Finding and characterizing Partially Methylated Domains in human haematopoietic cells

DNA cytosine methylation has been demonstrated to be a central epigenetic modification that has essential roles in a myriad of cellular processes. Some examples of these include gene regulation, DNA-protein interactions, cellular differentiation, X-inactivation, maintenance of genome integrity by suppressing transposable elements and viruses, embryogenesis, genomic imprinting and tumourigenesis. This list is increasingly growing thanks to recent advances in genome-wide technologies, like Whole Genome Bisulfite Sequencing (WGBS-Seq). The development of this technology in research has allowed the identification of new features of the DNA methylation landscape that was not possible using previous technologies, like Partially Methylated Domains (PMDs). PMDs have been found in several cell lines, as well as in both healthy and cancer primary samples. They have been described as regions with high variability in methylation levels across individual CpG sites and intermediate methylation levels on average with respect to the genome. Here, we performed an extensive search of PMDs in a big dataset of different haematopoietic primary cells from both myeloid and lymphoid lineages. We found and characterized significant PMDs in plasma B cells, confirming that PMDs are a phenomenon that is restricted to certain differentiated cells. Additionally, we found loci aberrantly hypomethylated in a myeloma sample which overlapped with plasma B cell PMDs. Genome-wide comparison of the myeloma and plasma B cell sample revealed that this is probably also the case for other loci.

Bat assemblages in the Nietoperek bat reserve (Western Poland) and their conservation strategies

Międzyrzecz Fortified Front, were Natura 2000 site PLH080003 Nietoperek is situated, was built by the Germans in the 1930s and during the World War II. It is composed of above ground bunkers connected by underground tunnels of ca. 32 km total length. Nietoperek is the eighth largest bats hibernation site in EU. Monthly censuses were carried out from October to April during three consecutive winter seasons (2011/12 – 2013/14) in area covering ca. 30% of the undergrounds. The aims of the study were: (1) to describe changes in numbers of each species in the course of hibernation season, (2) to suggest deadlines for counting particular bat species to obtain maximal numbers and (3) to describe negative impact of tourism on hibernating bats. The results will be useful for restriction of winter tourism in Nietoperek. The total number of bats observed during the study was 37869 individuals of 9 species. Because of difficulties in distinguishing without handling M. mystacinus and M. brandtii were treated as one group. M. myotis constituted from 53% (first season) to 64% (last season) of all hibernating bats. The maximal numbers of individuals were observed in November (first two seasons) and in December (third season). M. daubentonii constituted from 27% (first season) to 21% (last season) and M. nattereri from 10% (first season) to 11% (second season) of all bats. During the three seasons the maximal numbers of M. daubentonii and M. nattereri were observed in November and December respectively. B. barbastellus and P. auritus constituted from 4% (first season) to 2% (last season) of the multi species colony. The maximal numbers of B. barbastellus were observed in January and P. auritus in January (first and second seasons) and in December (third season). Results indicated that the best period for counting maximal numbers of M. myotis and M. daubentonii is November, for M. nattereri is December and for B. barbastellus and P. auritus is January. The study undertaken in the part visited by tourists in winter (total length of 900 m) proved negative effect caused by human disturbance with 23% decline of total bat numbers.

Enhanced capture of healthcare-related harms and injuries in the 11th revision of the International Classification of Diseases (ICD-11).

The World Health Organization (WHO) plans to submit the 11th revision of the International Classification of Diseases (ICD) to the World Health Assembly in 2018. The WHO is working toward a revised classification system that has an enhanced ability to capture health concepts in a manner that reflects current scientific evidence and that is compatible with contemporary information systems. In this paper, we present recommendations made to the WHO by the ICD revision's Quality and Safety Topic Advisory Group (Q&S TAG) for a new conceptual approach to capturing healthcare-related harms and injuries in ICD-coded data. The Q&S TAG has grouped causes of healthcare-related harm and injuries into four categories that relate to the source of the event: (a) medications and substances, (b) procedures, (c) devices and (d) other aspects of care. Under the proposed multiple coding approach, one of these sources of harm must be coded as part of a cluster of three codes to depict, respectively, a healthcare activity as a 'source' of harm, a 'mode or mechanism' of harm and a consequence of the event summarized by these codes (i.e. injury or harm). Use of this framework depends on the implementation of a new and potentially powerful code-clustering mechanism in ICD-11. This new framework for coding healthcare-related harm has great potential to improve the clinical detail of adverse event descriptions, and the overall quality of coded health data.

Keeping the balance? Management of oxidative stress, body mass and reproduction under energetic constraints by dispersing and philopatric collared flycatchers.

Dispersal, i.e. individual movement between breeding sites, is a key process for metapopulation dynamics and gene flow. Its success can be modulated by phenotypic differences between dispersing and philopatric individuals, or dispersal syndromes. However, the environmental (external) and physiological (internal) constraints underlying such syndromes remain poorly known. This project aimed at clarifying the impact of environmental variation and oxidative constraints, linked to the reactive oxygen species produced during respiration, on phenotypes associated to dispersal in a passerine bird, the collared flycatcher Ficedula albicollis. Energetic demand was experimentally (i) increased through a wing load manipulation or (ii) relieved through food supplementation. The oxidative balance of breeding flycatchers was influenced by complex interactions of dispersal status and extrinsic factors (breeding density, year, experimental treatments). Interestingly, antioxidant capacity was influenced both by permanent individual differences and by food availability, whereas measures of pro-oxidants were highly variables within individuals. Environmental variation and energetic constraints also modulated the differences in reproduction associated with dispersal: dispersing and philopatric birds differ in their management of the oxidative balance when it is competing with reproductive investment. This thesis highlights that reaction norms, rather than fixed differences, often shape traits associated to dispersal. ----- Le déplacement d'un individu entre sites de reproduction, ou dispersion, est un processus clé pour la dynamique des métapopulations et les flux de gènes. Son succès peut être modulé par des différences de phénotype, ou syndromes de dispersion. Cependant, les contraintes environnementales et physiologiques qui sous-tendent ces syndromes restent mal connues. Ce projet vise à clarifier l'impact des variations environnementales et des contraintes oxydatives (liées aux espèces réactives de l'oxygène produites durant la respiration) sur les phénotypes associés à la dispersion chez un passereau, le gobemouche à collier Ficedula albicollis. La demande énergétique a été expérimentalement (i) augmentée en manipulant la surface alaire ou (ii) diminuée par une supplémentation en nourriture. L'équilibre oxydo-réducteur des gobemouches en reproduction est influencé par des interactions complexes entre statut de dispersion et facteurs extrinsèques (densité de couples reproducteurs, année, traitement expérimental). La capacité antioxydante dépend principalement de différences permanentes entre individus, alors que les pro-oxydants présentent de grandes variations intra-individu. Environnement et contraintes énergétiques modulent aussi les différences de reproduction liées à la dispersion : les oiseaux dispersants et philopatriques diffèrent dans leur gestion de l'équilibre oxydo-réducteur lorsqu'il est en compétition avec l'investissement reproducteur. Ce travail souligne que les traits associés à la dispersion sont souvent déterminés par des normes de réaction à l'environnement et non des différences fixées entre individus.

Mitotic regulation by Polo-like kinase 1 and the Chromosomal Passenger Complex

During mitosis, the duplicated genome must be accurately divided between two daughter cells. Polo-like kinase 1 (Plk1) and Aurora B kinase, together with its binding partners Incenp, Survivin and Borealin (chromosomal passenger complex, CPC), have key roles in coordinating mitotic events. The accuracy of cell division is safeguarded by a signaling cascade termed the mitotic spindle checkpoint (SC), which ensures that chromosomes are not physically separated before correct bipolar attachments have been formed between kinetochores and spindle microtubules (MT). An inhibitory “wait anaphase” signal, which delays chromosome separation (anaphase onset), is created at individual kinetochores and broadcasted throughout the cell in response to lack of kinetochore-microtubule (kMT) attachment or proper interkinetochore tension. It is believed that the fast turnover of SC molecules at kinetochores contributes to the cell’s ability to produce this signal and enables rapid responses to changing cellular conditions. Kinetochores that lack MT attachment and tension express a certain phosphoepitope called the 3F3/2 phosphoepitope, which has been linked to SC signaling. In the experimental part, we investigated the regulation of the 3F3/2 phosphoepitope, analyzed whether CPC molecules turn over at centromeres, and dissected the mitotic roles of the CPC using a microinjection technique that allowed precise temporal control over its function. We found that the kinetochore 3F3/2 phosphoepitope is created by Plk1, and that CPC proteins exhibit constant exchange at centromeres. Moreover, we found that CPC function is necessary in the regulation of chromatid movements and spindle morphology in anaphase. In summary, we identified new functions of key mitotic regulators Plk1 and CPC, and provided insighs into the coordination of mitotic events.

Clinically occult metastases in patients with cutaneous melanoma. Detection with sentinel lymph node biopsy and whole body positron emission tomography

Objective: The aim of this study was to investigate the use of sentinel lymph node biopsy (SLNB) and whole body positron emission tomography (PET), with emphasis on surgical treatment and prognosis, in the detection of clinically occult metastases in patients with clinically localized cutaneous melanoma. Patients and methods: The study population consisted of 1255 patients with clinical stage I–II cutaneous melanoma, operated at Turku University Hospital between 1983 and 2007. 334 patients underwent SLNB and they were compared to 921 retrospective patients. A subgroup of 30 symptom-free patients with high risk melanoma underwent prospectively whole body PET 6–24 months postoperatively. Results: Overall, the disease-specific survival rate was 84.4 % at five years. Sex, Breslow thickness, age and nodal status were independent prognostic factors for survival. SLNB revealed occult nodal metastases in 17 % of the patients. There was no significant difference in disease-specific overall survival between SLNB patients and controls, but the nodal disease-free time was significantly longer suggesting better local control after SLNB and subsequent completion lymph node dissection. The followup time was different between the study cohorts and initial surgery was performed during different time periods. SLNB detected micrometastases in seven of 155 patients (4.5 %) with thin T1 primary melanoma and in four of 25 patients (16 %) with head and neck melanoma. In six of 30 asymptomatic patients with high risk melanoma (20 %), whole body PET detected occult distant metastases. Conclusion: Both SLNB and whole body PET were reliable methods to detect clinically occult metastases in patients with cutaneous melanoma. This upstaging altered the treatment in each case.

Neurophysiologic diagnosis, clinical symptoms and neuropathologic findings in polyneuropathies

Tausta: Polyneuropatia (PNP) on ääreishermoston sairaus, joka aiheuttaa laaja-alaisia, yleensä symmetrisiä vaurioita ääreishermostossa. PNP:aan johtavia syitä on satoja. Tavoitteet: Löytää parhaat neurofysiologiset menetelmät uremian, myelooman hoidossa käytettävän talidomidin sekä Fabryn taudin aiheuttaman PNP:n diagnosoimiseksi. Fabryn taudissa tutkin lisäksi ohutsäieneuropatian aiheuttamia neuropatologisia löydöksiä iholta otetusta koepalasta. Tutkimuksissa kartoitettiin lisäksi PNP:n aiheuttamien subjektiivisten oireiden korrelaatio neurofysiologisten ja neuropatologisten löydösten kanssa. Munuaisten vajaatoimintaa sairastavilla potilailla tavoitteena oli tutkia dialyysihoidon tehon vaikutusta autonomisen hermoston toimintaan sekä yhden dialyysikerran vaikutusta neurofysiologisiin löydöksiin. Aineisto ja menetelmät: I: Tutkittiin 21 uremiapotilaan sensoristen ja motoristen hermojen vasteet, värinä- sekä lämpötuntokynnykset ennen ja jälkeen hemodialyysin. Subjektiiviset PNP oireet kartoitettiin PNP oireita kysyvillä kaavakkeella. II:12 talidomidi hoitoa saavaa myeloomapotilasta, tutkimuksen menetelmät olivat samat kuin tutkimuksessa I. III: 12 Fabryn tautia sairastavaa potilasta, edellä mainittujen neurofysiologisten tutkimusten lisäksi potilailta otettiin ihobiopsia säären alueelta. Ihobiopsiasta laskettiin ohuiden hermosyiden määrä koepalan värjäyksen jälkeen. Subjektiiviset PNP oireet kartoitettiin kyselykaavakkeella. Sydämen sykevaihtelu tutkittiin levossa taajuustason analyysillä. IV: 32 uremiapotilaan autonomisen hermoston toimintaa tutkittiin sydämen sykevaihtelun aikatason analysillä, paksujen myelinoituneiden säikeiden toimintaa tutkittiin perifeeristen sensoristen hermojen mittauksilla toistetusti noin 2.9 vuoden aikana. Tulokset: Ureemisen PNP:n diagnostiikassa herkimmät tutkimukset ovat F-aaltojen parametrit alaraajojen motorisista hermoista, värinätuntokynnys alaraajoista sekä suralishermon amplitudi. Positiiviset PNP oireet uremiassa korreloivat värinätunto-kynnyksen sekä sensoristen hermojen neurografialöydösten kanssa. Neurofysiologisten tutkimusten ajankohdalla dialyysiajankohtaan nähden ei ole merkitystä. Talidomidi-PNP on pääasiassa sensorinen, mutta motoriset syyt ovat lievästi vaurioituneet. Talidomidi PNP:ssa subjektiiviset oireet korreloivat huonosti neurofysiologisten löydösten kanssa. Fabryn taudissa naisilla on oletettua enemmän ohutsäieneuropatian aiheuttamia oireita ja löydöksiä. Paksujen säikeiden löydöksiä ei tullut esiin. Ohutsäieneuropatian diagnostiikassa ihobiopsia ja kvantitatiiviset tuntokynnysmittaustestit täydentävät toisiaan. Tehokas dialyysi parantaa autonomisen hermoston toimintaa uremiapotilailla. Päätelmät: Erityyppisten polyneuropatioiden diagnostiikassa pitää etukäteen valita PNP tyypille oikeat tutkimusmenetelmät raskaiden tutkimuspatterien vähentämiseksi sekä diagnostiikan parantamiseksi. PNP:n aiheuttamat oireet ja kliiniset löydökset pitää aina tutkia, mutta yksin ne eivät ole herkkiä PNP:n diagnostiikassa.

Monomer conversion of composite dental resins photoactivated by a halogen lamp and a LED: a FT-Raman spectroscopy study

Eighteen circular blocks of resins cured either by a LED or a halogen lamp (20, 40 and 60 s), had their top (T) and bottom (B) surfaces studied using a FT-Raman spectrometer. Systematic changes in the intensity of the methacrylate C=C stretching mode at 1638 cm-1 as a function of exposure duration were observed. The calculated degree of conversion (DC) ranged from 45.0% (B) to 52.0% (T) and from 49.0% (B) to 55.0% (T) for the LED and halogen lamp, respectively. LED and halogen light produced similar DC values with 40 and 60 s of irradiation.

Free Flap Monitoring. Using Tissue Oxygen Measurement and Positron Emission Tomography

Aims:This study was carried out to evaluate the feasibility of two different methods to determine free flap perfusion in cancer patients undergoing major reconstructive surgery. The hypotheses was that low perfusion in the flap is associated with flap complications. Patients and methods: Between August 2002 and June 2008 at the Department of Otorhinolaryngology – Head and Neck Surgery, Department of Surgery, and at the PET Centre, Turku, 30 consecutive patients with 32 free flaps were included in this study. The perfusion of the free microvascular flaps was assessed with positron emission tomography (PET) and radioactive water ([¹⁵O] H₂O) in 40 radiowater injections in 33 PET studies. Furthermore, 24 free flaps were monitored with a continuous tissue oxygen measurement using flexible polarographic catheters for an average of three postoperative days. Results: Of the 17 patients operated on for head and neck (HN) cancer and reconstructed with 18 free flaps, three re-operations were carried out due to poor tissue oxygenation as indicated by p_tiO₂ monitoring results and three other patients were reoperated on for postoperative hematomas in the operated area. Blood perfusion assessed with PET (BF_PET) was above 2.0 mL / min / 100 g in all flaps and a low flap-to-muscle BFPET ratio appeared to correlate with poor survival of the flap. Survival in this group of HN cancer patients was 9.0 months (median, range 2.4-34.2) after a median follow-up of 11.9 months (range 1.0-61.0 months). Seven HN patients of this group are alive without any sign of recurrence and one patient has died of other causes. All of the 13 breast reconstruction patients included in the study are alive and free of disease at a median follow-up time of 27.4 months (range 13.9-35.7 months). Re-explorations were carried out in three patients due data provided by p_tiO₂ monitoring and one re-exploration was avoided on the basis of adequate blood perfusion assessed with PET. Two patients had donorsite morbidity and 3 patients had partial flap necrosis or fat necrosis. There were no total flap losses. Conclusions: P_tiO₂ monitoring is a feasible method of free flap monitoring when flap temperature is monitored and maintained close to the core temperature. When other monitoring methods give controversial results or are unavailable, [₁₅O] H₂O PET technique is feasible in the evaluation of the perfusion of the newly reconstructed free flaps.

Phytochemical study, antioxidant and antibacterial activities of Stemodia maritima

Stemodinol, a new natural compound, together with known compounds including jaceidin, stemodin, stemodinoside B, isocrenatoside, verbascoside, crenatoside, and isoverbascoside, were isolated from Stemodia maritima Linn. The antioxidant (DPPH method) and antimicrobial activities of stemodin, stemodinoside B, and crenatoside were investigated. Among the components tested, only crenatoside isolated from the roots showed a high antioxidant power. Stemodin and stemodinoside B exhibited antibacterial activities.

Sensitive spectrophotometric determination of lansoprazole in pharmaceuticals using ceric ammonium sulphate based on redox and complex formation reactions

Two simple sensitive and cost-effective spectrophotometric methods are described for the determination of lansoprazole (LPZ) in bulk drug and in capsules using ceric ammonium sulphate (CAS), iron (II), orthophenanthroline and thiocyanate as reagents. In both methods, an acidic solution of lansoprazole is treated with a measured excess of CAS followed by the determination of unreacted oxidant by two procedures involving different reaction schemes. The first method involves the reduction of residual oxidant by a known amount of iron(II), and the unreacted iron(II) is complexed with orthophenanthroline at a raised pH, and the absorbance of the resulting complex measured at 510 nm (method A). In the second method, the unreacted CAS is reduced by excess of iron (II), and the resulting iron (III) is complexed with thiocyanate in the acid medium and the absorbance of the complex measured at 470 nm (method B). In both methods, the amount CAS reacted corresponds to the amount of LPZ. In method A, the absorbance is found to increase linearly with the concentration of LPZ where as in method B a linear decrease in absorbance occurs. The systems obey Beer's law for 2.5-30 and 2.5-25 µg mL-1 for method A and method B, respectively, and the corresponding molar absorptivity values are 8.1×10³ and 1.5×10(4) L mol-1cm-1 . The methods were successfully applied to the determination of LPZ in capsules and the results tallied well with the label claim. No interference was observed from the concomitant substances normally added to capsules.

Spectrophotometric determination of lansoprazole in pharmaceuticals using bromate-bromide mixture based on redox and complexation reactions

Two sensitive spectrophotometric methods are described for the determination of lansoprazole (LPZ) in bulk drug and in capsule formulation. The methods are based on the oxidation of lansoprazole by insitu generated bromine followed by determination of unreacted bromine by two different reaction schemes. In one procedure (method A), the residual bromine is treated with excess of iron (II), and the resulting iron (III) is complexed with thiocyanate and measured at 470 nm. The second approach (method B) involves treating the unreacted bromine with a measured excess of iron (II) and remaining iron (II) is complexed with orthophenanthroline at a raised pH, and measured at 510 nm. In both methods, the amount of bromine reacted corresponds to the amount of LPZ. The experimental conditions were optimized. In method A, the absorbance is found to decrease linearly with the concentration of LPZ (r = -0.9986) where as in the method B a linear increase in absorbance occurs (r = 0.9986) The systems obey Beer's law for 0.5-4.0 and 0.5-6.0 µg mL-1 for method A and method B, respectively. The calculated molar absorptivity values are 3.97µ10(4) and 3.07µ10(4) L mol-1cm-1 for method A and method B, respectively, and the corresponding Sandell sensitivity values are 0.0039 and 0.0013 µg cm-2. The limit of detection (LOD) and quantification (LOQ) are also reported for both methods. Intra-day and inter-day precision, and accuracy of the methods were established as per the current ICH guidelines. The methods were successfully applied to the determination of LPZ in capsules and the results tallied well with the label claim and the results were statistically compared with those of a reference method by applying the Student's t-test and F-test. No interference was observed from the concomitant substances normally added to capsules. The accuracy and validity of the methods were further ascertained by performing recovery experiments via standard-addition method.

Cerimetric determination of simvastatin in pharmaceuticals based on redox and complex formation reactions

Two sensitive spectrophotometric methods are described for the determination of simvastatin (SMT) in bulk drug and in tablets. The methods are based on the oxidation of SMT by a measured excess of cerium (IV) in acid medium followed by determination of unreacted oxidant by two different reaction schemes. In one procedure (method A), the residual cerium (IV) is reacted with a fixed concentration of ferroin and the increase in absorbance is measured at 510 nm. The second approach (method B) involves the reduction of the unreacted cerium (IV) with a fixed quantity of iron (II), and the resulting iron (III) is complexed with thiocyanate and the absorbance measured at 470 nm. In both methods, the amount of cerium (IV) reacted corresponds to SMT concentration. The experimental conditions for both methods were optimized. In method A, the absorbance is found to increase linearly with SMT concentration (r = 0.9995) whereas in method B, the same decreased (r = -0.9943). The systems obey Beer's law for 0.6-7.5 and 0.5-5.0 µg mL-1 for method A and method B, respectively. The calculated molar absorptivity values are 2.7 X 10(4) and 1.06 X 10(5) Lmol-1 cm-1, respectively; and the corresponding sandel sensitivity values are 0.0153 and 0.0039µg cm-2, respectively. The limit of detection (LOD) and quantification (LOQ) are reported for both methods. Intra-day and inter-day precision, and accuracy of the methods were established as per the current ICH guidelines. The methods were successfully applied to the determination of SMT in tablets and the results were statistically compared with those of the reference method by applying the Student's t-test and F-test. No interference was observed from the common excipients added to tablets. The accuracy and validity of the methods were further ascertained by performing recovery experiments via standard addition procedure.

Spectrophotometric determination of ofloxacin in pharmaceuticals and human urine

Three simple and sensitive spectrophotometric methods are described for the determination of ofloxacin (OFX) in pharmaceuticals and in spiked human urine. First and second methods are based on the measurement of absorbance of OFX in 0.1 M HCl at 293 nm (method A) and 0.1 M NaOH at 287 nm, respectively. The third method is based on the measurement of 2:1 complex formed between OFX and iron(III) in H2SO4 medium, the complex peaking at 420 nm (method C). The optimum conditions for all the three methods are optimized. Beer's law is obeyed over the ranges 0.63-12.5 using method A and method B, and 10-120 µg mL-1 using method C. The apparent molar absorptivity values are calculated to be 3.5 × 10(4), 2.76 × 10(4) and 2.51 × 10³ L mol-1cm-1 for method A, method B and method C, respectively. The Sandell sensitivity, limit of detection (LOD) and limit quantification (LOQ) values are also reported. All the methods were validated in accordance with current ICH guidelines. The developed methods were employed with high degree of precision and accuracy for the estimation of total drug content in commercial tablet formulations of DOX. The results obtained from human spiked urine are satisfactory and recovery values are in the range 95.5-106.6%.

Sensitive spectrophotometric determination of lamotrigine in bulk drug and pharmaceutical formulations using bromocresol green

Two new, simple, rapid and reproducible spectrophotometric methods have been developed for the determination of lamotrigine (LMT) both in pure form and in its tablets. The first method (method A) is based on the formation of a colored ion-pair complex (1:1 drug/dye) of LMT with bromocresol green (BCG) at pH 5.02±0.01 and extraction of the complex into dichloromethane followed by the measurement of the yellow ion-pair complex at 410 nm. In the second (method B), the drug-dye ion-pair complex was dissolved in ethanolic potassium hydroxide and the resulting base form of the dye was measured at 620 nm. Beer's law was obeyed in the concentration range of 1.5-15 µg mL-1 and 0.5-5.0 µg mL-1 for method A and method B, respectively, and the corresponding molar absorptivity values are 1.6932 x 10(4) and 3.748 x 10(4) L mol-1cm-1. The Sandell sensitivity values are 0.0151 and 0.0068 µg cm-2 for method A and method B, respectively. The stoichiometry of the ion-pair complex formed between the dug and dye (1:1) was determined by Job's continuous variations method and the stability constant of the complex was also calculated. The proposed methods were applied successfully for the determination of drug in commercial tablets.