How Much Is Enough? an Analysis of the 5' Nontranslated Region of the Deformed Wing Virus in Honeybees

Honeybees are an essential component of today¿s agricultural system because of their role as pollinators. However, viruses, including a member of the Picornavirales order known commonly as Deformed Wing Virus (DWV), are compromising the health of honeybee colonies. Many picornaviruses, such as poliovirus, have been studied in depth because of their relation to human disease, but also because of their use of an Internal Ribosome Entry Site (IRES) to initiate translation. The primary goal of this thesis was to determine if the 5¿ Non-Translated Region (NTR) of Deformed Wing Virus (DWV) functions as an IRES. A secondary goal was to determine if there are specific parts of that 5¿ NTR that are important to IRES function. Six plasmids were constructed by inserting three different sections of the 5¿ NTR of DWV, in both sense and antisense directions, between two reporter genes. These plasmids, along with several control plasmids, were transfected into Sf9 cells, and post-transfection luciferase assays were conducted. Results were inconclusive. This could have been due to an inability of the plasmids to be expressed in Sf9 cells, an error in the construction of the plasmids, or a mechanical error in the assay procedure. At this time it appears most likely that the 5¿ NTR of DWV may be cell-type or species specific, and the next step would be to transfect the plasmids into a recently developed cultured honeybee cell line.

Identification of the p53 family-responsive element in the promoter region of the tumor suppressor gene hypermethylated in cancer 1

The tumor suppressor gene hypermethylated in cancer 1 (HIC1), located on human chromosome 17p13.3, is frequently silenced in cancer by epigenetic mechanisms. Hypermethylated in cancer 1 belongs to the bric à brac/poxviruses and zinc-finger family of transcription factors and acts by repressing target gene expression. It has been shown that enforced p53 expression leads to increased HIC1 mRNA, and recent data suggest that p53 and Hic1 cooperate in tumorigenesis. In order to elucidate the regulation of HIC1 expression, we have analysed the HIC1 promoter region for p53-dependent induction of gene expression. Using progressively truncated luciferase reporter gene constructs, we have identified a p53-responsive element (PRE) 500 bp upstream of the TATA-box containing promoter P0 of HIC1, which is sequence specifically bound by p53 in vitro as assessed by electrophoretic mobility shift assays. We demonstrate that this HIC1 p53-responsive element (HIC1.PRE) is necessary and sufficient to mediate induction of transcription by p53. This result is supported by the observation that abolishing endogenous wild-type p53 function prevents HIC1 mRNA induction in response to UV-induced DNA damage. Other members of the p53 family, notably TAp73beta and DeltaNp63alpha, can also act through this HIC1.PRE to induce transcription of HIC1, and finally, hypermethylation of the HIC1 promoter attenuates inducibility by p53.

[Intraoral lipoma in the region of the mental nerve--report of a case and review of the literature]

The intraoral lipoma is a benign, slowly growing, painless soft tissue neoplasia, which can cause esthetic or functional problems for the patient, depending on its size. All parts of the body can be affected, whereas the oral cavity is rarely involved. Clinically, the tumour often exhibits an exophytic growth pattern, a soft consistency, a broad base connected to the underlying tissue, and frequently has a reddish-yellowish colour. Instead of a superficial mucosal involvement, a deep localization in the soft tissues is also possible. Depending on the localization of the tumour, the diagnosis and the resulting therapy can turn out to be a challenge for the clinician. A clear differentiation to malign neoplasias of the fat tissues and other soft tissue expansions is essential. The following case report presents a female patient who is affected by a lipoma in the proximity of the mental nerve. The diagnostic work-up and resulting therapy including a review of the current literature are presented and discussed.

Functional relevance of DNA polymorphisms within the promoter region of the prion protein gene and their association to BSE infection

Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative diseases that can occur spontaneously or can be caused by infection or mutations within the prion protein gene PRNP. Nonsynonymous DNA polymorphisms within the PRNP gene have been shown to influence susceptibility/resistance to infection in sheep and humans. Analysis of DNA polymorphisms within the core promoter region of the PRNP gene in four major German bovine breeds resulted in the identification of both SNPs and insertion/deletion (indel) polymorphisms. Comparative genotyping of both controls and animals that tested positive for bovine spongiform encephalopathy (BSE) revealed a significantly different distribution of two indel polymorphisms and two SNPs within Braunvieh animals, suggesting an association of these polymorphisms with BSE susceptibility. The functional relevance of these polymorphisms was analyzed using reporter gene constructs in neuronal cells. A specific haplotype near exon 1 was identified that exhibited a significantly lower expression level. Genotyping of nine polymorphisms within the promoter region and haplotype calculation revealed that the haplotype associated with the lowest expression level was underrepresented in the BSE group of all breeds compared to control animals, indicating a correlation of reduced PRNP expression and increased resistance to BSE.

Short communication: duplication in the 5'-flanking region of the beta-lactoglobulin gene is linked to the BLG A allele

beta-Lactoglobulin (beta-LG) is the major whey protein in the milk of cows and other ruminants. It is well established that the predominant genetic variants beta-LG A and B are differentially expressed. Extensive investigation of the genetic variation in the promoter region of the BLG gene revealed the existence of specific haplotypes associated with the A and B variants. However, the genetic basis for the differentially expressed BLG A and B alleles is still elusive. In this study additional genetic variation further upstream in the 5'-flanking region of the BLG gene was identified, including 6 single nucleotide substitutions, a single nucleotide deletion, and a 7-bp duplication. Comparison of DNA sequences showed that the investigated 5'-flanking region is highly conserved between ruminants, and the duplication g.-1885_-1879dupCTCTCGC and the substitution g.-1888A>G are only found in the BLG A and D alleles in cattle. The cytosine at position g.-1957 and the thymines at positions g.-2008 and g.-2049 are only found in BLG B alleles of cattle. It is suggested that the described genetic variability contributes to the differential allelic expression of the BLG gene.

Evaluation of the chemical residue monitoring in animal-derived products in Switzerland

This paper evaluates whether the Swiss monitoring programme for foreign substances in animal products fulfils basic epidemiological quality requirements, and identifies possible sources of bias in the selection of samples. The sampling was analysed over a 4-year period (2002-05). The sampling frame in 37 participating abattoirs covered 51% of all slaughtered pigs, 73% of calves, 68% of beef and 36% of cows. The analysis revealed that some sub-populations as defined by the region of origin were statistically over-represented while others were under-represented. The programme that is in accordance with European Union requirements contained some relevant bias. Patterns of under-sampled regions characterized by management type differences were identified. This could lead to an underestimate of the number of contaminated animals within the programme. Although the current sampling was stratified and partially risk-based, its efficiency could be improved by adopting a more targeted approach.

A homologue of aliB is found in the capsule region of nonencapsulated Streptococcus pneumoniae

The epidemiology, phylogeny, and biology of nonencapsulated Streptococcus pneumoniae are largely unknown. Increased colonization capacity and transformability are, however, intriguing features of these pneumococci and play an important role. Twenty-seven nonencapsulated pneumococci were identified in a nationwide collection of 1,980 nasopharyngeal samples and 215 blood samples obtained between 1998 and 2002. On the basis of multilocus sequence typing and capsule region analysis we divided the nonencapsulated pneumococci into two groups. Group I was closely related to encapsulated strains. Group II had a clonal population structure, including two geographically widespread clones able to cause epidemic conjunctivitis and invasive diseases. Group II strains also carried a 1,959-bp homologue of aliB (aliB-like ORF 2) in the capsule region, which was highly homologous to a sequence in the capsule region of Streptococcus mitis. In addition, strains of the two major clones in group II had an additional sequence, aliB-like ORF 1 (1,968 to 2,004 bp), upstream of aliB-like ORF 2. Expression of aliB-like ORF 1 was detected by reverse transcription-PCR, and the corresponding RNA was visualized by Northern blotting. A gene fragment homologous to capN of serotypes 33 and 37 suggests that group II strains were derived from encapsulated pneumococci some time ago. Therefore, loss of capsule expression in vivo was found to be associated with the importation of one or two aliB homologues in some nonencapsulated pneumococci.

Performance evaluation of VIP latrines in the Upper West Region of Ghana

The prevalence of Ventilated Improved Pit (VIP) latrines in Ghana suggests that the design must have a high user acceptance. The two key factors attributed to user acceptance of a VIP latrine over an alternative latrine design, such as the basic pit latrine, are its ability to remove foul odors and maintain low fly populations; both of which are a direct result of an adequate ventilation flow rate. Adequate ventilation for odorless conditions in a VIP latrine has been defined by the United Nations Development Program (UNDP) and the World Bank, as an air flow rate equivalent to 6 air changes per hour (6 ACH) of the superstructure’s air volume. Additionally, the UNDP determined that the three primary factors that affect ventilation are: 1) wind passing over the mouth of the vent pipe, 2) wind passing into the superstructure, and 3) solar radiation on to the vent pipe. Previous studies also indicate that vent pipes with larger diameters increase flow rates, and the application of carbonaceous materials to the pit sludge reduces odor and insect prevalence. Furthermore, proper design and construction is critical for the correct functioning of VIP latrines. Under-designing could cause problems with odor and insect control; over-designing would increase costs unnecessarily, thereby making it potentially unaffordable for benefactors to independently construct, repair or replace a VIP latrine. The present study evaluated the design of VIP latrines used by rural communities in the Upper West Region of Ghana with the focus of assessing adequate ventilation for odor removal and insect control. Thirty VIP latrines from six communities in the Upper West Region of Ghana were sampled. Each VIP latrine’s ventilation flow rate and micro-environment was measured using a hot-wire anemometer probe and portable weather station for a minimum of four hours. To capture any temporal or seasonal variations in ventilation, ten of the latrines were sampled monthly over the course of three months for a minimum of 12 hours. A latrine usage survey and a cost analysis were also conducted to further assess the VIP latrine as an appropriated technology for sustainable development in the Upper West Region. It was found that the average air flow rate over the entire sample set was 11.3 m3/hr. The minimum and maximum air flow rates were 0.0 m3/hr and 48.0 m3/hr respectively. Only 1 of the 30 VIP latrines (3%) was found to have an air flow rate greater than the UNDP-defined odorless condition of 6 ACH. Furthermore, 19 VIP latrines (63%) were found to have an average air flow rate of less than half the flow rate required to achieve 6 ACH. The dominant factors affecting ventilation flow rate were wind passing over the mouth of the vent pipe and air buoyancy forces, which were the effect of differences in temperature between the substructure and the ambient environment. Of 76 usable VIP latrines found in one community, 68.4% were in actual use. The cost of a VIP latrine was found to be equivalent to approximately 12% of the mean annual household income for Upper West Region inhabitants.

An ethnobotanical survey of the economic and cultural significance of non-timber forest products in the southwest Rhodope Mountain region of Bulgaria

The people of the southwestern Rhodope Mountains of Bulgaria live in small, mountainous villages and rural areas. They rely on berries, herbs, and mushrooms provided by the forest and maintain a lifestyle and culture of gathering them. This study determined the economic and landscape concentration of Non-Timber Forest Products (NTFPs) and how this has changed in the past twenty years in the region of Garmen. The objective was to gauge the cultural and economic significance of NTFPs in the lives of the people who live there. Data was collected using informal, open-ended interviews and through participant observation. Results indicate that ethnicity influence how resources are utilized. Roma people collect mushrooms for income generation; Orthodox Bulgarians gather herbs, berries, and mushrooms for medicinal purposes, to supplement their diets, and to carry on traditions. Bulgarian Muslims collect for a combination of the aforementioned reasons. Changes that occur in the forests affect each of the ethnic groups in different ways and forest management practices should include people’s knowledge and uses of NTFPs.

Ecology of larval fishes and large zooplankton in the Keweenaw Current region of Lake Superior, with special focus on lake herring, Coregonus artedi

I assessed the influence of the Keweenaw Current and spring thermal bar on the distribution of larval fishes and large zooplankton in Lake Superior. In 1998 and 1999, samples were collected from inshore (0.2 – 3.0 km from shore) and offshore (5.0 – 9.0 km from shore) locations on three transects off the western coast of the Keweenaw Peninsula, Michigan. For larval fishes, density and size distribution patterns of lake herring (Coregonus artedi), rainbow smelt (Osmerus mordax), burbot (Lota lota), deepwater sculpin (Myoxocephalus thompsoni), and spoonhead sculpin (Cottus ricei) suggest a seasonal inshore to offshore movement. For zooplankton, seasonal warming appeared to be the major factor that limited planktonic catches of the primarily benthic Mysisrelicta and Diporeia spp., while simultaneously stimulated growth and reproduction of the cladocerans Daphnia spp., Holopedium gibberum, and Bythotrephes cederstroemi. In contrast, calanoid copepods as a group were abundant throughout the entire sampling season. The greatest abundances of zooplankton were generally encountered offshore, even for the cladocerans, which apparently expanded from inshore to offshore locations with seasonal warming. In 2000, sampling efforts focused on lake herring. Samples were collected from surface waters at 0.1 – 17.0 km from shore on two transects. Lake herring larvae were also reared in the laboratory from eggs in order to validate the use of otolith microstructure for aging. Increment deposition was not statistically different from a daily rate starting from 28 days after hatching, near the time of yolk-sac absorption, but larvae with lower growth rates could not be aged as accurately. In Lake Superior, lake herring tended to be slightly more abundant, larger, and older at inshore locations, but a dense patch of younger larvae was also encountered 7 – 13 km from shore. The distribution iiipatterns suggest that larvae were transported by prevailing currents into the study region, possibly from the more productive spawning regions in western Lake Superior. Growth rates were suppressed at offshore locations where temperatures were less than 8°C. These results indicate that lake herring larvae may be transported far distances from spawning concentrations by longshore currents, and water temperatures may largely control their growth.

Study of particle movement in the nearshore region of Lake Superior with radioisotope tracers

Biogeochemical processes in the coastal region, including the coastal area of the Great Lakes, are of great importance due to the complex physical, chemical and biological characteristics that differ from those on either the adjoining land or open water systems. Particle-reactive radioisotopes, both naturally occurring (210Pb, 210Po and 7Be) and man-made (137Cs), have proven to be useful tracers for these processes in many systems. However, a systematic isotope study on the northwest coast of the Keweenaw Peninsula in Lake Superior has not yet been performed. In this dissertation research, field sampling, laboratory measurements and numerical modeling were conducted to understand the biogeochemistry of the radioisotope tracers and some particulate-related coastal processes. In the first part of the dissertation, radioisotope activities of 210Po and 210Pb in a variability of samples (dissolved, suspended particle, sediment trap materials, surficial sediment) were measured. A completed picture of the distribution and disequilibrium of this pair of isotopes was drawn. The application of a simple box model utilizing these field observations reveals short isotope residence times in the water column and a significant contribution of sediment resuspension (for both particles and isotopes). The results imply a highly dynamic coastal region. In the second part of this dissertation, this conclusion is examined further. Based on intensive sediment coring, the spatial distribution of isotope inventories (mainly 210Pb, 137Cs and 7Be) in the nearshore region was determined. Isotope-based focusing factors categorized most of the sampling sites as non- or temporary depositional zones. A twodimensional steady-state box-in-series model was developed and applied to individual transects with the 210Pb inventories as model input. The modeling framework included both water column and upper sediments down to the depth of unsupported 210Pb penetration. The model was used to predict isotope residence times and cross-margin fluxes of sediments and isotopes at different locations along each transect. The time scale for sediment focusing from the nearshore to offshore regions of the transect was on the order of 10 years. The possibility of sediment longshore movement was indicated by high inventory ratios of 137Cs: 210Pb. Local deposition of fine particles, including fresh organic carbon, may explain the observed distribution of benthic organisms such as Diporeia. In the last part of this dissertation, isotope tracers, 210Pb and 210Po, were coupled into a hydrodynamic model for Lake Superior. The model was modified from an existing 2-D finite difference physical-biological model which has previously been successfully applied on Lake Superior. Using the field results from part one of this dissertation as initial conditions, the model was used to predict the isotope distribution in the water column; reasonable results were achieved. The modeling experiments demonstrated the potential for using a hydrodynamic model to study radioisotope biogeochemistry in the lake, although further refinements are necessary.