk and benefit assessment was found to be altered by the microembolization. It is concluded that the combination of the microembolization method and behavioral tests provides a valuable tool for further studies of the pathophysiology of, and potential treatment for, cerebral infarction.

Objective: To evaluate three different techniques to quantify retinal blood flow transit times in normal human eyes from fluorescein angiograms.Subjects and Methods: Fluorescein angiograms were recorded on two different occasions in 18 normal individuals with a scanning laser ophthalmoscope. The angiograms were digitized (5 frames per second) and the images were aligned. Mean transit times (MTT) were analysed with a newly developed technique based on an impulse-response analysis (MTTIR) and again with the conventional technique (MTT (SLOPE)). Arterio-venous passage times (AVP) were also calculated.Results: At the first determination, mean values (SD) for MTTIR , MTT (SLOPE), and AVP were 3.22 (0.78), 4.88 (1.86), and 1.46 (0.57) seconds, respectively. Detection of an increase of 25% with a power of 80% requires groups of 12, 86 and 17 individuals for the three techniques, respectively.Conclusions: Mean transit time is a well-defined physiological parameter. The technique based on impulse-response analysis allows for analysis of even badly defined dye curves. We found this technique to be superior to the conventional technique in terms of reproducibility.

PURPOSE:To determine the correlation between transit times of retinal blood flow calculated from fluorescein angiograms and retinal blood flow determined by the microsphere method.METHODS:Two fluorescein angiograms were obtained in each eye of six monkeys, followed by determination of retinal blood flow with labeled microspheres. Angiograms in 10 eyes were analyzed for mean transit time (MTT) and arteriovenous passage time (AVP). MTT was determined in two ways: from dye curves reconstructed by extrapolation of semilogarithmic plots of the recorded curves (MTT(slope)) and by a new technique based on an impulse-response analysis (MTT(ir)).RESULTS:Mean values (+/-SD) for retinal blood flow in 10 eyes were 23.2 +/- 6.9 mg/min. Corresponding values for MTT(ir), MTT(slope), and AVP were 2.22 +/- 0.38, 4.89 +/- 5.89, and 1.08 +/- 0.14 seconds. There was a weak, but not statistically significant, correlation between retinal blood flow and MTT(ir) (r = -0.60, P = 0.06) but no useful correlation between retinal blood flow and either MTT(slope) or AVP.CONCLUSIONS:The relationship between retinal blood flow and transit times determined from fluorescein angiograms is weak. Of the three transit parameters tested, MTT(ir), determined with the recently developed impulse-response technique, had the best correlation with retinal blood flow. Further studies are needed to determine the ability of these transit parameters to detect a change in retinal blood flow and the possibility that transit times may provide useful clinical information unrelated to absolute values of retinal blood flow.

This work describes changes in relative blood flow caused by discrete emboli reaching the brain of conscious rabbits. With [14C]iodoantipyrine autoradiography, small ischemic foci were observed scattered throughout the brain. After correction for tracer diffusion from the surroundings, the ischemic regions located in the deeper parts of the brain were found to have a lower blood flow than the foci in the cortex. Further, the cortical foci were significantly smaller than those in the basal ganglia (the area where the average size of the foci was found to be largest). The results and conclusions of this work should aid in interpretation of future experiments with potential treatments. Microinfarctions may well need different treatments depending on their localization.

ABSTRACT.Purpose: To evaluate a new technique for determing the Mean Transit Time (MTT) of retinal circulation, based on an impulse‐response analysis. The results obtained were compared to those obtained with a conventional method based on semilogarithmic extrapolation.Methods: 128 frames at a rate of 5 frames per second were digitized from video fluorescein angiograms and processed with a specially designed image analysis system. The MTT was determined from 25 curve pairs from 12 eyes in 8 young, healthy volunteers by the conventional technique (MTTSLOPE) and by our newly developed Impulse‐Response analysis (MTTIR).Results: MTTSLOPE and MTTIR calculated for the 25 curve pairs were 3.54 ± 1.00 and 2.67 ± 0.88 seconds, respectively (Mean ± SD). There was a good correlation between the two techniques (r2 = 0.81, p<0.001). Unlike MTTSLOPE MTTIR could be calculated also from curves with a badly defined bolus. Conclusion: We conclude that MTTiR‐analysis of the retinal circulation may be used for clinical studies on retinal blood flow from angiograms obtained in patients.

We have recently published an experimental method useful for causing discrete cerebral microischemic foci in rabbits. In that study it was shown that on reaching the brain, plastic beads (with an average diameter of 80 or 110 μm) give rise to foci of increased [14C]2-deoxyglucose accumulation, indicating anaerobic glycolysis. Further, it was suggested that the relatively low accumulation of [14C]2-deoxyglucose, as observed in the center of some of the ischemic foci located in areas which are thought to have a poor collateral blood supply, was an indication of glucose depletion. This work is intended to be a useful approach for the study of diffusion-limited consumption of glucose and oxygen in microischemic regions, located in endarterial regions. It is shown that a mathematical model with reasonable parameters can be fitted to a measured [14C]2-deoxyglucose profile. The results of this study are compatible with the view that the glucose concentration in the ischemic center is very low and limits the rate of energy turnover. Together with animal experiments, this mathematical model may impart new information of importance for evaluating the treatment of subcortical infarctions in humans.

We have measured the effectiveness of different standard cryogenic liquids (liquid nitrogen, chilled isopentane, chilled hexane, and chilled ethanol) and applied a mathematical model for calculating the temperature changes at different depths in rabbit and rat heads cooled in liquid nitrogen. We have also evaluated the extent to which the freezing time is shortened when the skin is removed prior to immersion. We conclude that: (i) of the coolants used, liquid nitrogen gives the most rapid freezing. (ii) dry ice-chilled ethanol is as effective as dry ice-chilled hexane. Liquid nitrogen and ethanol are safer for the environment than isopentane and hexane and should satisfy most needs. (iii) By removing the skin prior to immersion, the freezing time can be reduced by about 20 s for the rabbit cortex and rat hypothalamus, 30 s for the rat cortex, and 40 s for the rabbit hypothalamus.

Multiinfarct dementia is the second most common form of dementia in the elderly. An animal model of microischemia may provide information about the pathophysiology relevant when searching for prevention or treatment of microinfarctions in humans. The purpose of the present study was to develop an experimental model useful for studying discrete microischemic foci. In order to achieve single cerebral microischemic foci plastic beads with diameters of about 100 μm were injected into the left heart ventricle of anesthetized rabbits. 2-Deoxy-[14C]glucose (2-DG) and autoradiography were used to detect regions with disturbed metabolism. The tissue sections were inspected for impacted beads. Foci with markedly increased 2-DG accumulation and with diameters of about 1 mm were detected in all parts of the brain, indicating hypoxic regions with enhanced glycolysis. In some foci, located mainly in the basal ganglia, a central dip in the 2-DG profile was seen, suggesting poor glucose supply to the central ischemic region. The ratio foci/beads was about 1 in the brain stem (diencephalon included) and about 0.5 in the cortex. Twenty-four hours after embolization, infarctions, mainly in the deeper brain regions, were seen. There were still foci with increased 2-DG uptake, which were mainly located in the cortex. The results suggest that microemboli reaching the deeper brain regions give rise to metabolic disturbances more often than emboli reaching the cortex and that the ischemic foci in deeper brain regions are more prone to develop further into infarctions.

A magnetic resonance 3DFT multiple gradient-echo technique was used for measurements of the proton spectrum for each voxel in the measured slice. Water, fat, magnetic field and T2 distributions in the head of a normal volunteer and a patient with intracerebral hematoma were computed. Magnetic field variations caused by the head were calculated after correction for the static magnetic field inhomogeneity. Large local magnetic field variations up to 3 ppm were found in the human brain near interfaces between air or bone and brain tissues and 0.5 ppm between hematoma and brain tissue. Information about magnetic field variations could be useful for shimming procedures in vivo and for correcting artifacts in imaging and spectroscopy.

• Background: There are reasons to suspect that in patients with high intraocular pressure and glaucoma, there is underperfusion of the intraocular tissues and optic nerve head, leading to tissue hypoxia and neuronal damage. Studies in young, healthy monkeys have demonstrated that there is efficient autoregulation of the blood flow, and essentially normal glucose consumption, even at very high intraocular pressures that reduce the perfusion pressure to levels around 30 mmHg. It seemed likely that the conditions might be different in old monkeys that had been on atherogenic diet for long periods of time and that such monkeys were a better model for glaucomatous patients. • Methods: The perfusion pressure in one eye was reduced to 30–35 mmHg in four old rhesus monkeys that had been on atherogenic diet for 12.5 years, and the glucose consumption in the eyes and optic nerves was studied with the 14C-2-deoxyglucose (2DG) method of Sokoloff et al. • Results: There was enhanced uptake of 2DG in the inner as well as outer parts of the retina and in the optic nerve head in all four monkeys studied, indicating compromised supply of oxygen resulting in anaerobic glycolysis. • Conclusion: Old monkeys that have been on atherogenic diet seem more susceptible to elevation of the intraocular pressure than young, healthy monkeys, thereby suggesting defective autoregulation in them. Such differences in susceptibility may play a role also in the development of ischemic disorders of the optic nerve head and glaucomatous optic neuropathy.

This paper describes an MR imaging method for determining magnetic susceptibility constants of solutions containing paramagnetic contrast agents. The method's validity is demonstrated on Gd(DTPA) and Dy(DTPA) water solutions. The method can be used for measurement of the volume magnetic susceptibility or concentration of contrast agents in biological tissues.

In a previous study of 50 patients with non-Hodgkin lymphoma (NHL) it was shown that the inhomogeneous appearance of a tumor at MR imaging strongly indicated a high malignancy grade. In this study of 33 patients with NHL, the administration of an i.v. contrast medium, Gadolinium-DTPA, improved the subjective detectability of the inhomogeneities. A method of quantifying the degree of inhomogeneity in the tumors (inhomogeneity index, IH-index) was developed and tested. The mean value of IH-index in the T2-weighted image before contrast medium administration, and of the T1-weighted image after contrast medium administration, as well as the IH-index value in the T2-weighted image before contrast medium administration alone, was able to discriminate well between low- and high-grade NHL. This method of quantifying the degree of inhomogeneity in tumors improved sensitivity in detecting high-grade NHL.

Transverse relaxation times were estimated from numerical simulations on spin systems using multi-echo spinecho MRI protocols. The influence of T1 on the echo amplitudes via stimulated echo components was studied. The resulting effects on T2 estimates from the Carr-Purcell (CP), Carr-Purcell-Meiboom-Gill (CPMG), and Phase-Alternating-Phase-Shift (PHAPS; combination of CP and CPMG), multiple echo schemes were examined. Protocols with either spatially selective or nonselective refocusing pulses were studied. An intravoxel static field inhomogeneity of 0.1, 1, and 10 ppm was stimulated. The dependence on T1 of the T2 estimates was notable for T1 values below approximately 800 msec for all protocols. The PHAPS scheme provided rather accurate, but underestimated, T2 values when selective refocusing was used. With nonselective refocusing, PHAPS T2 values were overestimated and demonstrated a pronounced dependence on magnetic field inhomogeneity. In general, long T2 values were erroneous with the PHAPS protocol. The results indicate that a CPMG protocol structure provides a more robust method for T2 estimations than the PHAPS protocol.