Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Pan variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed1991

Pregnancy-associated murine protein-1 plasma levels during oestrus cycle, pseudopregnancy and pregnancy in the mouse.

A cyclic variation in plasma levels of pregnancy-associated murine protein-1 (PAMP-1) during the oestrus cycle in outbred Pan: Thei mice was recorded. PAMP-1 plasma levels were significantly elevated in dioestrus as compared with the three other stages of the murine oestrus cycle. Until day 7 of gestation the PAMP-1 plasma levels remained low, and no significant differences could be observed between pregnant and pseudopregnant female mice. The PAMP-1 levels increased markedly in the circulation on day 8 of pregnancy, and continued to increase until peak values were reached at day 11 of pregnancy. In the latter half of pregnancy the PAMP-1 levels declined until day 17 of pregnancy, at which stage the normal non-pregnant values were recorded.

Animals↗
PubMedDate not supplied

[Diurnal rhythm of cortisol and aldosterone plasma levels in patients with chronic renal insufficiency].

UNLABELLED: In patients with chronic renal failure (CRF) disturbances in cortical adrenal endocrine function were described previously. An increased plasma aldosterone level was documented in several studies [1-4]. The aim of this study was to investigate diurnal rhythms of plasma cortisol and aldosterone in CRF patients. In addition, in 3 patients on maintenance haemodialysis, the effect of dialysis procedure upon the plasma level of these hormones was studied. Ten patients with CRF of different etiologies, mean age 41.2 years, serum creatinine from 166-1336 mumol/L, creatinine clearance 4.2-29.2 ml/min, participated in the study. Blood samples were taken in the recumbent position at 6 am and at 6 h intervals thereafter for 24 h. Another group was made of 3 patients on maintenance haemodialysis for a mean 4.2 years. The effect of dialysis upon plasma cortisol and aldosterone levels was studied in the morning (7-11 h) and afternoon hours (14-18 h), with blood samples taken at one hour intervals. Patients were dialysed on cuprophan and polyacrilonitrile membranes. Plasma cortisol and aldosterone levels were determined using commercial RIA kits from Sorin Biomedica, Italy. The results obtained show that in 8 out of 10 patients with CRF in the predialysis period diurnal rhythm of cortisol was preserved. Investigation of the plasma aldosterone, with a 6 h sampling, however, shows in most of the patients studied no changes indicating a preserved diurnal rhythm. Investigation of the effect of haemodialysis treatment performed for 4 h on cuprophane as well as on PAN membrane, upon the plasma cortisol level has shown in morning hours the unchanged plasma cortisol level, compared to the same patients during the control study. Haemodialysis in the afternoon hours has produced, a small decrease of plasma cortisol during the first two hours, followed by an increase to the predialysis values. Plasma aldosterone levels during the morning and afternoon haemodialysis have shown variations similar to that observed in the same patients during the control study. CONCLUSIONS: This study has shown a preserved circadian rhythm of cortisol in kidney patients with CRF. A clear diurnal rhythm of aldosterone in these patients cannot be established. Investigation of the effect of haemodialysis procedure, performed on cuprophan and PAN, a more permeable membrane, upon the plasma levels of cortisol and aldosterone, has shown variations similar to that observed during the control study.

Adult↗
PubMed2025

Primulina pan-genome reveals differential gene retention following whole-genome duplications and provides insights into edaphic specialization.

Primulina, a genus of >200 species specialized to extreme soils, provides a model for edaphic adaptation. We assemble seven genomes and construct a pan-genome spanning nine species from karst, Danxia, and acidic soils. Comparative analyses reveal that karst-adapted species have smaller genomes. Two lineage-specific whole-genome duplications (WGDs) exhibit biased duplicate loss in large gene families but preferential retention of transcription factors, indicating combined adaptive and nonadaptive forces. Pan-genome analyses identify ion channel and transporter genes enriched in variant hotspots and under positive selection in karst lineages. Candidate genes for drought and salt stress tolerance include ABC transporters and ion channels. Notably, an ABC transporter shows positive selection in karst species and unique structural variation in non-karst species. Together, our findings show that genome downsizing, biased post-WGD retention, and evolution of ion-transport pathways shape adaptation to extreme soils. The Primulina pan-genome provides a resource for dissecting mechanisms underlying edaphic specialization.

Gene Duplication↗
PubMed1995

Complex changes of GABAA and GABAB receptor binding in the spinal cord dorsal horn following peripheral inflammation or neurectomy.

Chronic peripheral inflammation or peripheral neurectomy cause changes in GABA levels and GABA immunoreactivity in the spinal cord dorsal horn. The present study aimed to investigate if such changes are accompanied by alterations in GABA receptor binding. Neurectomy of the sciatic nerve caused an ipsilateral down-regulation of GABAB receptor binding in lamina II of the spinal cord 2-4 weeks after the nerve injury. Since approximately 50% of GABAB receptor binding in that region is located on primary afferent endings, degenerative changes of such endings caused by the nerve lesion can explain the observed reduction. In contrast, GABAA binding was substantially enhanced following neurectomy, which may be due to an up-regulation of the receptors issued by the concomitant decrease of endogenous GABA. In rats bearing unilateral chronic peripheral inflammation induced by intraarticular injection of complete Freund's adjuvant we found a reduction of GABAB binding in the superficial dorsal horn. This effect, which was maximal at 3-4 weeks after adjuvant injection, was attributed to an enhanced release of GABA by spinal interneurons. GABAA receptor binding was not changed in this experimental model. Together, these results suggest that the two receptor types may be located at different loci and are differently affected by variations in sensory input.

Animals↗
PubMed1995

Determination of microdialysis extraction fraction of cocaine by the no net flux method under high, low, and zero steady-state cocaine concentrations in rats.

The effect of different steady-state cocaine concentration maintenance on the microdialysis extraction fraction of cocaine (in situ recovery; Ed) in the medial prefrontal cortex (mPFC) was examined. Male, adult Sprague-Dawley rats anesthetized with chloral hydrate were used. All rats were randomly divided into three groups and were given cocaine i.v. infusion of either 0.6 mg/kg/min (group A), 0.3 mg/kg/min (group B), or 0.0 mg/kg/min (group C). A steady-state cocaine concentration in the blood was obtained for both A and B groups. They were 24.3 +/- 2.3 microM, respectively. We then applied the no net flux microdialysis method to determine the Ed of cocaine in vivo for all three groups. Results revealed that there was no significant difference of Ed under these three different infusion regimens (group A: 16 +/- 2%; group B: 17 +/- 1%; group C: 21 +/- 2%). The steady-state cocaine concentration in the mPFC was also estimated to be 17.7 +/- 1.3 microM, 11.3 +/- 2.0 microM, and 0.7 +/- 0.6 microM, respectively. We then concluded that the Ed of cocaine in the mPFC is invariable while the steady-state cocaine concentration in the mPFC was ranging from 0 to 18 microM. This information is useful in the cocaine pharmacokinetic study since scientists are concerned about the variations of Ed while cocaine concentration in the mPFC is changing.

Animals↗
PubMed2005

Functional analysis of the plant disease resistance gene Pto using DNA shuffling.

Pto is a serine/threonine kinase that mediates resistance in tomato to strains of Pseudomonas syringae pv. tomato expressing the (a)virulence proteins AvrPto or AvrPtoB. DNA shuffling was used as a combinatorial in vitro genetic approach to dissect the functional regions of Pto. The Pto gene was shuffled with four of its paralogs from a resistant haplotype to create a library of recombinant products that was screened for interaction with AvrPto in yeast. All interacting clones and a representative sample of noninteracting clones were sequenced, and their ability to signal downstream was tested by the elicitation of a hypersensitive response in an AvrPto-dependent or -independent manner in planta. Eight candidate regions important for binding to AvrPto or for downstream signaling were identified by statistical correlations between individual amino acid positions and phenotype. A subset of the regions had previously been identified as important for recognition, confirming the validity of the shuffling approach. Three novel regions important for Pto function were validated by site-directed mutagenesis. Several chimeras and point mutants exhibited a differential interaction with (a)virulence proteins in the AvrPto and VirPphA family, demonstrating distinct binding requirements for different ligands. Additionally, the identification of chimeras that are both constitutively active as well as capable of binding AvrPto indicates that elicitation of downstream signaling does not involve a conformational change that precludes binding of AvrPto, as previously hypothesized. The correlations between phenotypes and variation generated by DNA shuffling paralleled natural variation observed between orthologs of Pto from Lycopersicon spp.

Blotting, Western↗
PubMed1998

Polymorphisms of the apolipoprotein B 3' variable number of tandem repeats region associated with coronary artery disease in Taiwanese.

We studied the allelic frequency of the variable number of tandem repeats region 3' of the apolipoprotein B gene (apoB 3' VNTR) and its impact on coronary artery disease (CAD) in 150 patients with CAD and 153 normal controls in a Taiwan population. apoB 3' VNTR alleles were classified according to the number of repeats of a 15-bp hypervariable elements (HVE), the sequence of which was determined using the polymerase chain reaction and direct sequencing. Thirteen alleles comprising from 26 to 54 HVEs were identified. The CAD patients had greater heterozygosity (0.58 vs 0.42) and a higher frequency of long (> 36-HVE) apoB 3' VNTR alleles than the controls (18.7% vs 10.8%, p < 0.01). CAD patients with two HVE-36 alleles and no HVE-32 alleles (the two most common forms) had significantly higher concentrations of LDL-cholesterol, apolipoprotein B, and triglycerides, and significantly lower values of HDL-cholesterol and apolipoprotein AI than the control group (p < 0.01 for all comparisons). The length of the apoB 3' VNTR was not correlated with the plasma concentrations of any of the lipids. We conclude that long apoB 3' VNTR alleles occur more frequently in CAD patients, but that apoB 3'VNTR genotypic variation has little impact on the risk of dyslipidemia in Taiwanese.

Aged↗
PubMed2007

Measurement of eye-gaze in chimpanzees (Pan troglodytes).

Gaze cues are used as an index of social cognition in primates, yet the sensitivity to different forms of gaze, and consequently the cues required to test gaze-following abilities remain understudied. Whereas the eye is attributed special signal value in humans, the camouflaged ocular morphology of non-human primates has led to the consensus that head orientation may be a more salient cue. This study presents the first documentation of the surface eye movements of the chimpanzee, Pan troglodytes, in order to determine the behavioral forms of eye-gaze and their saliency as signals, document their functional variation, and address the signal value of the eyes distinct from head orientation. Movements of the eye were identified as Scan (continuous movement), Glance (a single movement <1 sec), or Fixate (no movement). Scans, glances, and fixations were reliably detected by humans during live observation and from video (Cohen's kappa over 0.70) and, therefore, are likely also to be detected by conspecifics. Eye-gaze comprised a nonunitary measure of visual attention, reflecting the attentional task demands of different activities. Specifically, chimpanzees spent significantly more time scanning while feeding and resting, than grooming, F(2,28) = 10.23, P<0.001, and spent significantly more time fixating while grooming, than feeding or resting, F(2,28) = 7.52, P<0.01. Further, eye-gaze was often incongruent with head movement, varying significantly with the form of eye-gaze: incongruence was found during 12-21% of fixations, during 42-49% of scans, and during 70-100% of glances, F(2,16) = 30.17, P<0.001. These findings provide the basis for discrimination of the adaptive significance of gaze-processing abilities with emphasis on sensitivity to eye-gaze distinct from head orientation. If we are to continue exploring gaze-processing abilities in primates, then we need greater consideration of the precise nature of the signals themselves. Here we present evidence for special consideration of the eyes as a salient signal in P. troglodytes.

Animals↗
PubMed1999

Cultures in chimpanzees.

As an increasing number of field studies of chimpanzees (Pan troglodytes) have achieved long-term status across Africa, differences in the behavioural repertoires described have become apparent that suggest there is significant cultural variation. Here we present a systematic synthesis of this information from the seven most long-term studies, which together have accumulated 151 years of chimpanzee observation. This comprehensive analysis reveals patterns of variation that are far more extensive than have previously been documented for any animal species except humans. We find that 39 different behaviour patterns, including tool usage, grooming and courtship behaviours, are customary or habitual in some communities but are absent in others where ecological explanations have been discounted. Among mammalian and avian species, cultural variation has previously been identified only for single behaviour patterns, such as the local dialects of song-birds. The extensive, multiple variations now documented for chimpanzees are thus without parallel. Moreover, the combined repertoire of these behaviour patterns in each chimpanzee community is itself highly distinctive, a phenomenon characteristic of human cultures but previously unrecognised in non-human species.

Animals↗
PubMed1995

Virologic and serologic characteristics of a natural chimpanzee lentivirus infection.

This study set out to characterize the unique features of natural lentivirus infection in chimpanzees over time. The virologic and serologic characteristics of this infection were followed longitudinally in a naturally infected chimpanzee together with a small cohort of experimentally HIV-1-infected chimpanzees. The subsequent isolates from the naturally infected chimpanzee were all non-syncytium forming (NSI) versus syncytium forming in the experimentally infected animals. In contrast to HIV-1-infected chimpanzees virus load was higher and plasma viremia occurred but in a cyclic pattern. Serologic follow-up suggested the development of neutralizing antibodies with subsequent escape of new isolates. Interestingly, the sequence of the principal neutralizing (V3 loop) domain (of HIV-1) remained constant over time. Antibodies to peptides from the V3 loop were type specific. The occurrence of persistent, fluctuating plasma viremia and NSI-type virus variants of this natural lentivirus infection are unique characteristics not previously reported in experimentally infected chimpanzees.

Acquired Immunodeficiency Syndrome↗
PubMed2005

Human polymorphism and human-chimpanzee divergence in pseudoautosomal region correlate with local recombination rate.

Previous studies have shown widespread correlation between nucleotide polymorphism and recombination rate, but the cause of this correlation is unresolved. One explanation is that recombination is associated with point mutations, potentially through mutagenic effects of meiotic crossover. This hypothesis predicts that regions of frequent recombination should show both elevated nucleotide diversity within a species and increased nucleotide divergence between species. Here we tested this hypothesis by studying the human short-arm pseudoautosomal region (PAR1), which recombines between X and Y chromosomes in men at a rate approximately 20 times the genome average. We sequenced dispersed intronic loci within PAR1 in a panel of humans and in the chimpanzee and directly measured sequence variation and recombination rate from these data. In line with previous reports, we saw a correlation between human polymorphism level and local recombination rate. Moreover, we also found a highly significant correlation between human-chimpanzee divergence and recombination rate. These results are consistent with the hypothesis that recombination is associated with point mutations, possibly because recombination is mutagenic.

Animals↗
PubMed2001

Genome of the apes.

The Human Genome Project has generated both the information and technological infrastructure needed to accelerate genetic comparisons between humans and the African great apes (chimpanzees and gorillas). Sequence and chromosomal organization differences between these highly related genomes will provide clues to the genetic basis for recently evolved, specifically human traits such as bipedal gait and advanced cognitive function. Recent studies comparing the primate genomes have the potential to affect many aspects of human biomedical research and could benefit primate conservation efforts.

Animals↗
PubMed1988

Immunohistochemical evaluation of neuroendocrine cells and neoplasms of the lung.

The dispersed neuroendocrine (NE) system is represented in the bronchopulmonary tract by submucosal nerves and ganglion cells and, in the mucosal lining by solitary NE cells and neuroepithalial bodies (NEB's). The latter two components variably express pan-NE markers including NSE, chromogranin (s) and, notably, synaptophysin. The expression of serotonin, bombesin, calcitonin and leu-enkephalin has been well established; additional eutopic materials include somatostatin and calcitonin gene-related peptide. Solitary NE cells and NEB's are epithelial structures as defined by their consistent cytokeratin expression. Hyperplasia and dysplasia of NE cells may be found in association with various forms of chronic injury; they have been noted in chronic bronchiectasis and in the vicinity of neoplasms of various types. Hyperplastic and dysplastic pulmonary NE cells frequently express ectopic materials particularly ACTH. NE neoplasms of the bronchopulmonary tract comprice a spectrum that includes a) carcinoids, b) well differentiated NE carcinomas, c) intermediate cell NE carcinomas and d) small cell NE carcinomas. The precise pathologic criteria defining these entities are discussed in detail as are their clinical implications. The entire spectrum of lung NE neoplasms express NE markers demonstrable by immunocytochemistry; these include pan-NE markers, serotonin and numerous neuropeptides. The expression of multiple hormonal materials is frequent. Within any given tumor, some variation in expression may be noted in different sites and in different periods of the "normal" or therapeutically modified lifespan of the tumor. The entire spectrum of lung NE neoplasms is epithelial for they express cytokeratin polypeptides and desmoplakin; subsets of the tumors coexpress cytokeratins and neurofilament proteins. Also, subsets of these NE neoplasms may be immunostained with monoclonal antibodies to antigens related to exocrine phenotype suggesting focal amphicrine features.

Carcinoid Tumor↗
PubMed2000

Molecular characterization and population study of an X chromosome homolog of the Y-linked microsatellite DYS391.

A novel microsatellite homologous to DYS391, a (GATA)(n) short tandem repeat on the human Y chromosome, was identified and characterized in the present work. Employing somatic cell hybrid and deletion panels in a PCR-based approach, we found out that the new microsatellite is located in Xp21.2-22.3, while its Y counterpart mapped to Yq11.21. This X-linked locus (provisionally called DXYS391) and its Y homolog constitute one more example of similarity outside the pseudoautosomal regions between the two human sex chromosomes. Sequencing data showed high levels of homology in the flanking regions of DXYS391 and DYS391 that differ primarily by the presence of a (GACA)(3) motif in the Y locus. Both loci were detected in chimpanzee DNA, suggesting that a putative transposition from the X to the Y occurred before the human/chimpanzee split. The allele frequencies of DYS391 and DXYS391 were investigated, respectively, in 271 Y and 337 X chromosomes from distinct human populations worldwide. DYS391 consistently displayed greater among-population component of the variance of the allele frequencies than DXYS391, as expected due to the three-times lower effective population size of Y chromosomes relative to the X. The intra-population diversity of DYS391, measured by Nei's locus diversity as well as by allele size variance, was lowest in Amerindians, while very low diversity of DXYS391 was seen in Africans. Since our African data are based on a small sample, further studies will be necessary to evaluate better this observation.

Alleles↗
PubMed2001

In search of hepatitis C virus receptor(s).

Since the genomic sequence of HCV was determined, significant progress has been made towards understanding the functions of the HCV-encoded proteins, despite the lack of an efficient in-vitro replication system or convenient small-animal model. The identity of the receptor for HCV remains elusive, however. Low-density lipoprotein receptor, CD81, and GAGs may all act as receptors for HCV, either sequentially or by different viral quasispecies. Recent work using pseudotypic VSV bearing E1 or E2 chimeric molecules showed that entry of the E1 pseudotype can be inhibited by recombinant LDLr, whereas the E2 pseudotype is more sensitive to inhibition by recombinant CD81 or heparin. These results suggest that E1 and E2 may be responsible for interactions with different cellular molecules. It is also conceivable that additional, yet unidentified, cellular proteins are involved in viral binding and entry. Intriguingly, the reports of HCV-RNA associated with PBMC suggest that HCV infection may not be restricted to hepatocytes. Thus, separate reservoirs of virus may exist, and HCV may use different receptors to access these different cell types.

Animals↗
PubMed2006

Genome variation and evolution of the malaria parasite Plasmodium falciparum.

Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.

Animals↗
PubMed2006

A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination.

Insights into the origins of structural variation and the mutational mechanisms underlying genomic disorders would be greatly improved by a genomewide map of hotspots of nonallelic homologous recombination (NAHR). Moreover, our understanding of sequence variation within the duplicated sequences that are substrates for NAHR lags far behind that of sequence variation within the single-copy portion of the genome. Perhaps the best-characterized NAHR hotspot lies within the 24-kb-long Charcot-Marie-Tooth disease type 1A (CMT1A)-repeats (REPs) that sponsor deletions and duplications that cause peripheral neuropathies. We investigated structural and sequence diversity within the CMT1A-REPs, both within and between species. We discovered a high frequency of retroelement insertions, accelerated sequence evolution after duplication, extensive paralogous gene conversion, and a greater than twofold enrichment of SNPs in humans relative to the genome average. We identified an allelic recombination hotspot underlying the known NAHR hotspot, which suggests that the two processes are intimately related. Finally, we used our data to develop a novel method for inferring the location of an NAHR hotspot from sequence variation within segmental duplications and applied it to identify a putative NAHR hotspot within the LCR22 repeats that sponsor velocardiofacial syndrome deletions. We propose that a large-scale project to map sequence variation within segmental duplications would reveal a wealth of novel chromosomal-rearrangement hotspots.

Alleles↗
PubMed1997

Survey of maximum CTG/CAG repeat lengths in humans and non-human primates: total genome scan in populations using the Repeat Expansion Detection method.

Repeat Expansion Detection (RED) is an efficient and simple method for detecting repeat expansions in the human genome, including expansion mutations resulting in disease. Here we report the first population survey of CTG/CAG repeat lengths in humans using the RED method; we have determined maximum CTG/CAG repeat length in 244 individuals from six human populations: Danes, Chinese, Japanese, Rondonian Surui, Maya and Mbuti/Biaka Pygmies. We have also sampled a number of non-human primates including eight orang-utans (Pongo pygmaeus), seven gorillas (Gorilla gorilla), seven pygmy chimpanzees (Pan paniscus), 13 common chimpanzees (Pan troglodytes) and three Hylobatidae (one Hylobates lar, one H.klossii, and one H.syndactylus). Our results demonstrate the existence of significant variation in the sizes and frequencies of the longest CTG/CAG repeat length seen per individual both within and between human populations. The population differences argue that overall mutation rates at CTG/CAG repeat loci are sufficiently low that mutation does not obliterate the effect of random genetic drift and clearly indicate that population stratification could occur in disease association studies using the RED method. No significant differences were detected among the non-human primates sampled. Our results also show that both common chimpanzees and pygmy chimpanzees (bonobos) are polymorphic for maximum length of any CTG/CAG repeats while no variation was found for gorillas and orang-utans.

Animals↗