Reindeer Parapoxvirus : Molecular Biology and Detection

Parapoxviruses (PPVs) are zoonotic viruses which cause contagious pustular skin infections of sheep, goats and cattle worldwide. In addition, they have more recently been shown to infect other animals such as red deer, seals, camels and reindeer. Cases of contagious pustular stomatitis in Finnish reindeer have been reported for many years. This economically important disease occurs typically during winter and is more common in the southern parts of the reindeer herding districts than in the north. The first severe outbreak occurred in the winter 1992-1993, and during the winter of 1999-2000 and in the late winter 2007 outbreaks of the disease were again observed. Usual symptoms include diminished appetite, drooling, fever, and later erosions and ulcerative lesions in the mouth. The aims of this study were to establish specific and rapid detection methods for the causative agent of the disease and characterize the viruses circulating in Finland. The causative agent of reindeer pustular stomatitis was originally considered to be Orf virus (ORFV) of the genus Parapoxvirus. PCR methods amplifying different regions of the PPV genomes were developed to analyse clinical samples obtained from outbreaks of the disease in reindeer and later from viruses isolated from the disease of sheep and cattle in Finland. Subsequent phylogenetic analyses of the Finnish PPVs, known members of the genus Parapoxvirus and selected members of the subfamily Chordopoxvirinae were conducted to identify the virus species isolated from reindeer. The results showed that the reindeer PPV from 1999-2000 is most closely related to the cattle PPV Pseudocowpox virus (PCPV) whereas the PPV strains from the winter of 1992-1993 outbreak grouped with sheep ORFV strains. Reindeer samples from the 2007 outbreak were identified as both PCPV and ORFV. Analysis of the similarity between genes of reindeer PCPV and ORFV isolates, Finnish sheep ORFV and cattle PCPV isolates indicated that these viruses have been circulating among Finnish reindeer, cattle and sheep at least ten years. Since the initial classification of the viruses causing pustular stomatitis in Finnish reindeer relied solely on the partial sequence analysis of virion core- and EEV envelope phospholipase protein sequences, the genome of PCPV-like reindeer isolate (F00.120R) was sequenced by shotgun sequencing of plasmid sublibraries of cosmids covering the central region of the genome, and by sequencing transposon random insertion libraries of plasmids derived from each end of the genome. The F00.120R and the genomic sequence of a reference strain of PCPV (VR634) were annotated and analyzed in this study. This first characterization of PCPV genomes revealed that F00.120R and VR634 are 135 and 145 kb in length and contain 131 and 134 putative genes, respectively. The organization of their genomes was found to be similar to that of other PPVs and both included 88 predicted genes that are conserved across all sequenced poxviruses. F00.120R was found to have four, possibly fragmented, genes at the left terminus and another near the central region of the genome that are not present in ORFV or Bovine papular stomatitis virus (BPSV; another PPV) genomes. In addition, the F00.120R genome was found to lack six genes seen near the right genome terminus of other PPVs. Comparing the PPV proteomes and whole genome phylogenetic analyses confirmed the classification of PCPV as a separate species within the PPV genus and verified that the virus causing pustular stomatitis in reindeer in 1999-2000 can be classified as PCPV. The observed six gene deletion at the right terminus of the F00.120R genome was further investigated in an attempt to use it in differentiating PCPV and ORFV causing pustular stomatitis in reindeer. The preliminary PCR analyses of wild type virus and early passages of F00.120R implied that the deletion of genes may have arisen during cell culture of the virus. The sequence around the deleted region was determined by sequencing two cloned overlapping PCR fragments from F00.120R wt virus isolated from lesion material. The same region was sequenced from an Italian PCPV field isolate (It1303). Further PCR analyses together with sequence determination showed that a 5431 bp sequence containing genes 116-121 was likely to have been deleted from the F00.120R genome prior to the 7th passage in cell culture. In addition, genes 116-121 were present in It1303 and in other isolates of reindeer and bovine PCPV isolated in Finland during the years 2005-2010. These results indicate that the genome of reindeer PCPV is about 140 kbp in length and has 137 genes instead of previously estimated length of 135 kbp and 131 genes; it contains homologues of all known ORFV genes and this analysis further reinforces the close genetic relationship between PCPV and ORFV

Reindeer Parapoxvirus

Parapoxviruses (PPVs) are zoonotic viruses which cause contagious pustular skin infections of sheep, goats and cattle worldwide. In addition, they have more recently been shown to infect other animals such as red deer, seals, camels and reindeer. Cases of contagious pustular stomatitis in Finnish reindeer have been reported for many years. This economically important disease occurs typically during winter and is more common in the southern parts of the reindeer herding districts than in the north. The first severe outbreak occurred in the winter 1992-1993, and during the winter of 1999-2000 and in the late winter 2007 outbreaks of the disease were again observed. Usual symptoms include diminished appetite, drooling, fever, and later erosions and ulcerative lesions in the mouth. The aims of this study were to establish specific and rapid detection methods for the causative agent of the disease and characterize the viruses circulating in Finland. The causative agent of reindeer pustular stomatitis was originally considered to be Orf virus (ORFV) of the genus Parapoxvirus. PCR methods amplifying different regions of the PPV genomes were developed to analyse clinical samples obtained from outbreaks of the disease in reindeer and later from viruses isolated from the disease of sheep and cattle in Finland. Subsequent phylogenetic analyses of the Finnish PPVs, known members of the genus Parapoxvirus and selected members of the subfamily Chordopoxvirinae were conducted to identify the virus species isolated from reindeer. The results showed that the reindeer PPV from 1999-2000 is most closely related to the cattle PPV Pseudocowpox virus (PCPV) whereas the PPV strains from the winter of 1992-1993 outbreak grouped with sheep ORFV strains. Reindeer samples from the 2007 outbreak were identified as both PCPV and ORFV. Analysis of the similarity between genes of reindeer PCPV and ORFV isolates, Finnish sheep ORFV and cattle PCPV isolates indicated that these viruses have been circulating among Finnish reindeer, cattle and sheep at least ten years. Since the initial classification of the viruses causing pustular stomatitis in Finnish reindeer relied solely on the partial sequence analysis of virion core- and EEV envelope phospholipase protein sequences, the genome of PCPV-like reindeer isolate (F00.120R) was sequenced by shotgun sequencing of plasmid sublibraries of cosmids covering the central region of the genome, and by sequencing transposon random insertion libraries of plasmids derived from each end of the genome. The F00.120R and the genomic sequence of a reference strain of PCPV (VR634) were annotated and analyzed in this study. This first characterization of PCPV genomes revealed that F00.120R and VR634 are 135 and 145 kb in length and contain 131 and 134 putative genes, respectively. The organization of their genomes was found to be similar to that of other PPVs and both included 88 predicted genes that are conserved across all sequenced poxviruses. F00.120R was found to have four, possibly fragmented, genes at the left terminus and another near the central region of the genome that are not present in ORFV or Bovine papular stomatitis virus (BPSV; another PPV) genomes. In addition, the F00.120R genome was found to lack six genes seen near the right genome terminus of other PPVs. Comparing the PPV proteomes and whole genome phylogenetic analyses confirmed the classification of PCPV as a separate species within the PPV genus and verified that the virus causing pustular stomatitis in reindeer in 1999-2000 can be classified as PCPV. The observed six gene deletion at the right terminus of the F00.120R genome was further investigated in an attempt to use it in differentiating PCPV and ORFV causing pustular stomatitis in reindeer. The preliminary PCR analyses of wild type virus and early passages of F00.120R implied that the deletion of genes may have arisen during cell culture of the virus. The sequence around the deleted region was determined by sequencing two cloned overlapping PCR fragments from F00.120R wt virus isolated from lesion material. The same region was sequenced from an Italian PCPV field isolate (It1303). Further PCR analyses together with sequence determination showed that a 5431 bp sequence containing genes 116-121 was likely to have been deleted from the F00.120R genome prior to the 7th passage in cell culture. In addition, genes 116-121 were present in It1303 and in other isolates of reindeer and bovine PCPV isolated in Finland during the years 2005-2010. These results indicate that the genome of reindeer PCPV is about 140 kbp in length and has 137 genes instead of previously estimated length of 135 kbp and 131 genes; it contains homologues of all known ORFV genes and this analysis further reinforces the close genetic relationship between PCPV and ORFV

Digitaalinen muovaustyökalu ja 3D-tulostaminen taiteen tuottamisessa

Insinöörityön tarkoitus oli selvittää digitaalisen muovaustyökalun ja 3D-tulostuksen mahdollisuuksia ja käytännöllisyyttä taiteen tuottamisessa. Käyttötestauksessa oli mukana kuvanveistäjä, joka on erikoistunut metallivalutöihin ja jolla ei ollut aikaisempaa kokemusta 3D-mallinnuksesta. Teknologinen edistyminen tietokone- ja 3D-tulostusteknologiassa, niiden yleistyminen ja halpeneminen, on mahdollistanut harrastustason tulostamisen kotioloissa ja ammattitason tulostamisen esimerkiksi auto-, lentoteollisuudelle sekä terveydenhuollolle. Tämä avaa uusia luovia käyttötarkoituksia 3D-tulostukselle. Projektissa luotiin digitaalinen veistos Sculptris-muotoiluohjelmalla, ja työ tulostettiin muovista oppilaitoksen omalla 3D-tulostimella. Työnkulku, ongelmat, mahdollisuudet, ja mietteet dokumentoitiin, ja ne sisällytettiin lopulliseen arviointiin. Tulostetussa patsaassa ilmeni jonkin verran virheitä tulostusprosessin teknisten ongelmien vuoksi, mutta patsas oli muilta osin onnistunut. Digitaalinen muotoilu- ja 3D-tulostustekniikka luovat uusia mahdollisuuksia taiteen tuottamiseen ja voivat olla apuna taiteilijoille varsinkin töiden suunnittelussa ja metallivalutöissä. Ammattikäyttöön tarkoitetut nopeat ja tarkat tulostimet ovat vielä liian kalliita, mutta niiden käyttö taiteen tuottamisessa varmasti lisääntyy lähitulevaisuudessa

Transnational Kinship Ties and Welfare State Resistance

In contemporary kinship studies, state and family appear to be closely related. This forceful affiliation is a result of complex historical and social contestation where reproduction, socialization and ties of affection are not only naturally intimate but also politically public. Anthropologists have much to comment on this; alas, their educated and comparative observations often go unnoticed. The speakers in this debate more often seem to represent the social policy  rofessions, state bureaucracies and legal expertise.   European immigration politics generally are illustrative. The tightening of residence permits and the control of particular migration groups seem to be  emergent trends. Though state policies and the rationales behind them are often promoted as protection against threats like human trafficking or terrorism, applications of this institutional thinking are largely interpreted as acts of discrimination by the migrants or family members involved. Furthermore, less attention has been paid to how the state classifies families and family members, something which is reproducing rather unrealistic ideals and norms for families and kin groups in general. In fact, the criteria of family relatedness for immigrant families differ from those very practices which are assumed to define family within most welfare states in Europe. In this context, I argue, more comparative, anthropologically-informed analysis would be useful

Circulating tumor DNA (ctDNA) in precision oncology of ovarian cancer

Non peer reviewe

POIBM : batch correction of heterogeneous RNA-seq datasets through latent sample matching

Motivation: RNA sequencing and other high-throughput technologies are essential in understanding complex diseases, such as cancers, but are susceptible to technical factors manifesting as patterns in the measurements. These batch patterns hinder the discovery of biologically relevant patterns. Unbiased batch effect correction in heterogeneous populations currently requires special experimental designs or phenotypic labels, which are not readily available for patient samples in existing datasets. Results: We present POIBM, an RNA-seq batch correction method, which learns virtual reference samples directly from the data. We use a breast cancer cell line dataset to show that POIBM exceeds or matches the performance of previous methods, while being blind to the phenotypes. Further, we analyze The Cancer Genome Atlas RNA-seq data to show that batch effects plague many cancer types; POIBM effectively discovers the true replicates in stomach adenocarcinoma; and integrating the corrected data in endometrial carcinoma improves cancer subtyping.Peer reviewe

PerPAS: Topology-Based Single Sample Pathway Analysis Method

Identification of intracellular pathways that play key roles in cancer progression and drug resistance is a prerequisite for developing targeted cancer treatments. The era of personalized medicine calls for computational methods that can function with one sample or very small set of samples. Developing such methods is challenging because standard statistical approaches pose several limiting assumptions, such as number of samples, that prevent their application when n approaches to one. We have developed a novel pathway analysis method called PerPAS to estimate pathway activity at a single sample level by integrating pathway topology and transcriptomics data. In addition, PerPAS is able to identify altered pathways between cancer and control samples as well as to identify key nodes that contribute to the pathway activity. In our case study using breast cancer data, we show that PerPAS can identify highly altered pathways that are associated with patient survival. PerPAS identified four pathways that were associated with patient survival and were successfully validated in three independent breast cancer cohorts. In comparison to two other pathway analysis methods that function at a single sample level, PerPAS had superior performance in both synthetic and breast cancer expression datasets. PerPAS is a free R package (http://csbi.ltdk.helsinki.fi/pub/czliu/perpas/).Peer reviewe

Levelling aeromagnetic survey data without the need for tie-lines

A new methodology that levels airborne magnetic data without orthogonal tie-lines is presented in this study. The technique utilizes the low-wavenumber content of the flight-line data to construct a smooth representation of the regional field at a scale appropriate to the line lengths of the survey. Levelling errors are then calculated between the raw flight-line data and the derived regional field through a least squares approach. Minimizing the magnitude of the error, with a first-degree error function, results in significant improvements to the unlevelled data. The technique is tested and demonstrated using three recent airborne surveys

Amorfisten disakkaridien molekylaarisen mobiliteetin tutkiminen

In pharmaceuticals amorphous state can be obtained either intentionally or unintentionally. Intentional production is used, for example, to improve the dissolution of poorly soluble compounds, to stabilize the structure of proteins, or to improve the mechanical properties of excipients (e.g., lactose). Unintentional introduction of amorphous phases can result from general manufacturing procedures of pharmaceuticals, such as coating, granulation, drying, milling, and compression. The presence of amorphous regions, even in small quantities, can exhibit a significant influence on the physical and chemical stability of pharmaceutical products. Molecular mobility in formulation with amorphous content is believed to be the key factor of their stability. Therefore, evaluating of molecular mobility is an important step in pharmaceutical product development. The aim of this study was to estimate molecular motions in amorphous disaccharides using calorimetric approach at temperatures below the glass transition temperature (Tg), where relaxation process is very slow as compared to the time of experiment. When temperature is low enough, the initial relaxation time parameter (œÑi) can be used as an estimate for relaxation process on the timescale of pharmaceutical product shelf life. The results of the present study revealed similar trend in stability of amorphous forms for the disaccharides (sucrose experiencing the fastest structural relaxation), which can be assumed on the basis of Tg alone, where higher Tg would result in more stable glassy state (Tg of sucrose is the lowest). Storage temperature of Tg - 55oC or lower would suffice for amorphous trehalose, melibiose and cellobiose to achieve at least 2 year's relaxation time, while for sucrose the temperature is Tg - 70oC. Fragility has been used as a helpful mean for classifying amorphous materials. All the compounds can be classified as fragile. Fragility ranking in the present study contains some degree of uncertainty, while 3 different approaches revealed somewhat different results for ranking the disaccharides. The variation in the results can be attributed to the overall sensitivity of DSC. The method described in the present study is quite difficult to apply without supportive information from other techniques. The results, obtained with the method, are very dependent on the slope in plotting ln q vs. 1/Tg, and even small fluctuations in the estimation can lead to different fragility values and consequently to different relaxation times. However, the final results reveal values for relaxation times well below Tg, which are in reasonable agreement with modern theoretical understanding of glassy state dynamics.Lääkevalmistuksessa amorfista muotoa käytetään, esimerkiksi parantamaan liukoisuusnopeutta, stabiloimaan proteiinien rakennetta säilytyksen aikana ja parantamaan apuaineiden käsiteltävyyttä. Aine voi muuttua osittain tai kokonaan amorfiseen muotoon monen tavallisen lääkevalmistusprosessin, kuten kalvopäällystyksen, rakeistuksen, kuivauksen, jauhatuksen ja puristuksen seurauksena. Amorfisten alueiden läsnä ollessa aineen fysikaaliset ominaisuudet muuttuvat merkittävästi, mikä vaikuttaa lääkevalmisteen fysikaaliseen ja kemialliseen säilyvyyteen. Amorfisen aineen molekyylimobiliteetti on tärkeä lasitilan pysyvyyttä kuvaava parametri. Tämän vuoksi on tärkeää arvioida se lääkekoostumussuunnittelun alkuvaiheessa. Tutkimuksen tavoitteena oli määrittää differentiaalista pyyhkäisykalorimetriaa (DSC) apuna käyttäen neljän amorfisen disakkaridin molekyylimobiliteettia alhaisissa (verrattuna Tg:seen) lämpötiloissa. Relaksaatio tapahtuu tutkituissa lämpötiloissa hyvin hitaasti. Niin hitaasti, että alkurelaksaationopeutta voidaan käyttää hyväksi relaksaatioprosessin kokonaisuuden arvioinnissa. Tutkimuksessa käytetyillä disakkarideilla on todettu olevan samanlainen relaksaatiotaipumus, kun tätä arvioidaan lasisiirtymälämpötilan (Tg) -arvon perusteella. Korkeamman Tg:n omaavilla yhdisteillä lasitila on tavallisesti pysyvämpi. Sakkaroosin Tg on alhaisin tutkimuksessa käytetyistä disakkarideista. Amorfisella mellibioosilla, trehaloosilla ja selibioosilla on kahden vuoden relaksaatioaika säilytettäessä lämpötilassa Tg-55oC. Amorfisen sakkaroosin kohdalla tarvitaan alhaisempi säilytyslämpötila (Tg-70oC) samansuuruisen relaksaationopeuden saavuttamiseen. Fragiliteettia voidaan käyttää amorfisten aineiden luokitteluun ja vertailuun. Kaikki tutkimuksessa käytetyt disakkaridit voidaan luokitella hauraiksi yhdisteiksi. Fragiliteetin arvot laskettiin kolmen eri menetelmän avulla. Tuloksina saatiin kolme jossain määrin erilaista fragiliteettijärjestystä. Tulosten epäyhtenevyys johtuu ainakin osittain DSC -laitteiston ominaisuuksista. Tutkimuksessa käytettyä menetelmää on vaikea soveltaa ilman muiden menetelmien tukitietoja. Tg:n riippuvuudella lämmitysnopeudesta on tärkeä merkitys, tästä syystä pienikin poikkeama ko. arvoissa saa aikaan merkittävät muutokset lopputulokseen. Tästä huolimatta tutkimuksen lopputuloksena saatujen relaksaatioajan arvojen voidaan todeta olevan yhdenmukaisia aikaisimpien tutkimuksien kanssa