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PubMed2025

Comparative phylogeographic patterns in three pan-Amazonian antwren lineages (Aves: Passeriformes: Thamnophilidae: Myrmotherula and Isleria).

We examined DNA sequences of 328 individuals of three lineages (species or species complexes) of Amazonian antwrens to evaluate their degree of geographical and historical concordance. All lineages (Myrmotherula longipennis, M. menetriesii, and the Isleria guttata-hauxwelli species complex) consist of small insectivorous birds that occupy understory or midstory of terra firme forest and are widely distributed across the Amazon Basin. Individuals of each of the three lineages grouped into genetic clades mainly separated by the Amazon and some major tributaries, although members of different clades of both M. menetriesii and I. hauxwelli were documented in the Madeira-Tapajós interfluvium. Branching patterns differed among taxa, but all taxa were highly differentiated across the lower or upper Amazon. Despite the morphological, ecological, and phylogenetic similarities among lineages, and despite the fact that nearly all taxa are bounded by rivers, the effect of the other major rivers as biogeographic barriers was highly variable. The Marañón, Ucayali, Madeira, Tapajós, Xingu, Napo, Negro, and Branco all separated main clades in one or two lineages but not in the others. Levels of genetic differentiation along the Teles Pires were substantially higher than those across the Tapajós in M. menetriesii and I. hauxwelli, consistent with a proposed historical change of river course for the Tapajós. Genetic units in this study were comparable for the most part to taxonomic units delineated by analyses of vocal and morphological variation, and identical, with one exception, to units defined solely by vocal variation in a companion paper (Isler et al. 2025). These results, in conjunction with those of Isler et al. (2025), provide additional instances of the variability of responses to the historical dynamism of Amazonia, in this case in closely related and ecologically similar species; highlight the consistency of genetic differentiation with vocal differentiation in additional species of Neotropical suboscine birds; support the importance of Amazonian rivers in creating conditions that result in the differentiation of independent evolutionary lineages; and demonstrate that species richness in two of the lineages studied (M. longipennis and M. menetriesii) was previously underestimated.

Passeriformes↗
PubMed1987

Presence of episomal and integrated human papillomavirus DNA sequences in cervical carcinoma.

Thirty surgical samples of squamous cell carcinoma of the cervix obtained from Chinese women were analysed for the presence of human papillomavirus (HPV) types 16 and 18 using Southern blot hybridization procedure. HPV16 was detected in 53% while HPV18 was found in only 6% of the samples analyzed. When compared with other reports, variation in the geographic distribution of these two HPV types in association with cervical carcinoma is noted. Thirty-seven and a half percent of the HPV16-positive samples contained this HPV type in episomal form and an equal number in cellular DNA-integrated form. The simultaneous presence of both episomal and integrated forms was found in the remaining 25% of the positive samples. The two HPV18-positive cases harbored only episomal viral genome and were not superinfected by HPV16. Analysis of the HPV16 integration samples showed that single integration events had probably occurred and some of the viral sequences had been lost on or subsequent to integration.

Carcinoma, Squamous Cell↗
PubMed2004

Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method.

Abstract Genetic analysis using noninvasively collected samples such as faeces continues to pose a formidable challenge because of unpredictable variation in the extent to which usable DNA is obtained. We investigated the influence of multiple variables on the quantity of DNA extracted from faecal samples from wild mountain gorillas and chimpanzees. There was a small negative correlation between temperature at time of collection and the amount of DNA obtained. Storage of samples either in RNAlater solution or dried using silica gel beads produced similar results, but significantly higher amounts of DNA were obtained using a novel protocol that combines a short period of storage in ethanol with subsequent desiccation using silica.

Animals↗
PubMed1990

[Hypercarotenemia, amenorrhea and a vegetarian diet].

In order to analyse the role of hypercarotenemia in amenorrhoea, we have studied the ovarian function of 20 patients presenting with hypercarotenemia (serum carotene greater than 5 mumol/l). 12 of these were complaining of secondary amenorrhoea (group I), 7 with a normal weight (group I A) and 5 with a weight below 85% of ideal weight (group I B). Another group of 8 patients had normal menstrual cycles and a body weight within normal limits (group II). Group I presented an ovarian insufficiency of hypothalamic origin with an increase in the FSH/LH ratio. The patients in group I A although of normal weight differed from group II by a history of important weight variations, strenuous sports activity and an essentially vegetarian diet, the most likely reason for their hypercarotenemia. The high carotene levels however do not seem to be directly responsible for the amenorrhoea, in view of the normal menstrual cycles of the patients in group II. Hypercarotenemia can be considered as a biologic marker of weight loss with fat mobilisation and low T3 levels. It can also be due to a vegetarian diet. The latter may be an aetiological factor in anovulation by increasing faecal excretion of oestrogens and thus decreasing blood levels of oestradiol particularly when associated with other compounding factors such as excessive physical activity, loss of weight or affective problems.

Amenorrhea↗
PubMed1995

Microsatellite evolution--evidence for directionality and variation in rate between species.

Microsatellite DNA sequences are rapidly becoming the dominant source of nuclear genetic markers for a wide range of applications, from genome mapping to forensic testing to population studies. If misinterpretation is to be avoided, it is vital that we understand fully the way in which microsatellite sequences evolve. We have therefore compared allele length distributions for 42 microsatellites in humans with their homologues in a range of related primates. We find a highly significant trend for the loci to be longer in humans, showing that microsatellites can evolve directionally and at different rates in closely related species.

Alleles↗
PubMed2003

Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome.

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.

Arabidopsis↗
PubMed2002

Selected contribution: circadian rhythm of tumor necrosis factor-alpha uptake into mouse spinal cord.

Circadian variations in the actions of tumor necrosis factor-alpha (TNF-alpha) have been observed. Because a saturable transport system at the blood-brain barrier mediates most of the influx of TNF-alpha from blood to the central nervous system (CNS), the circadian variation of the CNS effects of TNF-alpha could be related to changes in this transport system. Accordingly, we measured the uptake of intravenously injected TNF-alpha into various CNS regions at different times and compared these measurements with the uptake into a peripheral control (muscle). We found that the spinal cord, but not the brain, showed a circadian rhythm in the uptake of TNF-alpha. This pattern is similar to that of leptin but different from that of interleukin-1. The circadian rhythm of the influx of TNF-alpha into this region of the CNS suggests a functional role for the spinal cord in the physiological actions of TNF-alpha.

Animals↗
PubMed1990

Human monoclonal antibody Ha6D3, a candidate for treatment of leukaemia? In vitro reactivity of Ha6D3 with leukaemic cells and in vivo applications in a chimpanzee.

The human monoclonal antibody Ha6D3 of the IgM type was used to stain malignant lymphoma cells from peripheral blood in flow cytometry and from cryosections of lymph nodes using the immunoperoxidase technique. It was found to react with peripheral white blood cells of all 12 cases of leukaemia and with lymph node cells of seven out of 11 B cell lymphomas and with the one T cell lymphoma tested so far. For in vivo experiments a batch of 70 mg Ha6D3 was purified and 6 mg Ha6D3 was injected intravenously into a chimpanzee with time intervals of 10 months and 1 month. The side effects observed were shivering, some muscular spasms and variations in the heart frequency. A decrease of lymphocytes of more than 50% was documented by haematogram analysis. The flow cytometry data showed that the Ha6D3 antigen does not modulate. Even after three repeated injections applied in a time interval of several months no immune response to Ha6D3 could be detected in vivo or in vitro. Based on these data we suggest that Ha6D3 may become a candidate for the treatment of certain leukaemias in vivo.

Animals↗
PubMed2000

Quantitative analysis of mutagenic heterocyclic aromatic amines in cooked meat using liquid chromatography-atmospheric pressure chemical ionisation tandem mass spectrometry.

Five mutagenic heterocyclic aromatic amines (HAAs) were quantified from meat extracts, and grilled and pan fried bacon samples using stable isotopically labeled internal standards. These compounds were isolated from the matrices by a tandem solid-phase extraction procedure, followed by separation on reversed-phase liquid chromatography (HPLC) and quantified by atmospheric pressure chemical ionization tandem mass spectrometry (APCIMS-MS). Tandem mass spectrometry (MS-MS) acquisition was done in selected reaction monitoring (SRM) mode to provide a high degree of sensitivity and selectivity for accurate quantification of HAAs. The detection and quantification limits of these HAAs approached 0.015 and 0.045 microg/kg (part-per-billion), respectively, with only 4 g of meat. The HAA levels ranged widely from 0.045 to 45.500 microg/kg, and 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) was the predominant HAA found in these samples. The amount of HAAs formed was highly dependent upon the type of meat and method of preparation. An intralaboratory comparison of the extraction procedure showed that estimates of these HAAs obtained by three different individuals at HAA levels below 2 microg/kg were within 5% with coefficients of variation below 19%, indicating the robustness of the analytical method. Moreover, because all of these HAAs from this class of molecules undergo facile cleavage at the N-methylimidazole moiety under collision-induced dissociation (CID) conditions, MS-MS analysis in the constant neutral loss mode of [M+H]+-15 enabled the identification of two other HAAs, 2-amino-3-methylimidazo[4,5-f]quinoxaline (IQx) and 2-amino-1,7,9-trimethylimidazo[4,5-g]quinoxaline (7,9-DiMeIgQx), which have rarely been reported in cooked meats.

Amines↗
PubMed1995

Absence of polymorphism at the ZFY locus on the human Y chromosome.

DNA polymorphism in the Y chromosome, examined at a 729-base pair intron located immediately upstream of the ZFY zinc-finger exon, revealed no sequence variation in a worldwide sample of 38 human males. This finding cannot be explained by global constraint on the intron sequence, because interspecific comparisons with other nonhuman primates revealed phylogenetically informative sequence changes. The invariance likely results from either a recent selective sweep, a recent origin for modern Homo sapiens, recurrent male population bottlenecks, or historically small effective male population sizes. A coalescence model predicts an expected time to a most recent common ancestral male lineage of 270,000 years (95 percent confidence limits: 0 to 800,000 years).

Animals↗
PubMed2006

Dental morphometric variation between African and Asian colobines, with special reference to the other Old World monkeys.

In order to reveal differences between Asian and African colobines (nonhuman primates) in terms of dietary adaptation and evolutionary development, a large number of the species of the cercopithecoids (Old World monkeys) was analyzed with morphometric methods. In addition to the raw data and ratios, deviations of the colobines, predicted from allometric baselines derived from the cercopithecines, were analyzed by univariate and multivariate analyses. Some results indicated that there exists significant differentiation between colobines and cercopithecines; the latter exhibit a larger dental scale relative to body size, and the less developed front teeth of the colobines may be related to their fewer frequent incisal use, compared with those of the cercopithecines. With regard to variations between the two subtribes of the colobines, which are found in African (Colobina) and Asia (Presbytina), the Asian subtribe displays a larger scale of postcanine teeth, referring to the results of the raw data. This may correspond to their larger body size. While ratios were considered, the variation between Presbytina and Colobina was diminished greatly. This implies that, unlike the scenario postulated to reflect the relationships between colobines and cercopithecines--which supposes that their differentiation is in both size and shape--the variation between the two subtribes is principally size associated: relative to body size Colobina exhibits more emphasized incisors, but less developed postcanine teeth--with the exception of width of M3s. In other words, the relationships between teeth and body size of the African colobines are more similar to those of the cercopithecines. This implies, compared to their Asian partners, that African colobines share more similarities with cercopithecines. This may be related to the episodes in which African species underwent a longer period of sharing environmental and climatic patterns with the cercopithecines that moved to Asia about 5 or 8 million years ago. Canines were found to be important in distinguishing colobines from cercopithecines and in separating one subtribe from the other.

Adaptation, Physiological↗
PubMedDate not supplied

Determination of flavonol aglycones in Ginkgo biloba dietary supplement crude materials and finished products by high-performance liquid chromatography: single laboratory validation.

A single laboratory validation (SLV) was completed for a method to determine the flavonol aglycones quercetin, kaempferol, and isorhamnetin in Ginkgo biloba products. The method calculates total glycosides based on these aglycones formed following acid hydrolysis. Nine matrixes were chosen for the study, including crude leaf material, standardized dry powder extract, single and multiple entity finished products, and ethanol and glycerol tinctures. For the 9 matrixes evaluated as part of this SLV, the method appeared to be selective and specific, with no observed interferences. The simplified 60 min oven heating hydrolysis procedure was effective for each of the matrixes studied, with no apparent or consistent differences between 60, 75, and 90 min at 90 degrees C. A Youden ruggedness trial testing 7 factors with the potential to affect quantitative results showed that 2 factors (volume hydrolyzed and test sample extraction/hydrolysis weight) were the most important parameters for control during sample preparation. The method performed well in terms of precision, with 4 matrixes tested in triplicate over a 3-day period showing an overall repeatability (relative standard deviation, RSD) of 2.3%. Analysis of variance testing at alpha = 0.05 showed no significant differences among the within- or between-group sources of variation, although comparisons of within-day (Sw), between-day (Sb), and total (St) precision showed that a majority of the standard deviation came from within-day determinations for all matrixes. Accuracy testing at 2 levels (approximately 30 and 90% of the determined concentrations in standardized dry powder extract) from 2 complex negative control matrixes showed an overall 96% recovery and RSD of 1.0% for the high spike, and 94% recovery and RSD of 2.5% for the low spike. HorRat scores were within the limits for performance acceptability, ranging from 0.4 to 1.3. Based on the performance results presented herein, it is recommended that this method progress to the collaborative laboratory trial.

Calibration↗
PubMed2002

Novel ultrasonic fusion imaging method based on cyclic variation in myocardial backscatter.

Quantitative ultrasonic tissue characterisation of the myocardium based on integrated backscatter (IB) has the potential of becoming an effective method for detecting and evaluating myocardial ischaemia. To facilitate IB-based clinical applications, a new imaging method has been developed that combines the anatomical information of a B-mode image with the contractile performance of a selected myocardial region. To produce such a fusion image, a region of interest (ROI) in a B-mode cardiac image was first selected by the user. Algorithms for detection of the endocardium and epicardium were developed, and the resulting mean distance between the computer-detected curve and the manually traced curve was 0.83mm for the endocardium and 0.58mm for the epicardium. The cyclic variation of IB (CVIB) of each myocardial tissue element within the ROI was then calculated over one cardiac cycle. Finally, a grey-scale B-mode image at the end of diastole was displayed as a still image, and the pixels representing the myocardial tissue in the ROI colour-coded according to the corresponding CVIB over the past heart cycle. Both the B-mode image and the colour-coded region were refreshed (up-dated) at the next end-of-diastole. Preliminary results from normal (CVIB= 10-12dB) and ischaemic (CVIB = 5-7 dB) canine hearts are presented that demonstrate the utility of this new imaging method.

Diagnosis, Computer-Assisted↗
PubMed1991

Genotyping and haplotyping of polymorphisms directly from genomic DNA via coupled amplification and sequencing (CAS).

Coupled amplification and sequencing (CAS) allows a segment of DNA to be sequenced directly from genomic DNA. An initial PCR amplification stage selects and amplifies the target. During a subsequent stage both strands of the target segment are sequenced simultaneously and amplified further. We show that CAS can readily identify variant base pairs. Genotyping of a population for known sequence variation can be achieved simply and directly from genomic DNA of each organism by performing CAS only for the variant bases. The procedure supercedes development and optimization of alternative typing assays based on oligonucleotide hybridization or ligation. In addition, we show that competitive oligonucleotide priming with allelic primers can be readily performed in concert with the second stage of CAS. The combination of techniques allows sequencing of a single chromosome from a heterozygous genomic sample and direct haplotyping of the polymorphism at the priming site with any others encompassed within the amplified segment.

Animals↗
PubMed2005

Effect of expanded graphite lattice in exfoliated graphite nanofibers on hydrogen storage.

A graphite exfoliation technique, using intercalation of a concentrated sulfuric/nitric acid mixture followed by a thermal shock, has successfully exfoliated a herringbone graphite nanofiber (GNF). The exfoliated GNF retains the overall nanosized dimensions of the original GNF, with the exfoliation temperature determining the degree of induced defects, lattice expansion, and resulting microstructure. High-resolution transmission electron microscopy indicated that the fibers treated at an intermediate temperature of 700 degrees C for 2 min had dislocations in the graphitic structure and a 4% increase in graphitic lattice spacing to 3.5 A. The fibers treated at 1000 degrees C for 36 h were expanded along the fiber axis, with regular intervals of graphitic and amorphous regions ranging from 0.5 to >50 nm in width. The surface area of the starting material was increased from 47 m(2)/g to 67 m(2)/g for the 700- degrees C treatment and to 555 m(2)/g for the 1000- degrees C treatment. Hydrogen uptake measurements at 20 bar indicate that the overall hydrogen uptake and operative adsorption temperature are sensitive to the structural variations and graphitic spacing. The increased surface area after the 1000- degrees C treatment led to a 1.2% hydrogen uptake at 77 K and 20 bar, a 3-fold increase in hydrogen physisorption of the starting material. The uptake of the 700- degrees C-treated material had a 0.29% uptake at 300 K and 20 bar; although low, this was a 14-fold uptake over the starting material and higher than other commonly used pretreatment methods that were tested in parallel. These results suggest that selective exfoliation of a nanofiber is a means by which to control the relative binding energy of the hydrogen interaction with the carbon structure and thus vary the operative adsorption temperature.

Journal Article↗
PubMedDate not supplied

Androgens in human evolution. A new explanation of human evolution.

Human evolution consists of chronological changes in gene regulation of a continuous and relatively stable genome, activated by hormones, the production of which is intermittently affected by endogenous and exogenous forces. Periodic variations in the gonadal androgen, testosterone, and the adrenal androgen, dehydroepiandrosterone (DHEA), significantly participated in all hominid transformations. The hominid characteristics of early Australopithecines are primarily a result of increased testosterone. The first significant cold of the early Pleistocene resulted in an increase in DHEA that simultaneously produced Homo and the robust Australopithecines. Subsequent Pleistocene climatic changes and differential reproduction produced changes in DHEA and testosterone ratios that caused extinction of the robust Australopithecines and further changes and continuation of Homo. Changes in testosterone and DHEA produce allometric and behavioral changes that are identifiable and vigorous in modern populations.

Adolescent↗
PubMed2002

Cloning and high expression of hbFGF with a new strategy.

Computer program DNASIS v2.5 was used to help designing the site-directed mutations for optimizing the expression of hbFGF in E. coli. The secondary structure of the translation initiation region (TIR) is a determinant factor for translation initiation rate, meanwhile, codon preference plays an important role, too. According to the two principles, 4 sites in 5' end of hbFGF cDNA were definitely changed, and another 4 sites randomly changed. These mutations will lead to potential variation in the secondary structure of TIR. Then computer program DNASIS v2.5 was utilized to analyse the total 32 TIR sequences resulted from the combination of the 4 randomly mutated sites. Ten sequences with highest free formation energy (delta G0) were chosen for subsequent cloning. By PCR using synthetic primers containing the 8 changed sites described above, ten hbFGF cDNA were amplified and cloned to pET-3c respectively. E. coli strain BL21 (DE3) was transformed and induced to express recombinant hbFGF. Two high-expression clones were obtained by SDS-PAGE and MTT assay, indicating that computer program-aided design for optimizing expression of foreign genes in E. coli is useful.

Cloning, Molecular↗
PubMed1984

Development and evaluation of enteric-coated penicillamine tablets.

Commercially available 250-mg penicillamine tablets were converted into enteric-coated tablets. Based on in vitro dissolution and disintegration tests, tablets coated with five layers of a cellulose acetate phthalate formulation by a modified pan coating technique were judged to be superior to other coated tablets. These tablets resisted disintegration in simulated gastric fluid over a 4-h period and disintegrated in an average of 21 min in simulated intestinal fluid. Enteric-coated penicillamine tablets were tested in vivo in nine weanling pigs divided into three groups: a negative control group, a test group dosed with enteric-coated penicillamine tablets, and a positive control group dosed with uncoated tablets. The incidence of GI tract bleeding, as determined by daily occult blood tests of the stools, was significantly less in the animals receiving the enteric-coated tablets when compared with the positive control group. The enteric-coated dosage form appeared to decrease GI tract irritation caused by penicillamine. Plasma concentration-time curves for penicillamine in the pigs were similar in shape to those reported in humans. Atypical double peaks occur in both species. Relative bioavailability of the enteric-coated tablet was found to be 67% when compared with the uncoated tablet. This apparent reduction is probably due to a large intrasubject variation in areas under the plasma concentration-time curves and not to a dosage form effect.

Animals↗