DNA sequence variation in a 3.7-kb noncoding sequence 5' of the CYP1A2 gene: implications for human population history and natural selection

CYP1A2 is a cytochrome P450 gene that is involved in human physiological responses to a variety of drugs and toxins. To investigate the role of population history and natural selection in shaping genetic diversity in CYP1A2, we sequenced a 3.7-kb region 5' from CYP1A2 in a diverse collection of 113 individuals from three major continental regions of the Old World (Africa, Asia, and Europe). We also examined sequences in the 90-member National Institutes of Health DNA Polymorphism Discovery Resource (PDR). Eighteen single-nucleotide polymorphisms (SNPs) were found. Most of the high-frequency SNPs found in the Old World sample were also found in the PDR sample. However, six SNPs were detected in the Old World sample but not in the PDR sample, and two SNPs found in the PDR sample were not found in the Old World sample. Most pairs of SNPs were in complete linkage disequilibrium with one another, and there was no indication of a decline of disequilibrium with physical distance in this region. The average +/- SD nucleotide diversity in the Old World sample was 0.00043+/-0.00026. The African population had the highest level of nucleotide diversity and the lowest level of linkage disequilibrium. Two distinct haplotype clusters with broadly overlapping geographical distributions were present. Of the 17 haplotypes found in the Old World sample, 12 were found in the African sample, 8 were found in Indians, 5 were found in non-Indian Asians, and 5 were found in Europeans. Haplotypes found outside Africa were mostly a subset of those found within Africa. These patterns are all consistent with an African origin of modern humans. Seven SNPs were singletons, and the site-frequency spectrum showed a significant departure from neutral expectations, suggesting population expansion and/or natural selection. Comparison with outgroup species showed that four derived SNPs have achieved high (>0.90) frequencies in human populations, a trend consistent with the action of positive natural selection. These patterns have a number of implications for disease-association studies in CYP1A2 and other genes.     

Influence of anthropogenic pollution on ostracod assemblages of Amurskii Bay,Sea of Japan

The species composition and distribution of ostracods were investigated at two sites with different pollution levels on the eastern coast of Amurskii Bay within the limits of Vladivostok City. A total of 41 species were found. In all, thirty-eight species (28 of them alive) were found at the first site between Krasnyi and Groznyi capes. Another twenty-seven species were found at a depth of 1.5–3 m in the phytal zone with a diversity of microbiotopes. As the bottom became increasingly silty and the depth increased, the number of species decreased. A total of 25 species (only 15 of them alive) were found at the mouth of the Vtoraya Rechka River, which is heavily polluted by municipal and industrial sewage discharge. No valves of ostracods were found in surface sediments on silts at a depth down to 5.5m. At 4 m, only 2 species were found alive on stones overgrown with Saccharina japonica. At 500 m from a sewage discharge site, few ostracod valves were found that seemed to have died recently. At a distance of over 1 km, an ostracod assemblage typical of the silty substrates of Amurskii Bay was found below a 7 m depth (21 species, 12 of them alive).     

Developmental changes of free amino acids in bovine fetal fluids with gestational age and the interrelationships between the amino acid concentrations in the fluid compartments.

Thirty ninhydrin-positive compounds were determined in the sera, amniotic fluid, stomach content and allantoic fluid from 29 bovine fetuses of various gestational ages. Fetal serum was found to contain about 3-fold higher concentrations of free amino acids (FAA) than maternal serum, and allantoic fluid contained about 3-fold higher concentration of FAA than fetal serum. Decreasing concentrations of FAA were found in serum as a function of the crown-rump length for the amino acids taurine, aspartic acid, threonine, serine, ornithine and lysine. Decreasing concentrations of FAA in allantoic fluid were found for threonine, alanine and ornithine, whereas increasing concentrations were found for phosphoserine and methionine as a function of the crown-rump length. Correlations were found between the concentrations of most amino acids in amniotic fluid and stomach content, but fewer correlations were found between the other fluid compartments. The transport of amino acids between compartments is discussed.     

Intranuclear inclusions containing melanosomes observed after PUVA therapy: a study of five psoriatic patients

Skin biopsies were obtained before and after PUVA therapy from five psoriatic patients and epidermal melanocytes surveyed for the presence of intranuclear melanosome-like bodies and nuclear bodies. Intranuclear melanosome-like bodies were observed after PUVA therapy whereas none were found before therapy. Nuclear bodies were found to increase in frequency after PUVA therapy. Remnants of a nuclear envelope membrane were not found around the intranuclear melanosome-like bodies. Nor were remnants of a nuclear envelope membrane found in or around the nuclear bodies. The results are discussed in view of the possible sites of origin of intranuclear melanosome-like bodies and nuclear bodies.     

Mycotoxins in maize products of the 1994/95 marketing season

The levels of mycotoxins found were generally lower the more refined the maize products were. The highest levels of deoxynivalenol, nivalenol and fumonisins were found in maize bran and maize screenings. Ochratoxin A was found in a defatted germ meal sample at 50 μg/kg. Zearalenone was found randomly in samples at low levels (50 – 100 μg/kg). All other mycotoxins tested for, except in maize bran and maize screenings, were absent above the detection limits     

Isolation and characterization of a reservosome fraction from Trypanosoma cruzi

Resistance to different antibiotics was found in 26 of the 30 strains analyzed, more than 70% of the strains analyzed were resistant to carbenicillin and ampicillin and a significant correlation was found between the resistance to both antibiotics. Plasmids were found in 80% of the strains analyzed, and 11 different plasmid profiles were observed. The most common profile obtained had only a 21.2-kbp plasmid, a significant correlation was found between the presence of this plasmid and resistance to carbenicillin, although some exceptions could be detected. Plasmids were cured from a cephalothin resistant strain and reintroduced into the plasmid-free cell and into Escherichia coli DH5alpha, both strains gained resistance to this antibiotic.     

D-amino acid levels in human physiological fluids

Plasma, urine, cerebrospinal fluid (CSF), and amniotic fluid were examined to determine whether free D-amino acids were present and if so at what levels. It was found that D-amino acids exist in all physiological fluids tested, but that their level varied, considerably. The lowest levels of D-amino acids were usually found in amniotic fluid or CSF (almost always <1% of the corresponding L-amino acid). The highest levels were found in urine (usually tenth percent to low percent levels). Pipecolic acid seemed to be different from the other amino acids tested in that it was excreted primarily as the D-enantiomer (often >90%). Correspondingly high levels of D-pipecolic acid were not found in plasma. Some of the trends found in this work seemed to be analogous to those found in a recent rodent study. © 1993 Wiley-Liss, Inc.     

Neuropeptide Y in the human male genital tract

Neuropeptide Y (NPY) was found in high concentrations in the male genital tract. NPY levels were highest in the seminal vesicles, prostate, corpus cavernosum and vas deferens, where large numbers of immunoreactive nerve fibres were detected. Considerable quantities were also found in the epididymis and spongiosum. Lower concentrations were found in the glans penis, testis and foreskin. The presence of a large number of nerves containing NPY suggest that this active neuropeptide may play a role in control of genital function.     

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.

A 0.7-ns molecular dynamics simulation of the DNA-EcoRI complex in a 7.0-A solvent shell indicated a stable behavior of the system. No significant evaporation or smearing of the solvent's outer boundary occurred. The structure and the intermolecular interactions were found to be well maintained during the simulation. The interaction pattern in the simulation was found to be very similar to that in the crystal structure. Most of the specific interactions between the DNA and the protein were found to be enhanced in the simulation compared to that in the crystal structure as a result of improved interaction geometry. The nonspecific interactions were found to be stronger than the specific ones. The specific interactions between the N7 atoms of Gua(4) or Ade(5) or Ade(6) and the protein were found to be present over almost the entire time of the simulation, whereas hydrogen bonds involving the amino groups of the Ade(5) and Ade(6) with the protein were found to be relatively weaker, with lower probability and shorter lifetime. The time evolution of the root mean square deviations of the DNA and the protein were highly correlated even at the later part of the simulation, showing the tight binding between them. Several long-lived water bridges were found between the DNA backbone atoms and the protein and also between the two protein monomers, which increased the overall stability of the complex. The two protein monomers were found to interact strongly with each other. The energy of the DNA kink deformation was estimated as approximately 31 kcal/mol.     

A SCUBA-diving investigation of Baltic herring (Clupea harengus membras L.) spawning grounds in the Askö-Landsort area, northern Baltic proper

In a spawning area survey in the Askö area, northern Baltic proper, undertaken in the beginning of summer 1978, 100 randomly established and sampled transects were studied by diving. Herring spawn was found at 45 of the transects. The eggs were usually found on Pilayella littoralis , a filamentous brown algae, at the more exposed transects. Eggs were only found down to a depth of 11 m. In a neighbouring oil spill area spawn were found at only four out of 20 transects. Of eggs taken to the laboratory for hatching, 54% of those from the unaffected area hatched but only 25% of those from the oil spill area.     

Cryptosporidium genotypes in wildlife from a new york watershed

To identify the animal sources for Cryptosporidium contamination, we genotyped Cryptosporidium spp. in wildlife from the watershed of the New York City drinking water supply, using a small-subunit rRNA gene-based PCR-restriction fragment length polymorphism analysis and DNA sequencing. A total of 541 specimens from 38 species of wildlife were analyzed. One hundred and eleven (20.5%) of the wildlife specimens were PCR positive. Altogether, 21 Cryptosporidium genotypes were found in wildlife samples, 11 of which were previously found in storm runoff in the watershed, and six of these 11 were from storm water genotypes of unknown animal origin. Four new genotypes were found, and the animal hosts for four storm water genotypes were expanded. With the exception of the cervine genotype, most genotypes were found in a limited number of animal species and have no major public health significance.     

Extraintestinal sporozoites of chicken Eimeria in chickens and turkeys

Oocysts were found in the feces of chickens (recipients) dosed orally with whole blood, liver, lung, or heart homogenates from chickens and turkeys (donors) inoculated 3 and 4 days previously with a mixture of 3.5 X 10(6) oocysts of chicken Eimeria. No oocysts were found in the feces of recipients given spleen homogenates from these same chickens and turkeys and none were found in the feces of recipients given similar material from uninoculated donors. Intracellular sporazoites were found in the peripheral blood of a turkey inoculated with chicken Eimeria. The results indicate that a small number of sporozoites are capable of invading and surviving for at least 4 days in the peripheral blood of chickens and turkeys.     

Rapid purification of the 30 kDa calcimedin using DNase I affinity chromatography

The 30 kDa calcimedin was found to bind directly to phenyl-Sepharose in a calcium dependent manner similar to calmodulin. The 30 kDa calcimedin was also found to bind to and inhibit DNase I. This calcium-dependent binding was exploited to develop a two-step purification scheme for this calcimedin. In addition, affinity-purified antibodies to the 30 kDa calcimedin were used to examine its tissue distribution. The highest levels were found in lung, trachea and diaphragm while the lowest levels of the 30 kDa calcimedin were found in brain and skeletal muscle.     

Multiple molecular forms of murine thymocyte-stimulating factor

Murine thymocyte stimulating factor (TSF) was found to sediment in sucrose density gradients on a broad band with peaks at about 2.60 S and 2.0 S. Two main peaks of TSF activity (with buoyant densities of 1.34 and 1.28 g/ml) were found in CsCl density gradients. Gel chromatography on Sephadex G-100 columns of the material sedimented in sucrose or CsCl density gradients originated multiple peaks of TSF activity with various molecular weights. Heterogeneity of molecular forms of TSF was also found upon dilution of the factor. The lowest molecular weights found were 4000 and 4700 daltons. When Sephadex fractions containing the low molecular weight material were pooled and rerun on Sephadex columns, molecular species with a wide range of molecular weights were found. Temperature also affects the appearance of the low molecular weight forms of TSF. Most of the experiments presented in this work were carried out with Sephadex-purified TSF. Multiple molecular forms, however, and, in particular, the forms with molecular weights of 4000 and 4700 daltons were found also with TSF-Fraction IIIa, a highly purified preparation of this factor.     

Mandibular gland chemistry of four Caribbean species of Camponotus (Hymenoptera: Formicidae)

The volatile components of whole-body extracts of males, females and workers were analyzed in four species of Neotropical ants in the formicine genus, Camponotus. The species, C. kaura, C. sexguttatus, C. ramulorum and C. planatus, represent three different subgenera. Volatile mandibular gland components were found only in male extracts in three of the species. In C. ramulorum, volatile components were found in male and female reproductives and workers. 3,4-Dihydro-3,5-dihydroxy-6-methylpyran-4-one and octanic acid were found in different sets of three of the species. Methyl 6-methyl salicylate was found in two species and the isocoumarin, mellein, was found in a third species. The significance of the mandibular gland secretion for formicid systematics is discussed.     

Caryospora uptoni and Frenkelia sp.-like coccidial infections in red-tailed hawks (Buteo borealis)

The feces from 16 red-tailed hawks (Buteo borealis) were examined by fecal flotation for the presence of coccidial oocysts or sporocysts. Oocysts of Caryospora uptoni were found in five (31%), sporocysts of a Frenkelia sp.-like coccidium were found in eight (50%), and mixed infections with both species of coccidia were found in three (19%) red-tailed hawks. Neither oocysts nor sporocysts were found in six (38%) red-tailed hawks. Sexual stages of C. uptoni were found in the duodenum and jejunum of a naturally infected red-tailed hawk. Sexual stages were located in enterocytes on the distal three-fourths of the villi. This study shows that over 60% of red-tailed hawks may be passing coccidial oocysts/sporocysts in their feces and provides morphological information for diagnosing C. uptoni infections in histological sections.     

Longitudinal study on methicillin-resistant Staphylococcus pseudintermedius in households

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an emerging pathogen in dogs and has been found in Europe, Asia and North America. To date most studies are one-point prevalence studies and therefore little is known about the dynamics of MRSP in dogs and their surrounding. In this longitudinal study MRSP colonization in dogs and the transmission of MRSP to humans, contact animals and the environment was investigated. Sixteen dogs with a recent clinical MRSP infection were included. The index dogs, contact animals, owners and environments were sampled once a month for six months. Samples taken from the nose, perineum and infection site (if present) of the index cases and contact animals, and the nares of the owners were cultured using pre-enrichment. Index cases were found positive for prolonged periods of time, in two cases during all six samplings. In five of the 12 households that were sampled during six months, the index case was intermittently found MRSP-positive. Contact animals and the environment were also found MRSP-positive, most often in combination with a MRSP-positive index dog. In four households positive environmental samples were found while no animals or humans were MRSP-positive, indicating survival of MRSP in the environment for prolonged periods of time. Genotyping revealed that generally similar or indistinguishable MRSP isolates were found in patients, contact animals and environmental samples within the same household. Within two households, however, genetically distinct MRSP isolates were found. These results show that veterinarians should stay alert with (former) MRSP patients, even after repeated MRSP-negative cultures or after the disappearance of the clinical infection. There is a considerable risk of transmission of MRSP to animals in close contact with MRSP patients. Humans were rarely MRSP-positive and never tested MRSP-positive more than once suggesting occasional contamination or rapid elimination of colonization of the owners.     

Studies on bacteriophage distribution: virulent and temperate bacteriophage content of mammalian feces.

Freshly voided samples of the feces of cows, pigs, and humans were analyzed for the enumeration of cell-free plaque-forming units (PFU) of coliphages and Salmonella phages. Coliphage PFU counts per gram (wet weight) of feces were found to range from less than 10(1) to greater than 10(7). Salmonella phages were found in three out of five porcine samples, but none were found in the four bovine samples analyzed. Virulent coliphages related to the phiX174/S13 serological group showed some "habitat preference" in that the S13 type of phages was found only in pig feces, whereas the phiX174 type of phages was found only in cow dung. Temperate coliphages were detectable in a majority of samples of both human and porcine origin but were infrequently found in bovine samples. About 80% of the temperate coliphages of fecal origin have been found to be serologically related to phage HK022 (Dhillon and Dhillon, 1973), and all are efficiently inducible by ultraviolet light irradiation. However, considerable diversity with the group was found when the prophage immunity pattern of 10 randomly selected isolates was examined.     

Effect of a honey and arginine-glutamine-hydroxymethylbutyrate mixture on the healing of colon anastomosis in rats immunosuppressed with tacrolimus

ABSTRACT

We compared the effect of honey and a mixture of arginine-glutamine-hydroxymethylbutyrate (AGHMB) on healing of a descending colon anastomosis in rats that were immunosuppressed with tacrolimus (Tac). Sprague-Dawley rats were divided into four groups: untreated control, Tac, Tac + honey and Tac + AGHMB. Colon resection and anastomosis were performed on day 14 and re-laparotomy was performed on the day 21 of the study. Anastomotic bursting pressure, macroscopic adhesion score, weekly body weight changes, histopathological features and immunohistochemical staining of TGF-β1 were determined for all groups. We found no significant difference in anastomotic bursting pressure among the experimental groups. We found significant weekly increases in body weight for the Tac + honey group. We found no significant difference in the weekly body weight measurements for the Tac + AGHMB group. We found significant increases in TGF-β1 expression in the Tac + honey group compared to the control and Tac groups. No significant differences in inflammatory cell infiltration, fibroblast proliferation or collagen deposition were found between the Tac + honey and Tac + AGHMB groups; however, a significant difference in neovascularization between these groups was found. Neovascularization in the Tac + honey group was significantly greater than for the Tac + AGHMB group. We found that both honey and the AGHMB mixture were beneficial for anastomotic wound healing in rats that were immunosuppressed using Tac.