Genome-wide gene expression responses to experimental manipulation of Saccharomyces cerevisiae repressor activator protein 1 (Rap1) expression level.

Precise regulation of transcription in gene expression is critical for all aspects of normal organism form, fitness, and function and even minor alterations in the level, location, and timing of gene expression can result in phenotypic variation within and between species including evolutionary innovations and human disease states. Eukaryotic transcription is regulated by a complex interplay of multiple factors working both at a physical and molecular levels influencing this process. In Saccharomyces cerevisiae, the TF with the greatest number of putative regulatory targets is the essential gene Repressor Activator Protein 1 (RAP1). While much is known about the roles of Rap1 in gene regulation and numerous cellular processes, the response of Rap1 target genes to systematic titration of RAP1 expression level remains unknown. To fill this knowledge gap, we used a strain with a tetracycline-titratable promoter replacing wild-type regulatory sequences of RAP1 to systematically reduce the expression level of RAP1 and followed this with RNA sequencing (RNA-seq) to measure genome-wide gene expression responses. Previous research indicated that Rap1 plays a significant regulatory role in particular groups of genes including telomere-proximal genes, homothallic mating (HM) loci, glycolytic genes, DNA repair genes, and ribosomal protein genes; therefore, we focused our analyses on these groups and downstream targets to determine how they respond to reductions in RAP1 expression level. Overall, despite being known as both an activator and as a repressor of its target genes, we found that Rap1 acts as an activator for more target genes than as a repressor. Additionally, we found that Rap1 functions as an activator of ribosomal protein genes and a repressor for HM loci genes consistent with predictions from the literature. Unexpectedly, we found that Rap1 functions as a repressor of glycolytic enzyme genes contrary to prior reports of it having the opposite effect. We also compared the expression of RAP1 to five different genes related to DNA repair pathway and found that decreasing RAP1 downregulated four of those five genes. Finally, we found no effect of RAP1 depletion on telomere-proximal genes despite its functioning to silence telomeric repeat-containing RNAs. Together our results enrich our understanding of this important transcriptional regulator.

Engineered Unique Elastic Modes at a BaTiO_{3}/(2×1)-Ge(001) Interface.

The strong interaction at an interface between a substrate and thin film leads to epitaxy and provides a means of inducing structural changes in the epitaxial film. These induced material phases often exhibit technologically relevant electronic, magnetic, and functional properties. The 2×1 surface of a Ge(001) substrate applies a unique type of epitaxial constraint on thin films of the perovskite oxide BaTiO_{3} where a change in bonding and symmetry at the interface leads to a non-bulk-like crystal structure of the BaTiO_{3}. While the complex crystal structure is predicted using first-principles theory, it is further shown that the details of the structure are a consequence of hidden phases found in the bulk elastic response of the BaTiO_{3} induced by the symmetry of forces exerted by the germanium substrate.

Application of X-ray microcomputed tomography in the characterization of irradiated nuclear fuel and material specimens.

X-ray microcomputed tomography (µCT) was applied in characterizing the internal structures of a number of irradiated materials, including carbon-carbon fibre composites, nuclear-grade graphite and tristructural isotropic-coated fuel particles. Local cracks in carbon-carbon fibre composites associated with their synthesis process were observed with µCT without any destructive sample preparation. Pore analysis of graphite samples was performed quantitatively, and qualitative analysis of pore distribution was accomplished. It was also shown that high-resolution µCT can be used to probe internal layer defects of tristructural isotropic-coated fuel particles to elucidate the resulting high release of radioisotopes. Layer defects of sizes ranging from 1 to 5 µm and up could be isolated by tomography. As an added advantage, µCT could also be used to identify regions with high densities of radioisotopes to determine the proper plane and orientation of particle mounting for further analytical characterization, such as materialographic sectioning followed by optical and electron microscopy. In fully ceramic matrix fuel forms, despite the highly absorbing matrix, characterization of tristructural isotropic-coated particles embedded in a silicon carbide matrix was accomplished using µCT and related advanced image analysis techniques.

X-ray microdiffraction analysis of radiation-induced defects in single grains of polycrystalline Fe.

Single-crystal diffuse X-ray scattering was used to characterize radiation-induced defects in individual grains of a polycrystalline proton-irradiated Fe foil. The grains were probed with an intense 1 microm X-ray beam to demonstrate that both polycrystalline and micrometer-scale samples can be studied with single-crystal-like signal-to-noise. Scattering was measured with an X-ray-sensitive area detector, which measures intensity over a surface in reciprocal space. By scanning the X-ray energy, the intensity was measured over reciprocal-space volumes. Since the sample is not rotated, the real-space scattering volume does not change. Methods to minimize experimental artifacts arising from the use of an area detector are described.

Prevalence of bovine trypanosomosis in Central Mozambique from 2002 to 2005.

The study is the result of analyzing 16895 blood smears of cattle collected at 180 sites in the provinces of Manica, Sofala, Zambézia and Tete in Mozambique. Of the blood smears 73.9% were from Manica, 11.8% from Tete, 8.5% from Sofala and 5.8% from Zambézia; 75.6% of these were collected from smallholder cattle. Infections with trypanosomes were highest in smallholder cattle from Sofala Province with 36.8% of the 872 blood smears examined positive for trypanosomes, and lowest in cattle of commercial farmers in Manica Province with only 6.2% of 2252 blood smears being positive. Trypanosoma congolense was the predominant species, followed by Trypanosoma vivax and Trypanosoma brucei sensu lato. Trypanosoma brucei, which also infects humans, was more frequent in the districts of Buzi, Mutarara and Morrumbala with 15.1%, 10.5% and 9.8% of all examined cattle in 2005 being infected with it, respectively. The results show a significant increase in the infection rate with trypanosomes compared with results obtained in previous years by the Regional Veterinary Laboratory in Manica Province and by the Regional Tsetse and Trypanosomiasis Control Programme in Zambézia, Tete and Sofala provinces.

The arachidonic acid cascade, eicosanoids, and signal transduction.

Eicosanoid biosynthesis in animal cells either results from agonist-stimulated phospholipase activation (endogenous pathway) or from lipoprotein receptor-mediated uptake and lysosomal lipid hydrolase-dependent release of AA (exogenous pathway) (see Fig. 1 for schematic representation). LDL stimulates eicosanoid formation through delivery of substrate AA to enzymes of oxidative AA metabolism. The classical LDL receptor is a control point of the effects of LDL AA on eicosanoid formation in different tissues: LDL AA metabolism occurs in several cell types of mesenchymal and epithelial origin and generates the formation of distinct eicosanoid patterns in each case. The LDL AA pathway does appear to couple directly to the PGH synthase reaction, whereas it does not couple directly to the 5-lipoxygenase reaction. We expect that a more complete characterization of the LDL unsaturated fatty acid pathway in different tissue will yield additional information on the biochemistry of lipoproteins, AA, and eicosanoids.

Congenital paralytic vertical talus. An anatomical study.

Dissections of the feet of a three-month-old infant with paralytic congenital vertical talus secondary to lumbar myelomeningocele were compared with a dissection of a normal foot. The major differences appeared to be absence of the plantar intrinsic muscles and dorsal dislocation of the talonavicular joint. It is postulated that the pathological process begins as a failure of the intrinsic muscles to oppose the unbalanced, active dorsiflexion forces of the anterior crural muscles. This imbalance then allows disruption of the talonavicular joint, mechanically the least stable joint in the mid-part of the foot. All dorsiflexion forces acting on the ankle then become ineffective and plantar flexion forces serve only to pull the calcaneus and talus into equinus, causing a "vertical" talus. Treatment must be directed at reducing the talonavicular dislocation, correcting the equinus deformity of the hind part of the foot, and substituting for the undeveloped plantar intrinsic muscles.

Evaluation of a computerised image analyser for studying alterations in radiographic bone density in the rat.

A computerised image analyser has been used experimentally to determine its possible usefulness in quantifying bone density. Rats were prepared for this purpose and ash weight/volume readings were obtained on femora which had been radiographed and studied to estimate radiographic density by means of the image analyser. The findings indicated that rats can be prepared by administering oestradiol or by allowing an additional week's growth, both of which give a statistically significant increase of bone density. The computerised image analyser was able to detect these differences but the correlations, although real and linear, between ash weight/volume and radiographic density were not large. Further refinements in techniques will be needed before the system is applied clinically.

Seasonal incidence of helminths in sheep and goats in south Mozambique.

The seasonal fluctuations in faecal worm egg counts were studied at monthly intervals for over a year in 20 male sheep and goats on extensive grazing tracts at a farm near Maputo, Mozambique. Larval differentiation from faecal cultures showed that Haemonchus contortus and Oesophagostomum columbianum were the most prevalent worm species. Trichostrongylus colubriformis, Cooperia spp., Strongyloides papillosus, Moniezia spp., Paramphistomum spp. and Trichuris spp. also occurred. After the onset of heavy rains in October 1978, the mean total egg counts increased due to a higher egg-output of Haemonchus contortus, reaching peak values in January 1979 in sheep and in February 1979 in goats. A second smaller peak in the mean total egg counts occurred in both groups in May 1979. With the beginning of the drier season the mean total egg counts in the goats fell to a low level, those of the sheep had a third rise in July 1979 due in that case to Oesophagostomum columbianum. The mean total strongyloids egg counts were generally much higher in sheep than in goats. Only at the beginning of February 1979, did the goats have a mean total egg count nearly as high as that of the sheep. Paramphistomum spp. are reported for the first time from sheep and goats in Mozambique.

The effect of double infections with trypanosomes and gastrointestinal nematodes on the productivity of sheep and goats in south Mozambique.

The effect of simultaneous infections with trypanosomes (Trypanosoma vivax and Trypanosoma congolense) and gastrointestinal nematodes on the productivity of sheep and goats was studied in 20 animals (6 male goats and 14 male sheep) at a farm near Maputo. The animals were divided into 4 groups which received either treatment against gastrointestinal nematodes, or against trypanosomes, or treatment against both, or no treatment at all. In two-weekly and later in weekly intervals body weight, packed cell volume, body temperature, worm egg burdens and occurrence of trypanosomes in the peripheral blood were recorded. Body temperature and packed cell volume did not show the expected close relation to an infection with either trypanosomes or gastrointestinal nematodes, but the differences in the increase of body weight among the 4 groups were very considerable. Animals receiving both treatments gained an average of 13.5 kg in body weight in 40 weeks compared with 5.1 kg (surviving animals with treatment against worm parasites), 6.5 kg (surviving animals with treatment against trypanosomes) and 3.4 kg (surviving animals without any treatment). Of the last 3 groups 1 sheep (21 kg), 2 sheep (50 kg) and 1 sheep (21 kg), respectively, died. One goat, treated against gastrointestinal nematodes, but suffering from an infection with Trypanosoma vivax and Trypanosoma congolense was killed at the end of the experiment. A striking finding during the post-mortem examination was the complete hyperplasis of the red-marrow of the right and left femur.

Predictors of nonattendance at the first newborn health supervision visit.

Failure to attend the first newborn health supervision visit is an important problem for the Continuity Care Clinic of Children's Hospital Medical Center of Akron, Ohio. The goal of this study was to use objective data from the neonatal record to identify newborns at high risk of failure to attend. Clinical and social risk factors of the mother and newborn were abstracted from the neonatal progress notes of 319 infants. The relative risk (RR) of nonattendance was calculated for each factor, and rules for predicting failure to attend were evaluated. The best predictors were multiparous mother (RR = 2.4, P = .01), no telephone in home (RR = 2.6, P = .002), and unmarried teenage mother (RR = 5.8, P = .05). Newborns who had a medical problem and had a adult mother were more likely to attend (RR = 0.4, P = .02). These risk factors were easily identifiable from the medical record at birth. Because interventions may be labor-intensive, it is important to target the families at the highest risk.

Phonon localization drives polar nanoregions in a relaxor ferroelectric.

Relaxor ferroelectrics exemplify a class of functional materials where interplay between disorder and phase instability results in inhomogeneous nanoregions. Although known for about 30 years, there is no definitive explanation for polar nanoregions (PNRs). Here we show that ferroelectric phonon localization drives PNRs in relaxor ferroelectric PMN-30%PT using neutron scattering. At the frequency of a preexisting resonance mode, nanoregions of standing ferroelectric phonons develop with a coherence length equal to one wavelength and the PNR size. Anderson localization of ferroelectric phonons by resonance modes explains our observations and, with nonlinear slowing, the PNRs and relaxor properties. Phonon localization at additional resonances near the zone edges explains competing antiferroelectric distortions known to occur at the zone edges. Our results indicate the size and shape of PNRs that are not dictated by complex structural details, as commonly assumed, but by phonon resonance wave vectors. This discovery could guide the design of next generation relaxor ferroelectrics.

Hip fracture, skeletal fragility, osteoporosis and hormonal deprivation in elderly women.

Fractures of the hip have been shown to have a significant personal and societal impact in Western countries; this impact is largely borne by elderly women, and represents a substantial health care commitment in modern society. For many people a fracture of the proximal end of the femur represents a preterminal event of considerable cost, both in economic loss and psychosocial well-being. These fractures are generally recognized as a clinical complication of osteoporosis, and are one index of general skeletal fragility which is also manifested in fractures of the vertebrate and of the distal radius (Colles fracture). There is increasing evidence that hormonal deprivation in elderly women is directly related to loss of skeletal integrity and consequent fragility. There is also increasing evidence that hormonal substitution is effective in preventing this structural loss and fragility. Unfortunately, a therapeutic dilemma has arisen in that the preparation that seems to give optimal protection, conjugated estrogens, has also been reported to cause an increased incidence of endometrial carcinoma. The search for a preparation or dosage regimen of estrogens which simultaneously prevents skeletal atrophy and fragility and avoids the increased risk of malignancy must be a long-term goal.

Congenital dislocation of the hip.

Congenital dislocation or subluxation of the hip (congenital acetabular dysplasia) is a complete or partial displacement of the femoral head out of the acetabulum. The physical signs essential for diagnosis are age related. In newborns the tests for instability are the most sensitive. After the neonatal period, and until the age of walking, tightness of the adductor muscles is the most reliable sign. Early diagnosis is vital for successful treatment of this partially genetically determined condition. Various therapeutic measures, ranging from abduction splinting to open reduction and osteotomy, may be required. Following diagnosis in the first month of life, the average treatment time in one recent series was only 2.3 months from initiation of therapy to attainment of a normal hip. When the diagnosis was not made until 3 to 6 months of age, ten months of treatment was required to achieve the same outcome. When the diagnosis is not made, or the treatment is not begun until after the age of 6, a normal hip will probably not develop in any patient.

Candida pyarthrosis of the hip and renal homotransplant. Report of a case treated by femoral head and neck resection and 5-fluorocytosine.

A 54-year-old female with chronic renal failure who had undergone renal homotransplantation and who was being maintained for 3 months on immunosuppressive therapy, developed Candida pyarthrosis of the hip. The patient posed a management problem because of the nephrotoxicity of the antibiotics required to control Candida. The literature was of little help in resolving the treatment dilemma because only 4 other cases of Candida pyarthrosis in adults, and only one other on immunosuppressive therapy, have been reported. Surgical excision of the head and neck of the femur was elected because the combined use of Amphotericin B and 5-fluorocytosine posed an unacceptable risk of renal damage while the use of 5-fluorocytosine alone might allow development of step-wise resistance to the drug. Femoral head and neck resection and a 7-month course of 5-fluorocytosine brought the infection under control and allowed normal would healing. With increasing number of compromised susceptible patients, the frequency of serious infections caused by ordinarily saphrophytic organisms is likely to increase. There is a need for more case reports on management, including the consequences of surgical excision of Candida infected tissues.