Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells

The aim of this study was to identify in human cells common targets of histone H3 lysine 9 (H3-Lys9) methylation, a modification that is generally associated with gene silencing. After chromatin immunoprecipitation using an H3-Lys9 methylated antibody, we cloned the recovered DNA and sequenced 47 independent clones. Of these, 38 clones (81%) contained repetitive elements, either short interspersed transposable element (SINE or Alu elements), long terminal repeat (LTR), long interspersed transposable element (LINE), or satellite region (ALR/Alpha) DNA, and three additional clones were near Alu elements. Further characterization of these repetitive elements revealed that 32 clones (68%) were Alu repeats, corresponding to both old Alu (23 clones) and young Alu (9 clones) subfamilies. Association of H3-Lys9 methylation was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. In addition, we randomly selected 5 Alu repeats from the recovered clones and confirmed association with H3-Lys9 by PCR using primer sets flanking the Alu elements. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine rapidly decreased the level of H3-Lys9 methylation in the Alu elements, suggesting that H3-Lys9 methylation may be related to the suppression of Alu elements through DNA methylation. Thus H3-Lys9 methylation is enriched at human repetitive elements, particularly Alu elements, and may play a role in the suppression of recombination by these elements.     

Microscopic study of cortical explants from lamb kidney in culture

Cortical explants from lamb kidney have been maintained in organ culture for up to 12 days. Early in culture, the tissue showed limited necrosis, but most tissue elements, especially those closest to the medium, significantly recovered by day 5. Glomerular peripolar cells were present for at least the first 3 days of culture. Neotubular formation was noted by day 5, often appearing as cyst-like structures. Glomerular podocytes lost their foot processes early in culture but apparently remained viable throughout the total culture period.     

Effect of recovery method on yield of bovine oocytes per ovary and their developmental competence after maturation, fertilization and culture in vitro

An important aim of an oocyte recovery method is to maximize the number of oocytes per ovary which can be employed for in vitro maturation (IVM), in vitro fertilization (IVF) and in vitro culture (IVC). In this study, primary bovine oocytes were collected by 2 methods: aspiration of visible follicles (2 to 6mm in diameter) or surface dissection in which the ovary surface is finely dissected. The oocytes were classified on the basis of cumulus cover and cytoplasmic appearance. The total number of oocytes and the yield of good-quality oocytes recovered per ovary by surface dissection and aspiration were 44.2 and 13.9 and 13.5 and 4.6 (P<0.05), respectively. When a sample group of selected oocytes recovered by each method was measured, no significant difference was found in the mean diameter (144.11m vs 142.54m). A representative sample of good-quality oocytes recovered by each method was put through the IVM/IVF/IVC procedure: no significant difference in cleavage rate, cleavage index or blastocyst yield was found. However, when the blastocyst yield was compared on a per ovary basis, a significant difference was observed in favor of surface dissection (3.30+/-0.46 vs 0.96+/-0.16;P<0.05). When unselected oocytes recovered by surface dissection of the ovaries were put through the standard embryo production system, an average of 15.4 blastocysts per dam was obtained.     

Altered nucleic acid partitioning during phenol extraction or silica adsorption by guanidinium and potassium salts

Nucleic acids were found to partition into the phenol phase during phenol extraction in the presence of guanidinium at certain concentrations under acidic conditions. The guanidinium-concentration-dependent nucleic acid partitioning patterns were analogous to those of the nucleic acid adsorption/partitioning onto silica mediated by guanidinium, which implied that phenol and silica interact with nucleic acids through similar mechanisms. A competition effect was observed in which the nucleic acids that had partitioned into the phenol phase or onto the silica solid phase could be recovered to the aqueous phases by potassium in a molecular weight–salt concentration-dependent manner (the higher molecular weight nucleic acids needed higher concentrations of potassium to be recovered, and vice versa). Methods were developed based on these findings to isolate total RNA from Escherichia coli. By controlling the concentrations of guanidinium and potassium salts used before phenol extraction or silica adsorption, we can selectively recover total RNA but not the high molecular weight genomic DNA in the aqueous phases. Genomic DNA-free total RNA obtained by our methods is suitable for RT-PCR or other purposes. The methods can also be adapted to isolate small RNAs or RNA in certain molecular weight ranges by changing the salt concentrations used.     

On the association of DNA polymerase alpha activity with the nuclear matrix in HeLa cells

The association of DNA polymerase alpha activity with the nuclear matrix has been reinvestigated in HeLa cells. Isolated nuclei were extracted with 2M NaCl and then digested with Dnase I and the final structures were recovered by centrifugation through a sucrose cushion. Typically over 98% of the total DNA synthesized in the matrix fraction on either endogenous matrix-associated DNA or activated calf thymus DNA was due to DNA polymerase alpha as defined by inhibition to n-ethylmaleimide or aphidicolin. DNA polymerase beta activity was absent or recovered in only trace amounts. Matrix-bound DNA polymerase alpha activity demonstrated a remarkable degree of stability: DNA synthesis was essentially linear up to 3 hours at 37 degrees C. Overall, these results substantiate previous findings from regenerating rat liver, unlike other data obtained from tissue culture cells.     

Engineering the Drosophila Genome: Chromosome Rearrangements by Design

We show that site-specific recombination can be used to engineer chromosome rearrangements in Drosophila melanogaster. The FLP site-specific recombinase acts on chromosomal target sites located within specially constructed P elements to provide an easy screen for the recovery of rearrangements with breakpoints that can be chosen in advance. Paracentric and pericentric inversions are easily recovered when two elements lie in the same chromosome in opposite orientation. These inversions are readily reversible. Duplications and deficiencies can be recovered by recombination between two elements that lie in the same orientation on the same chromosome or on homologues. We observe that the frequency of recombination between FRTs at ectopic locations decreases as the distance that separates those FRTs increases. We also describe methods to determine the absolute orientation of these P elements within the chromosome. The ability to produce chromosome rearrangements precisely between preselected sites provides a powerful new tool for investigations into the relationships between chromosome arrangement, structure, and function.     

In vitro embryo production and embryo transfer in domestic and non-domestic cats

Over a 5-year interval, multiple laparoscopic oocyte retrievals were done in fishing cats (Prionailurus viverrinus), caracals (Caracal caracal) and domestic cats after ovarian stimulation with gonadotropins. From 21 retrievals in five fishing cats, 579 preovulatory oocytes (mean = 27.6) were recovered and 348 embryos were produced in vitro (mean = 16.6). A total of 452 preovulatory oocytes (mean = 25.1) were recovered from 18 of 24 retrievals in six caracals and 297 (mean = 16.6) embryos were produced. An additional 16 caracal embryos (19%) were produced after in vitro maturation of 83 oocytes, 59 of which came from six retrievals producing only immature oocytes. The presence of corpora lutea at oocyte retrieval occurred in each species (1) at a similar frequency (33%) and (2) more frequently during January through May (11 of 15 retrievals) than during the latter half of the year (4 of 30 retrievals). Of the 12 embryo transfer procedures done in fishing cats, one pregnancy (8%) was obtained and one live kitten born after the auto-transfer of 10 Day-6 embryos. In caracals, a total of 46 Day-4 or Day-5 embryos were auto-transferred to six recipients, one of which delivered two live kittens. Then, 109 caracal embryos were cryopreserved before thawing and transferring to nine recipients (mean = 12.1) on Days 5 or 6. From three pregnancies established (33%), a total of three kittens were born. Two to six gonadotropin treatments/oocyte retrievals were done in domestic cats during 1999 through 2003; an average of 24.9, 23.5, 22.0, 23.1, 23.5 and 40.9 oocytes (P > 0.05) were recovered at the first through the sixth treatment cycles from 138, 138, 97, 49, 22, and seven retrievals, respectively.     

Trace elements in soils and crops.

To demonstrate the total amounts to be expected in soils, the ranges of contents of some 60 trace elements in ten representative Scottish arable surface soils are compared with ranges in soil-forming rocks and with crustal averages. It is, however, the amounts potentially available to plants rather than the total contents that are biologically significant. In temperate climates, trace element mobilization is greatest when weathering takes place under conditions of impeded pedological drainage, leading to the formation of gleyed soils. Mobilized trace elements occur in arable surface soils largely in adsorbed and chelated forms, which are available to plants to a greater or smaller extent depending on the prevailing soil parameters and on the element in question. Different species take up different amounts of trace elements: the proportions in the various plant parts vary with the element and the stage of growth. Information is required about the mobilization and uptake of many elements about which little is at present known but which may affect the functions of essential elements through inter-element interactions. Systematic soil surveys in which soils are mapped by associations related to parent material, with their series related to genetic soil types, provide a useful countrywide guide to trace element status.     

Effect of corticosteroid treatment on cell recovery by lung lavage in acute radiation-induced lung injury

The purpose of this study was to quantitate cell populations recovered by lung lavage up to 6 weeks following thoracic irradiation (24 Gy) as an index of the acute inflammatory response within lung structures. Additionally, rats were treated five times weekly with intraperitoneal saline (0.3 cc) or methylprednisolone (7.5 mg/kg/week). Lung lavage of irradiated rats recovered increased numbers of total cells compared to controls beginning 3 weeks after irradiation (P less than 0.05). The initial increase in number of cells recovered was attributable to an influx of neutrophils (P less than 0.05), and further increases at 4 and 6 weeks were associated with increased numbers of recovered macrophages (P less than 0.05). Lung lavage of steroid-treated rats at 6 weeks after irradiation recovered increased numbers of all cell populations compared to controls (P less than 0.05); however, numbers of recovered total cells, macrophages, neutrophils, and lymphocytes were all significantly decreased compared to saline-treated rats (P less than 0.05). The number of inflammatory cells recovered by lung lavage during acute radiation-induced lung injury is significantly diminished by corticosteroid treatment. Changes in cells recovered by lung lavage can also be correlated with alteration in body weight and respiration rate subsequent to treatment with thoracic irradiation and/or corticosteroids.     

An unstable family of large DNA elements in the center of the mouse t complex

We have cloned 363 kb (× 10³ bases) from a novel, locally dispersed family of 11 large DNA elements, called T66 elements, within the center of complete mouse t haplotypes. Homologies among individual members of the T66 family are observed along a repeated unit of at least 75 kb in length. Individual T66 homology units are classified into three subfamilies through hybridization studies with a series of diagnostic subfamily-specific probes. The organization and number of elements in wild-type forms of chromosome 17 are very different from those found within t haplotype forms of this chromosome. The number of T66 elements present within individual chromosomes is highly polymorphic among both inbred strains of mice and among independently derived t haplotypes. Wild-type chromosomes have between five and nine T66 elements distributed between two loci that are separated by a genetic distance of at least three map units, whereas t haplotypes have between 9 and 11 T66 elements within a single cluster. Many of the rare recovered products of recombination between a t haplotype and a wild-type form of chromosome 17 have resulted from recombination within or near the T66 regions present on each chromosome. Molecular and genetic data lead to the speculation that portions of individual T66 homology units could be involved in t haplotype effects on sperm differentiation.     

Sieve size effects on root length and biomass measurements of maize (Zea mays) and Grevillea robusta

The purpose of this study was to investigate the effects of different mesh sizes on the recovery of root length and biomass and to determine whether the degree of recovery was influenced by plant species and sample location. Sieves of 2.0, 1.0, 0.5 and 0.25 mm (4.0, 1.0, 0.25 and 0.06 mm2) mesh sizes were used to recover and measure the root length and biomass of Zea mays L. (maize) at 0–15 cm and 30–45 cm depths and of Grevillea robusta A. Cunn. ex R. Br. (grevillea) at the same depths 1.0 m and 4.5 m from a line of grevillea trees. At 0–15 cm, the coarser sieves (sum collected with 2.0 and 1.0 mm sieves) recovered approximately 80% of the total root biomass measured, but only 60% of the root length. The proportion of total maize root length and biomass recovered by the coarser sieves decreased with soil depth. The proportion of total grevillea root length recovered by the coarser sieves was similar at the two soil depths, but increased slightly with distance from the tree line. The ≥ 0.5 mm sieves recovered between 93 and 96% of grevillea and maize root biomass and between 73 and 98% of their root length, depending on the sample location. Roots passing through the 0.5 mm sieve, but recovered by the 0.25 mm sieve were about 20% of total maize root length and grevillea root length at 1.0 m from the tree line but < 5% of the total grevillea root length at 4.5 m from the tree. Roots passing through the 0.5 mm sieve but recovered by the 0.25 mm sieve contributed only slightly to root biomass. Although the ≥ 0.5 mm sieves provided adequate measurements of root biomass, the ≥ 0.25 mm sieves were required for accurate measurement of fine root length. There was no universal correction for root length and biomass underestimation when large sieve sizes were used because the proportions of length and biomass recovered depended on the plant species and on soil depth and distance from the plant. This revised version was published online in August 2006 with corrections to the Cover Date.     

Identification of dorsal-spined larvae from free-ranging wapiti (Cervus elaphus) in southwestern Manitoba, Canada

Dorsal-spined first-stage larvae recovered from feces of free-ranging wapiti (Cervus elaphus) were passaged through snails (Triodopsis multilineata) and two hand-raised white-tailed deer fawns (Odocoileus virginianus). A total of 74 adult Parelaphostrongylus tenuis were recovered from the fawns; no other protostrongylid nematodes were recovered. The study indicates that wapiti may be infected with natural infections of meningeal worm and pass larvae suitable for transmission to gastropod intermediate hosts. Wapiti from areas endemic with P. tenuis should not be translocated to areas currently free of the parasite.     

Estimation of volume of epithelial lining fluid recovered by lavage using urea as marker of dilution

Bronchoalveolar lavage is a powerful technique for sampling the epithelial lining fluid (ELF) of the lower respiratory tract but also results in a significant dilution of that fluid. To quantify the apparent volume of ELF obtained by bronchoalveolar lavage, urea was used as an endogenous marker of ELF dilution. Since urea diffuses readily through the body, plasma and in situ ELF urea concentrations are identical; thus ELF volume can be calculated using simple dilution principles. Using this approach, we determined that with a standard lavage procedure, the volume of ELF recovered from a normal human is 1.0 +/- 0.1 ml/100 ml of recovered lavage fluid. Time course experiments in which the saline used for lavage was permitted to remain in the lower respiratory tract for various "dwell times" suggested that diffusion of urea from sources other than recovered ELF can contribute to the total urea recovered resulting in an overestimate of the volume of ELF recovered. Thus, while reasonably accurate, the volume of ELF determined by urea must be considered an overestimate, or "apparent" volume. The ELF albumin concentration based on the apparent ELF volume was 3.7 +/- 0.3 mg/ml, a value that is in good agreement with direct measurements made by other techniques in experimental animals. The density of all inflammatory and immune effector cells on the epithelial surface of the lower respiratory tract, based on the apparent ELF volume, was 21,000 +/- 3,000 cells/microliter, a value that is twofold greater than that in blood.(ABSTRACT TRUNCATED AT 250 WORDS)     

Pregnancies and live birth from in vitro fertilization of calf oocytes collected by laparoscopic follicular aspiration

Oocytes were recovered by laparoscopic aspiration from 3- to 8-week-old calves treated with follicle-stimulating hormone (FSH) followed by human chorionic gonadotropin (hCG) to induce follicular growth and oocyte maturation in vivo. Most of the recovered oocytes either had resumed meiotic maturation at the time of aspiration or were competent to undergo maturation during subsequent culture in vitro. Oocytes matured in vivo following FSH and hCG treatment underwent in vitro fertilization (70%) at rates not significantly different from those of control oocytes recovered from adult cow ovaries at abattoirs and matured in vitro (75%). Calf oocytes that were immature at aspiration exhibited lower fertilization rates after in vitro maturation (36%) but their rate of development to morulae and blastocysts did not differ from that of mature oocytes at aspiration. A total of 91% of the zygotes produced from calf oocytes developed to morula and 27% to blastocyst stages during 6 days of culture. The proportion developing to morulae was significantly higher (P<0.05) than that observed for zygotes resulting from in vitro maturation and fertilization of oocytes recovered from cow ovaries obtained at an abattoir and processed concomitantly (59% to morulae and 18% to blastocysts). Morulae or blastocysts developed from oocytes from 5 to 6-week-old calves, when transferred to synchronized recipient heifers, resulted in 2 confirmed pregnancies, one of which produced a single full-term live calf. The ability to produce embryos from oocytes recovered from newborn or prepubertal calves offers the potential for markedly reducing the generation interval in cattle, thereby substantially accelerating the rate of genetic gain that can be achieved through embryo transfer.     

暖温带两种针叶林生态系统中茎流和穿透雨的养分特征研究

通过对暖温带地区两种典型人工针叶林生态系统内树干茎流和穿透雨的收集,对其中Ｎ、Ｐ、Ｋ、Ｃａ、Ｍｇ、Ｓ和Ａｌ等７种元素进行了测定。研究发现这些养分元素在树干茎流和穿透雨中的含量在年内有明显的时间动态变化,这些变化主要受元素在水分中的含量和它们在植物生命活动中的活跃程度等影响,甚至在不同的针叶林生态系统之间都有一定的差异,其中表现为明显的是Ｎ、Ｋ和Ｓ。