Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

Abstract Background RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. Results A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. Conclusion We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.

Dual effect of Lutzomyia longipalpis saliva on Leishmania braziliensis infection is mediated by distinct saliva-induced cellular recruitment into BALB/c mice ear

Abstract Background Leishmania parasites are transmitted to their vertebrate hosts by infected Phlebotomine sand flies during the blood meal of the flies. Sand fly saliva is known to enhance Leishmania spp. infection, while pre-exposure to saliva protects mice against parasitic infections. In this study, we investigated the initial inflammatory leucocyte composition induced by one or three inocula of salivary gland extract (SGE) from Lutzomyia longipalpis in the presence or absence of Leishmania braziliensis. Results We demonstrated that inoculating SGE once (SGE-1X) or three times (SGE-3X), which represented a co-inoculation or a pre-exposure to saliva, respectively, resulted in different cellular infiltrate profiles. Whereas SGE-1X led to the recruitment of all leucocytes subtypes including CD4+ T cells, CD4+CD25+ T cells, dendritic cells, macrophages and neutrophils, the immune cell profile in the SGE-3X group differed dramatically, as CD4+ T cells, CD4+CD25+ T cells, dendritic cells, macrophages and neutrophils were decreased and CD8+ T cells were increased. The SGE-1X group did not show differences in the ear lesion size; however, the SGE-1X group harbored a higher number of parasites. On the other hand, the SGE-3X group demonstrated a protective effect against parasitic disease, as the parasite burden was lower even in the earlier stages of the infection, a period in which the SGE-1X group presented with larger and more severe lesions. These effects were also reflected in the cytokine profiles of both groups. Whereas the SGE-1X group presented with a substantial increase in IL-10 production, the SGE-3X group showed an increase in IFN-γ production in the draining lymph nodes. Analysis of the inflammatory cell populations present within the ear lesions, the SGE-1X group showed an increase in CD4+FOXP3+ cells, whereas the CD4+FOXP3+ population was reduced in the SGE-3X group. Moreover, CD4+ T cells and CD8+ T cells producing IFN-γ were highly detected in the ears of the SGE-3X mice prior to infection. In addition, upon treatment of SGE-3X mice with anti-IFN-γ monoclonal antibody, we observed a decrease in the protective effect of SGE-3X against L. braziliensis infection. Conclusions These results indicate that different inocula of Lutzomyia longipalpis salivary gland extract can markedly modify the cellular immune response, which is reflected in the pattern of susceptibility or resistance to Leishmania braziliensis infection.

Natural regeneration in abandoned fields following intensive agricultural land use in an Atlantic Forest Island, Brazil

The time required to regrowth a forest in degraded areas depends on how the forest is removed and on the type of land use following removal. Natural regeneration was studied in abandoned old fields after intensive agricultural land use in areas originally covered by Brazilian Atlantic Forests of the Anchieta Island, Brazil in order to understand how plant communities reassemble following human disturbances as well as to determine suitable strategies of forest restoration. The fields were classified into three vegetation types according to the dominant plant species in: 1) Miconia albicans (Sw.) Triana (Melastomataceae) fields, 2) Dicranopteris flexuosa (Schrader) Underw. (Gleicheniaceae) thickets, and 3) Gleichenella pectinata (Willd.) Ching. (Gleicheniaceae) thickets. Both composition and structure of natural regeneration were compared among the three dominant vegetation types by establishing randomly three plots of 1 x 3 m in five sites of the island. A gradient in composition and abundance of species in natural regeneration could be observed along vegetation types from Dicranopteris fern thickets to Miconia fields. The gradient did not accurately follow the pattern of spatial distribution of the three dominant vegetation types in the island regarding their proximity of the remnant forests. A complex association of biotic and abiotic factors seems to be affecting the seedling recruitment and establishment in the study plots. The lowest plant regeneration found in Dicranopteris and Gleichenella thickets suggests that the ferns inhibit the recruitment of woody and herbaceous species. Otherwise, we could not distinguish different patterns of tree regeneration among the three vegetation types. Our results showed that forest recovery following severe anthropogenic disturbances is not direct, predictable or even achievable on its own. Appropriated actions and methods such as fern removal, planting ground covers, and enrichment planting with tree species were suggested in order to restore the natural forest regeneration process in the abandoned old fields.

Comparison of primers for RAPD-PCR from environmental isolates of Cryptococcus neoformans, Cryptococcus albidus and Cryptococcus laurentii complex

Various organisms have been characterized by molecular methods, including fungi of the genus Cryptococcus. The purposes of this study were: to determine the discriminatory potential of the RAPD (Random Amplified Polymorphic DNA) primers, the pattern of similarity of the Cryptococcus species, and discuss their useful application in epidemiological studies. We analyzed 10 isolates of each specie/group: C. albidus, C. laurentii complex, C. neoformans var. grubii, all from environmental source, and two ATCC strains, C. neoformans var. grubii ATCC 90112, and C. neoformans var. neoformans ATCC 28957 by RAPD-PCR using the primers CAV1, CAV2, ZAP19, ZAP20, OPB11 and SEQ6. The primers showed a good discriminatory power, revealing important differences between them and between species; the SEQ6 primer discriminated a larger number of isolates of three species. Isolates of C. laurentii showed greater genetic diversity than other species revealed by all six primers. Isolates of C. neoformans were more homogeneous. Only the primer CAV2 showed no amplification of DNA bands for C. albidus. It was concluded that the use of limited number of carefully selected primers allowed the discrimination of different isolates, and some primers (e.g., CAV2 for C. albidus) may not to be applied to some species.

Comparative analysis of shell occupation by two southern populations of the hermit crab Loxopagurus loxochelis (Decapoda, Diogenidae)

The present study aimed to comparatively verify the relation between the hermit crabs and the shells they use in two populations of Loxopagurus loxochelis. Samples were collected monthly from July 2002 to June 2003, at Caraguatatuba and Ubatuba Bay, São Paulo, Brazil. The animals sampled had their sex identified, were weighed and measured; their shells were identified, measured and weighed, and their internal volume determined. To relate the hermit crab's characteristics and the shells' variables, principal component analysis (PCA) and a regression tree were used. According to the PCA analysis, the three gastropod shells most frequently used by L. loxochelis varied in size. The regression tree successfully explained the relationship between the hermit crab's characteristics and the internal volume of the inhabited shell. It can be inferred that the relationship between the morphometry of an individual hermit crab and its shell is not straightforward and it is impossible to explain only on the basis of direct correlations between the body's and the shell's attributes. Several factors (such as the morphometry and the availability of the shell, environmental conditions and inter- and intraspecific competition) interact and seem to be taken into consideration by the hermit crabs when they choose a shell, resulting in the diversified pattern of shell occupancy shown here and elsewhere.

Occurrence of bipolar spectrum disorder and comorbidities in women with eating disorders

Abstract Background Eating disorder (ED) patients often have comorbidities with other psychiatric disorders, especially with mood disorders. Although recent studies suggest an intimate relationship between ED and bipolar disorder (BD), the study on a broader bipolar spectrum definition has not been done in this population. We aimed to study the occurrence of bipolar spectrum (BS) and comorbidities in eating disorder patients of a tertiary service provider. Methods Sixty-nine female patients diagnosed with anorexia nervosa, bulimia nervosa, or eating disorder not otherwise specified were evaluated. The assessment comprised the Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), clinical criteria for diagnosis of the Zurich bipolar spectrum. Mann–Whitney tests compared means of continuous variables. The association between categorical variables and the groups was described using contingency tables and analyzed using the chi-square or Fisher's exact test. The level of significance alpha was set at 5%. Results The results showed that 68.1% of patients had comorbidity with bipolar spectrum, and this was associated with higher family income, proportion of married people, and comorbidity with substance use. The ED with BS group showed higher rates of substance use comorbidity (40.4%) than the ED without BS group (13.6%). Discussion These results showed that the bipolar spectrum is a common comorbidity in patients with eating disorders and is associated with correlates of clinical importance, notably the comorbidity with substance use. Due to the pattern of similarity between the groups with and without comorbid bipolar spectrum in relation to various outcomes evaluated, the identification of comorbidity can be difficult. However, the precise diagnosis and careful identification of clinical correlates may contribute to future advances in treating these conditions. Further studies are necessary to evaluate the association of other clinical correlates and its possible causal association.

Expression of the repressor element-1 silencing transcription factor (REST) is regulated by IGF-I and PKC in human neuroblastoma cells

The repressor element 1-silencing transcription factor (REST) was first identified as a protein that binds to a 21-bp DNA sequence element (known as repressor element 1 (RE1)) resulting in transcriptional repression of the neural-specific genes [Chong et al., 1995; Schoenherr and Anderson, 1995]. The original proposed role for REST was that of a factor responsible for restricting neuronal gene expression to the nervous system by silencing expression of these genes in non-neuronal cells. Although it was initially thought to repress neuronal genes in non-neuronal cells, the role of REST is complex and tissue dependent. In this study I investigated any role played by REST in the induction and patterning of differentiation of SH-SY5Y human neuroblastoma cells exposed to IGF-I. and phorbol 12- myristate 13-acetate (PMA) To down-regulate REST expression we developed an antisense (AS) strategy based on the use of phosphorothioate oligonucleotides (ODNs). In order to evaluate REST mRNA levels, we developed a real-time PCR technique and REST protein levels were evaluated by western blotting. Results showed that nuclear REST is increased in SH-SY5Y neuroblastoma cells cultured in SFM and exposed to IGF-I for 2-days and it then declines in 5-day-treated cells concomitant with a progressive neurite extension. Also the phorbol ester PMA was able to increase nuclear REST levels after 3-days treatment concomitant to neuronal differentiation of neuroblastoma cells, whereas, at later stages, it is down-regulated. Supporting these data, the exposure to PKC inhibitors (GF10923X and Gö6976) and PMA (16nM) reverted the effects observed with PMA alone. REST levels were related to morphological differentiation, expression of growth coneassociated protein 43 (GAP-43; a gene not regulated by REST) and of synapsin I and βIII tubulin (genes regulated by REST), proteins involved in the early stage of neuronal development. We observed that differentiation of SH-SY5Y cells by IGF-I and PMA was accompanied by a significant increase of these neuronal markers, an effect that was concomitant with REST decrease. In order to relate the decreased REST expression with a progressive neurite extension, I investigated any possible involvement of the ubiquitin–proteasome system (UPS), a multienzymatic pathway which degrades polyubiquinated soluble cytoplasmic proteins [Pickart and Cohen, 2004]. For this purpose, SH-SY5Y cells are concomitantly exposed to PMA and the proteasome inhibitor MG132. In SH-SY5Y exposed to PMA and MG 132, we observed an inverse pattern of expression of synapsin I and β- tubulin III, two neuronal differentiation markers regulated by REST. Their cytoplasmic levels are reduced when compared to cells exposed to PMA alone, as a consequence of the increase of REST expression by proteasome inhibitor. The majority of proteasome substrates identified to date are marked for degradation by polyubiquitinylation; however, exceptions to this principle, are well documented [Hoyt and Coffino, 2004]. Interestingly, REST degradation seems to be completely ubiquitin-independent. The expression pattern of REST could be consistent with the theory that, during early neuronal differentiation induced by IGF-I and PKC, it may help to repress the expression of several genes not yet required by the differentiation program and then it declines later. Interestingly, the observation that REST expression is progressively reduced in parallel with cell proliferation seems to indicate that the role of this transcription factor could also be related to cell survival or to counteract apotosis events [Lawinger et al., 2000] although, as shown by AS-ODN experiments, it does not seem to be directly involved in cell proliferation. Therefore, the decline of REST expression is a comparatively later event during maturation of neuroroblasts in vitro. Thus, we propose that REST is regulated by growth factors, like IGF-I, and PKC activators in a time-dependent manner: it is elevated during early steps of neural induction and could contribute to down-regulate genes not yet required by the differentiation program while it declines later for the acquisition of neural phenotypes, concomitantly with a progressive neurite extension. This later decline is regulated by the proteasome system activation in an ubiquitin-indipendent way and adds more evidences to the hypothesis that REST down-regulation contributes to differentiation and arrest of proliferation of neuroblastoma cells. Finally, the glycosylation pattern of the REST protein was analysed, moving from the observation that the molecular weight calculated on REST sequence is about 116 kDa but using western blotting this transcription factor appears to have distinct apparent molecular weight (see Table 1.1): this difference could be explained by post-translational modifications of the proteins, like glycosylation. In fact recently, several studies underlined the importance of O-glycosylation in modulating transcriptional silencing, protein phosphorylation, protein degradation by proteasome and protein–protein interactions [Julenius et al., 2005; Zachara and Hart, 2006]. Deglycosilating analysis showed that REST protein in SH-SY5Y and HEK293 cells is Oglycosylated and not N-glycosylated. Moreover, using several combination of deglycosilating enzymes it is possible to hypothesize the presence of Gal-β(1-3)-GalNAc residues on the endogenous REST, while β(1-4)-linked galactose residues may be present on recombinant REST protein expressed in HEK293 cells. However, the O-glycosylation process produces an immense multiplicity of chemical structures and monosaccharides must be sequentially hydrolyzed by a series of exoglycosidase. Further experiments are needed to characterize all the post-translational modification of the transcription factor REST.

Distribution and state of fishery resources in the Northern and Central Adriatic Sea using trawl surveys data

The Ecosystem Approach to Fisheries represents the most recent research line in the international context, showing interest both towards the whole community and toward the identification and protection of all the “critical habitats” in which marine resources complete their life cycles. Using data coming from trawl surveys performed in the Northern and Central Adriatic from 1996 to 2010, this study provides the first attempt to appraise the status of the whole demersal community. It took into account not only fishery target species but also by-catch and discharge species by the use of a suite of biological indicators both at population and multi-specific level, allowing to have a global picture of the status of the demersal system. This study underlined the decline of extremely important species for the Adriatic fishery in recent years; adverse impact on catches is expected for these species in the coming years, since also minimum values of recruits recently were recorded. Both the excessive exploitation and environmental factors affected availability of resources. Moreover both distribution and nursery areas of the most important resources were pinpointed by means of geostatistical methods. The geospatial analysis also confirmed the presence of relevant recruitment areas in the North and Central Adriatic for several commercial species, as reported in the literature. The morphological and oceanographic features, the relevant rivers inflow together with the mosaic pattern of biocenoses with different food availability affected the location of the observed relevant nursery areas.

Development of control-oriented models of Dual Clutch Transmission systems

A control-oriented model of a Dual Clutch Transmission was developed for real-time Hardware In the Loop (HIL) applications, to support model-based development of the DCT controller. The model is an innovative attempt to reproduce the fast dynamics of the actuation system while maintaining a step size large enough for real-time applications. The model comprehends a detailed physical description of hydraulic circuit, clutches, synchronizers and gears, and simplified vehicle and internal combustion engine sub-models. As the oil circulating in the system has a large bulk modulus, the pressure dynamics are very fast, possibly causing instability in a real-time simulation; the same challenge involves the servo valves dynamics, due to the very small masses of the moving elements. Therefore, the hydraulic circuit model has been modified and simplified without losing physical validity, in order to adapt it to the real-time simulation requirements. The results of offline simulations have been compared to on-board measurements to verify the validity of the developed model, that was then implemented in a HIL system and connected to the TCU (Transmission Control Unit). Several tests have been performed: electrical failure tests on sensors and actuators, hydraulic and mechanical failure tests on hydraulic valves, clutches and synchronizers, and application tests comprehending all the main features of the control performed by the TCU. Being based on physical laws, in every condition the model simulates a plausible reaction of the system. The first intensive use of the HIL application led to the validation of the new safety strategies implemented inside the TCU software. A test automation procedure has been developed to permit the execution of a pattern of tests without the interaction of the user; fully repeatable tests can be performed for non-regression verification, allowing the testing of new software releases in fully automatic mode.

Applications of GIS and remote sensing techniques for studying the housing patterns in Cairo Governorate

The main objective of this study is to reveal the housing patterns in Cairo as one of the most rapidly urbanizing city in the developing world. The study outlines the evolution of the housing problem and its influencing factors in Egypt generally and in Cairo specifically. The study takes into account the political transition from the national state economy to the open door policy, the neo-liberal period and finally to the housing situation after the January 2011 Revolution. The resulting housing patterns in Cairo Governorate were identified as (1) squatter settlements, (2) semi-informal settlements, (3) deteriorated inner pockets, and (4) formal settlements. rnThe study concluded that the housing patterns in Cairo are reflecting a multifaceted problem resulting in: (1) the imbalance between the high demand for affordable housing units for low-income families and the oversupply of upper-income housing, (2) the vast expansion of informal areas both on agricultural and desert lands, (3) the deterioration of the old parts of Cairo without upgrading or appropriate replacement of the housing structure, and (4) the high vacancy rate of newly constructed apartmentsrnThe evolution and development of the current housing problem were attributed to a number of factors. These factors are demographic factors represented in the rapid growth of the population associated with urbanization under the dictates of poverty, and the progressive increase of the prices of both buildable land and building materials. The study underlined that the current pattern of population density in Cairo Governorate is a direct result of the current housing problems. Around the depopulation core of the city, a ring of relatively stable areas in terms of population density has developed. Population densification, at the expense of the depopulation core, is characterizing the peripheries of the city. The population density in relation to the built-up area was examined using Landsat-7 ETM+ image (176/039). The image was acquired on 24 August 2006 and considered as an ideal source for land cover classification in Cairo since it is compatible with the population census 2006.rnConsidering that the socio-economic setting is a driving force of change of housing demand and that it is an outcome of the accumulated housing problems, the socio-economic deprivations of the inhabitants of Cairo Governorate are analyzed. Small administrative units in Cairo are categorized into four classes based on the Socio-Economic Opportunity Index (SEOI). This index is developed by using multiple domains focusing on the economic, educational and health situation of the residential population. The results show four levels of deprivation which are consistent with the existing housing patterns. Informal areas on state owned land are included in the first category, namely, the “severely deprived” level. Ex-formal areas or deteriorated inner pockets are characterized as “deprived” urban quarters. Semi-informal areas on agricultural land concentrate in the third category of “medium deprived” settlements. Formal or planned areas are included mostly in the fourth category of the “less deprived” parts of Cairo Governorate. rnFor a better understanding of the differences and similarities among the various housing patterns, four areas based on the smallest administrative units of shiakhat were selected for a detailed study. These areas are: (1) El-Ma’desa is representing a severely deprived squatter settlement, (2) Ain el-Sira is an example for an ex-formal deprived area, (3) El-Marg el-Qibliya was selected as a typical semi-informal and medium deprived settlement, and (4) El-Nozha is representing a formal and less deprived area.rnThe analysis at shiakhat level reveals how the socio-economic characteristics and the unregulated urban growth are greatly reflected in the morphological characteristics of the housing patterns in terms of street network and types of residential buildings as well as types of housing tenure. It is also reflected in the functional characteristics in terms of land use mix and its degree of compatibility. It is concluded that the provision and accessibility to public services represents a performance measure of the dysfunctional structure dominating squatter and semi-informal settlements on one hand and ample public services and accessibility in formal areas on the other hand.rn

3D bloodstain pattern analysis: ballistic reconstruction of the trajectories of blood drops and determination of the centres of origin of the bloodstains

For crime scene investigation in cases of homicide, the pattern of bloodstains at the incident site is of critical importance. The morphology of the bloodstain pattern serves to determine the approximate blood source locations, the minimum number of blows and the positioning of the victim. In the present work, the benefits of the three-dimensional bloodstain pattern analysis, including the ballistic approximation of the trajectories of the blood drops, will be demonstrated using two illustrative cases. The crime scenes were documented in 3D, using the non-contact methods digital photogrammetry, tachymetry and laser scanning. Accurate, true-to-scale 3D models of the crime scenes, including the bloodstain pattern and the traces, were created. For the determination of the areas of origin of the bloodstain pattern, the trajectories of up to 200 well-defined bloodstains were analysed in CAD and photogrammetry software. The ballistic determination of the trajectories was performed using ballistics software. The advantages of this method are the short preparation time on site, the non-contact measurement of the bloodstains and the high accuracy of the bloodstain analysis. It should be expected that this method delivers accurate results regarding the number and position of the areas of origin of bloodstains, in particular the vertical component is determined more precisely than using conventional methods. In both cases relevant forensic conclusions regarding the course of events were enabled by the ballistic bloodstain pattern analysis.

Perception of non-invasive ventilation in adult Swiss intensive care units

The real utilisation scenario of non-invasive ventilation (NIV) in Swiss ICUs has never been reported. Using a survey methodology, we developed a questionnaire sent to the directors of the 79 adult ICUs to identify the perceived pattern of NIV utilisation. We obtained a response rate of 62%. The overall utilisation rate for NIV was 26% of all mechanical ventilations, but we found significant differences in the utilisation rates among different linguistic areas, ranging from 20% in the German part to 48% in the French part (p <0.01). NIV was mainly indicated for the acute exacerbations of COPD (AeCOPD), acute cardiogenic pulmonary edema (ACPE) and acute respiratory failure (ARF) in selected do-not-intubate patients. In ACPE, CPAP was much less used than bi-level ventilation and was still applied in AeCOPD. The first line interface was a facial mask (81%) and the preferred type of ventilator was an ICU machine with an NIV module (69%). The perceived use of NIV is generally high in Switzerland, but regional variations are remarkable. The indications of NIV use are in accordance with international guidelines. A high percentage of units consider selected do-not-intubate conditions as an important additional indication.

Hydrologic and Water Quality Assessment of Miller Run: A Study of Bucknell University’s Impact

Human development causes degradation of stream ecosystems due to impacts on channel morphology, hydrology, and water quality. Urbanization, the second leading cause of stream impairment, increases the amount of impervious surface cover, thus reducing infiltration and increasing surface runoff of precipitation, which ultimately affects stream hydrologic process and aquatic biodiversity. The main objective of this study was to assess the overall health of Miller Run, a small tributary of the Bull Run and Susquehanna River watersheds, through an integrative hydrologic and water quality approach in order to determine the degree of Bucknell University’s impact on the stream. Hydrologic conditions, including stage and discharge, and water quality conditions, including total suspended solids, ion, nutrient, and dissolved metal concentrations, specific conductivity, pH, and temperature, were measured and evaluated at two sampling sites (upstream and downstream of Bucknell’s main campus) during various rain events from September 2007 to March 2008. The primary focus of the stream analysis was based on one main rain event on 26 February 2008. The results provided evidence that Miller Run is impacted by Bucknell’s campus. From a hydrologic perspective, the stream’s hydrograph showed the exact opposite pattern of what would be expected from a ‘normal’ stream. Miller run had a flashier downstream hydrograph and a broader upstream hydrograph, which was more than likely due to the increased amount of impervious surface cover throughout the downstream half of the watershed. From a water quality perspective, sediment loads increased at a faster rate and were significantly higher downstream compared to upstream. These elevated sediment concentrations were probably the combined result of sediment runoff from upstream and downstream construction sites that were being developed over the course of the study. Sodium, chloride, and potassium concentrations, in addition to specific conductivity, also significantly increased downstream of Bucknell’s campus due to the runoff of road salts. Calcium and magnesium concentrations did not appear to be impacted by urbanization, although they did demonstrate a significant dilution effect downstream. The downstream site was not directly affected by elevated nitrate concentrations; however, soluble reactive phosphorus concentrations tended to increase downstream and ammonium concentrations significantly peaked partway through the rain event downstream. These patterns suggest that Miller Run may be impacted by nutrient runoff from the golf course, athletic fields, and/or fertilizers applications on the main campus. Dissolved manganese and iron concentrations also appeared to slightly increase downstream, demonstrating the affect of urban runoff from roads and parking lots. pH and temperature both decreased farther downstream, but neither showed a significant impact of urbanization. More studies are necessary to determine how Miller Run responds to changes in season, climate, precipitation intensity, and land-use. This study represents the base-line analysis of Miller Run’s current hydrologic and water quality conditions; based on these initial findings, Bucknell should strongly consider modifications to improve storm water management practices and to reduce the campus’s overall impact on the stream in order to enhance and preserve the integrity of its natural water resources.

The Sociolinguistics of Hungarian Outside Hungary

This study describes the sociolinguistic situation of the indigenous Hungarian national minorities in Slovakia (c. 600,000), Ukraine (c. 180,000), Romania (c. 2,000,000), Yugoslavia (c. 300,000), Slovenia (c. 8,000) and Austria (c. 6,000). Following the guidelines of Hans Goebl et al, the historical sociolinguistic portrait of each minority is presented from 1920 through to the mid-1990s. Each country's report includes sections on geography and demography, history, politics, economy, culture and religion, language policy and planning, and language use (domains of minority and/or majority language use, proficiency, attitudes, etc.). The team's findings were presented in the form of 374 pages of manuscripts, articles and tables, written in Hungarian and English. The core of the team's research results lies in the results of an empirical survey designed to study the social characteristics of Hungarian-minority bilingualism in the six project countries, and the linguistic similarities and differences between the six contact varieties of Hungarian and Hungarian in Hungary. The respondents were divided by age, education, and settlement group - city vs. village and local majority vs. local minority. The first thing to be observed is that Hungarian is tending to be spoken less to children than to parents and grandparents, a familiar pattern of language shift. In contact varieties of Hungarian, analytic constructions may be used where monolingual Hungarians would use a more synthetic form. Mr Kontra gives as an example the compound tagdij, which in Standard Hungarian means "membership fee" but which is replaced in contact Hungarian by the two-word phrase tagsagi dij. Another similar example concerns the synthetic verb hegedult "played the violin" and the analytic expression hegedun jatszott. The contrast is especially striking between the Hungarians in the northern Slavic countries, who use the synthetic form frequently, and those in the southern Slavic countries, who mainly use the analytic form. Mr. Kontra notes that from a structural point of view, there is no immediate explanation for this, since Slovak or Ukrainian are as likely to cause interference as is Serbian. He postulates instead that the difference may be attributable to some sociohistoric cause, and points out that the Turkish occupation of what is today Voivodina caused a discontinuity of the Hungarian presence in the region, with the result that Hungarians were resettled in the area only two and a half centuries ago. However, the Hungarians in today's Slovakia and Ukraine have lived together with Slavic peoples continuously for over a millennium. It may be, he suggests, that 250 years of interethnic coexistence is less than is needed for such a contact-induced change to run its course. Next Mr. Kontra moved on to what he terms "mental maps and morphology". In Hungarian, the names of cities and villages take the surface case (eg. Budapest-en "in Budapest") whereas some names denoting Hungarian settlements and all names of foreign cities take the interior case (eg. Tihany-ban "in Tihany" and Boston-ban "in Boston). The role of the semantic feature "foreign" in suffix-choice can be illustrated by such minimal pairs as Velence-n "in Velence, a village in Hungary" versus Velence-ben "in Velence [=Venice], a city in Italy", and Pecs-en "in Pecs, a city in Hungary" vs. Becs-ben "in Becs, ie. Vienna". This Hungarian vs. foreign distinction is often interpreted as "belonging to historical (pre-1920) Hungary" vs. "outside historical Hungary". The distinction is also expressed in the dichotomy "home" vs. "abroad'. The 1920 border changes have had an impact on both majority and minority Hungarians' mental maps, the maps which govern the choice of surface vs. interior cases with placenames. As there is a growing divergence between the mental maps of majority and minority Hungarians, so there will be a growing divergence in their use of the placename suffixes. Two placenames were chosen to scratch the surface of this complex problem: Craiova (a city in Oltenia, Romania) and Kosovo (Hungarian Koszovo) an autonomous region in southeast Yugoslavia. The assumption to be tested was that both placenames would be used with the inessive (interior) suffixes categorically by Hungarians in Hungary, but that the superessive suffix (showing "home") would be used near-categorically by Hungarians in Romania and Yugoslavia (Voivodina). Minority Hungarians in countries other than Romania and Yugoslavia would show no difference from majority Hungarians in Hungary. In fact, the data show that, contrary to expectation, there is considerable variation within Hungary. And although Koszovo is used, as expected, with the "home" suffix by 61% of the informants in Yugoslavia, the same suffix is used by an even higher percentage of the subjects in Slovenia. Mr. Kontra's team suggests that one factor playing a role in this might be the continuance of the former Yugoslav mentality in the Hungarians of Slovenia, at least from the geographical point of view. The contact varieties of Hungarian show important grammatical differences from Hungarian in Hungary. One of these concerns the variable use of Null subjects (the inclusion or exclusion of the subject of the verb). When informants were asked to insert either megkertem or megkertem ot - "I asked her" - into a test sentence, 54.9% of the respondents in the Ukraine inserted the second phrase as opposed to only 27.4% in Hungary. Although Mr. Kontra and his team concentrated more on the differences between Contact Hungarian and Standard Hungarian, they also discovered a number of similarities. One such similarity is demonstrable in the distribution of what Mr. Kontra calls an ongoing syntactic merger in Hungarian in Hungary. This change means effectively that two possibilities merge to form a third. For instance, the two sentences Valoszinuleg kulfoldre fognak koltozni and Valoszinu, hogy kulfoldre fognak koltozni merge to form the new construction Valszinuleg, hogy kulfoldre fognak koltozni ("Probably they will move abroad."). When asked to choose "the most natural" of the sentences, one in four chose the new construction, and a chi-square test shows homogeneity in the sample. In other words, this syntactic change is spreading across the entire Hungarian-speaking region in the Carpathian Basin Mr. Kontra believes that politicians, educators, and other interested parties now have reliable and up-to-date information about each Hungarian minority. An awareness of Hungarian as a pluricentric language is being developed which elevates the status of contact varieties of Hungarian used by the minorities, an essential process, he believes, if minority languages are to be maintained.

Genetic analysis of syndactyly in German Holstein cattle

Congenital syndactyly with a variable number of affected feet was observed in eight black and white German Holstein calves. Analysis of the pedigree data revealed that all affected individuals could be traced back to a single founder. The pedigree was consistent with monogenic autosomal recessive inheritance and variable expressivity. Bovine syndactyly or "mulefoot" has been previously shown to map on the telomeric end of bovine chromosome 15 and we performed PCR genotyping of microsatellite markers spanning 27 cM of this chromosomal region to test the new cases for genetic linkage with the phenotype. The haplotype segregation confirmed the suggested inheritance pattern of the mulefoot mutation in this family and markers RM004, BM848 and BMS820 showed significant linkage to the phenotype. The results confirmed the chromosomal location of the mulefoot gene in this pedigree. Furthermore the study demonstrated that although marker testing has been available for nearly a decade the use of mulefoot carriers in cattle breeding remains uncontrolled. The presented family provides a resource for positional cloning of the causative mutation.