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Crystal Structure of Exopolyphosphatase from Leishmania tarentolae : Structural Insights into a Kinetoplastid Polyphosphatase
No full textExopolyphosphatases (PPXs) are metal-dependent phosphoesterases that catalyze the stepwise removal of terminal phosphate residues from linear polyphosphate (polyP), a reaction fundamental to phosphate homeostasis in a wide range of organisms. This enzymatic activity reflects their conserved and central role in maintaining intracellular phosphate balance. In kinetoplastid parasites such as Leishmania and Trypanosoma, PPX has been proposed to participate not only in phosphate turnover also to the cellular adaptation to stress-related conditions. These include the regulation of osmotic balance under hypoosmotic conditions, the enhancement of phosphate import through feedback activation of the Pho91 transporter, the prevention of ionic imbalance during salt stress, and the provision of buffering capacity under elevated temperatures. However, despite these proposed roles, no structural data for kinetoplastid PPXs have previously been available. To date, the only reported crystal structure of a DHH-type exopolyphosphatase is that of ScPPX1 from Saccharomyces cerevisiae.
This thesis addresses the existing structural gap by presenting the crystal structure of Leishmania tarentolae exopolyphosphatase (LtPPX), the first such structure reported from a kinetoplastid parasite. Two crystal forms were determined: an apo structure at 2.7 Å resolution and a citrate bound structure at 1.65 Å. Both conformations adopt a closed interdomain arrangement characteristic of the DHH superfamily, with no significant rigid body displacement between domains. In the citrate bound structure, the ligand is tightly coordinated within the active site through a network of direct and water mediated hydrogen bonds involving conserved catalytic residues. The citrate molecule occupies the phosphate binding groove spanning from the PT to PE2 sites, as previously defined in the yeast homolog ScPPX1, offering insight into how the enzyme may accommodate polyphosphate like ligands.
Crystals consistently form under citrate and Tacsimate® containing conditions, suggesting that citrate binding may stabilize a more ordered and less flexible conformation that promotes lattice formation. Based on its positioning and interactions, citrate is proposed here as a potential competitive inhibitor of PPX. However, additional biochemical assays are required to support this hypothesis. In both the apo and citrate bound structures, a second divalent metal ion observed in the ScPPX1 tripolyphosphate complex is absent. This observation supports a model in which the second metal ion is recruited only upon substrate binding
Modified fast UHPLC method for quantification of soil amino sugars – improved sensitivity compared to the GC method
No full textSoil microbial necromass analysis through measurement of soil amino sugars is a common technique in soil science. Traditionally, the measurement is performed by aldononitrile acetate derivatization and gas chromatographic (GC) analysis. Long pretreatment times and high limits of quantification (LOQ) have led to the development of faster and more sensitive high performance liquid chromatography (HPLC) methods. In this study, we enhanced a previously discovered ortho-phthalaldehyde derivatization and HPLC separation method for soil samples by converting it to work with ultra-high performance liquid chromatography (UHPLC) column and equipment. We also added an internal standard to control for pretreatment variation. In addition, we explored the factors that must be optimized to establish the method with alternative equipment, and the differences in the results between the UHPLC and the GC methods. We found that the UHPLC method produced similar results to the GC methods with glucosamine and galactosamine, while the performance of the UHPLC method was significantly better in determining muramic acid, especially at low concentrations. Mannosamine results were not correlated between the methods. The speed of the UHPLC analysis was much higher and LOQ much lower compared to the GC method. In the majority of soil samples (13 out of 18), muramic acid concentrations were found to be below LOQ for the GC method, but clearly detectable with the developed UHPLC method. It was found that the UHPLC method is at least twice as fast as the GC method and requires only few of the hazardous chemicals traditionally used in amino sugar analysis. The UHPLC method also improved on the HPLC method by consuming only 1/5th of the total solvent and by reducing analysis time from 30 to 18 min.Peer reviewe
Tehokkaan kuvien luokittelun viitekehys yhteiskuntatieteellisessä tutkimuksessa : korkean luokkasisäisen visuaalisen vaihtelun haasteen ratkaiseminen
No full textThis article-based dissertation addresses a fundamental challenge in computational social science: how to accurately classify political imagery when images within the same theoretical category exhibit substantial visual diversity, a phenomenon the research identifies as High Intra-Class Visual Diversity. The work progresses through four interconnected studies that collectively develop a comprehensive methodological framework bridging ethnographic insights with artificial intelligence capabilities. Beginning with an exploration of Pepe the Frog meme adaptations during Hong Kong's Anti-Extradition Bill movement, the research reveals both the potential and limitations of a similarity-based unsupervised approach to political imagery analysis. The investigation then expands to European environmental activism, where extensive experimentation with supervised classification methods leads to the development of key practices including class solidification, category refinement, and subcategorization that transform theoretically meaningful but visually disparate categories into computationally manageable tasks. In the following study, the methodological framework and the computational approach produced by it, were put into practice for testing its robustness and effectiveness to assist in mapping regimes of online political visibility of activists on Instagram. The final study enhances zero-shot classification through strong embeddings derived from reference images, achieving substantial accuracy improvements while significantly maintaining computational efficiency and accuracy. The methodological framework that emerges offers several innovations that directly address the core challenge. Class solidification forces explicit definition of visual characteristics qualifying images for specific categories, while subcategorization breaks broad theoretical constructs into visually coherent subgroups, simultaneously addressing visual diversity and enriching theoretical understanding. Object detection serves as a post-classification verification system, identifying potential misclassifications based on compositional rules, and enhanced zero-shot learning incorporates visual information from carefully selected reference images to improve classification performance without requiring extensive training datasets. Perhaps most significantly, the research demonstrates that addressing High Intra-Class Visual Diversity requires sustained dialogue between computational methods and ethnographic understanding, creating a reciprocal relationship where computational requirements enhance theoretical clarity while ethnographic insights guide algorithmic development. This “bridge” transforms both computational capabilities and theoretical insights, offering social research scholars practical tools for developing computational systems to analyse large-scale visual datasets without sacrificing contextual sensitivity or analytical depth, and establishing a framework applicable across diverse political contexts from meme culture to environmental activism.Tässä artikkeliväitöskirjassa tarkastellaan, miten sosiaalisen median poliittisia kuvia voidaan luokitella luotettavasti ja tehokkaasti yhteiskuntatieteellisessä tutkimuksessa silloin, kun samaan luokkaan kuuluvat kuvat poikkeavat visuaalisesti paljon toisistaan. Tätä ilmiötä kutsun korkeaksi luokkasisäiseksi visuaaliseksi vaihteluksi (High Intra-Class Visual Diversity, HIVD). Väitöskirja koostuu neljästä toisiinsa kytkeytyvästä osatutkimuksesta, joissa yhdistetään etnografista tutkimusta ja tekoälymenetelmiä suurten kuvamassojen analysoimiseksi ilman, että kuvien poliittinen ja kulttuurinen konteksti kadotetaan.
Ensimmäisessä osatutkimuksessa analysoidaan Pepe the Frog -meemejä Hongkongin demokratialiikkeen aikana ja osoitetaan, miten samat visuaaliset hahmot voivat saada eri poliittisia merkityksiä eri tilanteissa. Seuraavissa tutkimuksissa keskitytään eurooppalaiseen ympäristöaktivismiin ja nuorten aktivistien Instagram-kuviin Suomesta, Ranskasta, Saksasta ja Portugalista. Kehitän vaiheittain menetelmällisen kehyksen, jossa poliittisesti merkitykselliset kuvakategoriat määritellään tarkemmin, jaotellaan visuaalisesti yhtenäisempiin alaluokkiin ja tarkistetaan tarvittaessa objektintunnistuksen avulla. Näin parannetaan koneoppimismallien tarkkuutta ja samalla selkeytetään sitä, millaisia visuaalisia piirteitä eri aktivismin muotoihin liittyy.
Väitöskirjan viimeisessä osassa arvioin nollashottiluokitteluun perustuvia kuvien luokittelumenetelmiä ja parannan niitä yhdistämällä tekstipohjaiset kehotteet tarkoin valittuihin esimerkkikuviin. Tämä mahdollistaa tutkijalle sen, että uusia kuvakokoelmia voidaan luokitella aiempaa tarkemmin ilman laajoja käsin annotoituja aineistoja tai raskasta mallien koulutusta. Kokonaisuutena väitöskirja osoittaa, että poliittisten kuvien automaattinen luokittelu on mahdollista toteuttaa tavalla, joka on sekä laskennallisesti tehokas että herkkä kuvien poliittisille merkityksille. Kehys tarjoaa käytännön työkaluja tutkijoille, jotka haluavat ymmärtää, miten visuaalinen aktivismi ja poliittinen osallistuminen rakentuvat eri maissa ja digitaalisilla alustoilla.
Enhancement the catalytic activity of TiO2 inverse opal nanostructures through binary and ternary heterojunction
No full textEfficient light harvesting through titania inverse opal nanostructures (TiO2 IOs) can be achieved by strategically engineering binary and ternary heterojunctions with various metal oxides. In this study, we developed two distinct binary heterojunctions involving titanium dioxide paired with tin oxide (TiO2-SnO2 IOs) and bismuth oxide (TiO2-Bi2O3 IOs), alongside a ternary heterojunction combining titanium dioxide, tin oxide, and bismuth oxide (TiO2-SnO2-Bi2O3 IOs). These IOs were synthesized using a soft template method. We employed transient absorption spectroscopy to assess the lifetime of photogenerated carriers in the IO systems, revealing a notably long lifetime exceeding 5 ns for all samples. Our investigation into photocatalytic activity demonstrated that both TiO2-Bi2O3 IOs and TiO2-SnO2 IOs binary heterojunctions exhibited enhanced performance, displaying 20 % and 5 % greater photocatalytic activity for acetylene degradation, respectively, compared to pure TiO2 IOs. Notably, the TiO2-SnO2-Bi2O3 IOs ternary heterojunction showcased a remarkable increase in photocatalytic activity, with a 53 % improvement over TiO2 IOs.Peer reviewe
Sedimentin eroosioherkkyys ja resuspensio rannikkoalueilla : Biologisten ja fysikaalisten prosessien vaikutus ekosysteemien dynamiikkaan
No full textCoastal areas play pivotal role for both human and marine life by providing essential ecosystem services and functions. Among the key processes in these environments, sediment resuspension is a frequent phenomenon that drives the transfer of matter and energy. It influences water quality, pollutant and organism dispersal, and biogeochemical cycles. Hydrodynamic forces, such as waves and currents, cause shear stress on the sediment surface, and if an erosion threshold (critical shear stress; τ) is exceeded, sediment is resuspended. Climate change is expected to intensify and increase the frequency of sediment resuspension events, highlighting the need to understand the factors controlling sediment erodibility and resuspension to maintain water quality and healthy ecosystems. Despite its ecological significance, measurements on natural subtidal sediments remain limited.
This thesis addresses these knowledge gaps by examining spatial and temporal variability in sediment erodibility and resuspension potential across a sedimentary gradient in the Hanko archipelago, Baltic Sea, using a core-based erosion device (EROMES) and a high-resolution wave modeling approach. Field studies (Publications I and II) revealed that sediment type, habitat structure, seasonal variability, and biological activity jointly regulate sediment erodibility and nutrient fluxes. Sandy sediments in exposed areas remained stable, while muddy sediments in sheltered areas were more vulnerable to erosion and nutrient release, with mixed sediments showing intermediate but unexpectedly high stability. Temporal analyses demonstrated that dry bulk density and macrofaunal community dynamics were key predictors of erodibility, particularly in muddy sediments.
Modeling (Publication III) demonstrated that grain size–based estimates underestimated empirical critical shear stresses, emphasizing the need for integrated approaches that combine biological, chemical, and physical processes. Discrepancies between modeled and measured erosion thresholds emphasize the influence of biogeochemical and biological properties that cannot be captured by simple grain-size models. Together these findings highlight the spatial and temporal variability of sediment erodibility and the importance of incorporating biological variables and sedimentary gradients into sediment transport models.Rannikkoalueet ovat elintärkeitä sekä ihmisille että meriluonnolle, sillä ne tarjoavat monia ekosysteemipalveluja ja toimintoja. Sedimentin resuspensio, eli pohja-aineksen sekoittuminen takaisin veteen, on yksi keskeisimmistä rannikkoekosysteemiin vaikuttavista ilmiöistä. Sedimentin resuspensio vaikuttaa veden laatuun, ravinteiden ja haitta-aineiden kulkeutumiseen sekä ekosysteemin aine- ja energiavirtoihin. Resuspensiota tapahtuu, kun kovat tuulet ja aallokko aiheuttavat merenpohjaan riittävän suuren leikkausvoiman ja pohjan eroosiokynnys ylittyy. Ilmastonmuutoksen myötä resuspension odotetaan yleistyvän ja voimistuvan, joten sedimentin eroosioherkkyyttä ja resuspensiota säätelevien tekijöiden ymmärtäminen on tärkeää veden laadun ja ekosysteemien hyvinvoinnin turvaamiseksi.
Tässä väitöskirjassa selvitettiin sedimentin eroosioherkkyyden ja resuspension alueellista ja ajallista vaihtelua Hangon saaristossa. Menetelminä hyödynnettiin sekä EROMES-laitteella tehtyjä laboratoriomittauksia että mallinnusta. Tulokset osoittivat, että sedimentin tyyppi, pohjan habitaatti, vuodenaikaisvaihtelu ja eliöstö yhdessä säätelevät eroosioherkkyyttä ja ravinnevirtoja. Avoimien alueiden hiekkapohjat olivat vakaampia kuin suojaisammilla alueilla sijainneet ja eroosiolle herkät mutapohjat. Mutapohjilta vapautui myös enemmän ravinteita resuspension aikana. Hiekan ja mudan sekoituksesta koostuvat pohjat olivat sen sijaan odotettua vakaampia. Lisäksi havaittiin, että sedimentin kuivatiheys ja pohjaeläinyhteisöt olivat tärkeitä eroosioherkkyydelle erityisesti mutapohjilla.
Mallinnus osoitti, että raekokokoon perustuvat arviot eroosiokynnyksestä aliarvioivat sedimentin eroosioherkkyyden. Erot mallinnettujen ja mitattujen arvojen välillä osoittivat, että yksinkertaiset sedimentin kulkeutumista kuvaavat mallit eivät pysty huomioimaan biologisia ja biogeokemiallisia tekijöitä. Tämä väitöstyö korostaa eroosioherkkyyden suurta alueellista ja ajallista vaihtelua sekä biologisten tekijöiden ja sedimenttigradientin tärkeyttä sedimentin kulkeutumista mallinnettaessa
Matala CD11c-ilmentyminen on merkki huonommasta selviytymisestä peräsuolensyöpäpotilailla
No full textThe immune landscape of the tumor microenvironment significantly influences the development and prognosis of colorectal cancer (CRC). High intratumoral and stromal expressions of CD3+ and CD8+ T-lymphocytes have been associated with a better prognosis in CRC patients. However, the prognostic role of antigen-presenting cells, such as dendritic cells and macrophages, has less attention. In this study, we assessed the impact of CD11c expression and the disease-specific survival (DSS) in CRC patients. Thus, we evaluated the CD11c expression on tissue microarray samples via immunohistochemistry from 516 patients who underwent surgery at Helsinki University Hospital between 2000 and 2005. Samples were categorized as low expression (= 5% positive). Colon and rectal cancer patients were analyzed separately using Cox regression for survival analysis. A lower CD11c expression associated with a worse DSS among rectal cancer patients (p = 5 % stroomapositiivisuus). Elossaoloanalyysit tehtiin Kaplan–Meier -menetelmällä ja log-rank-testillä, ja monimuuttujamalli muodostettiin Coxin regressioanalyysilla. Peräsuolensyövässä ja oikeanpuolisessa paksusuolensyövässä matalampi CD11c-ilmentyminen assosioitui potilaiden huonomman ennusteen kanssa (p=0,02 ja p<0,001 vastaavasti). Vasemmanpuolisessa paksusuolensyövässä korkean ja matalan CD11c-ilmentymän potilasryhmien ennusteissa ei ollut merkittävää eroa (p=0,89). Peräsuolensyöpäpotilailla tulokset olivat samansuuntaiset riippumatta siitä, olivatko potilaat saaneet sädehoitoa ennen leikkausta vai ei (p=0,003 ja p=0,03 vastaavasti). Monimuuttujamallissa matalampi CD11c-ilmentyminen oli syöpäspesifisen eloonjäämisen itsenäinen ennusteellinen tekijä peräsuolensyöpäpotilailla (hazard ratio [HR] 2,72; 95 % luottamusväli 1,56–4,76; p<0,001), kun otettiin huomioon potilaiden ikä ja sukupuoli sekä syövän levinneisyysaste, erilaistumisaste ja MMR (mismatch repair) -geenien ilmentymä. Paksusuolensyöpäpotilaille CD11c ei ollut merkitsevä tekijä (HR 1,50; 95 % luottamusväli 0,96–2,38; p=0,08) monimuuttujamallissa. Nämä tulokset viittaavat siihen, että tulevaisuudessa CD11c voisi toimia ennustemerkkiaineena peräsuolensyöpäpotilailla
From mapping to action : social network analysis as a strategic tool in cross-national community interventions
No full textCommunity interventions increasingly leverage Social Network Analysis (SNA) both to understand relational patterns and to facilitate structural changes within networks. Indeed, SNA serves not only as an analytical tool but also as a catalyst for reflection and change. Although SNA has been widely used as an intervention tool, its application in cross-national contexts remains underexplored. This study aims to address this research gap by investigating how SNA can contribute to cross-national community interventions. We use a case study approach based on a longitudinal analysis of the Assistance and Legal Program for Emigrant Support (ALPES) network, a cross-national project established at the Italian-French border. In this project, SNA has been used both as a diagnostic tool to map the information exchange network of third-sector organizations and as a strategic intervention strategy that produced behavioral changes in these organizations. Our results show that SNA functioned as both a translational monitoring tool and a catalytic intervention: network visualization prompted organizations to strategically alter their collaborative patterns and address structural gaps in migrant support services across borders. This demonstrates how network feedback processes can enhance inter-organizational collaboration in complex cross-national contexts.Peer reviewe
Vårens makter : drama i fyra akter, - tredje akten i tre skymningsbilder
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Association of bacterial biomarkers with current classification of periodontitis
No full textAim: To study whether saliva and serum lipopolysaccharide (LPS), as well as subgingival Gram-positive and Gram-negative bacteria, are associated with periodontitis staging and grading, the most recent classification system representing the disease severity and progression rate.
Materials and methods: The study population consisted of 505 patients from the Parogene cohort, which is a subpopulation of the Corogene study of Finnish patients. In addition to angiography, participants underwent oral and radiographic examinations. LPS activity in saliva and serum were determined with the Limulus amebocyte lysate assay with chromogenic substrate. Subgingival bacterial samples from the deepest pocket in each quadrant were analyzed for 29 species (18 Gram-negative and 11 Gram-positive bacteria). Associations of these bacterial biomarkers with periodontal staging and grading were assessed using regression analysis.
Results: Elevated saliva LPS levels and subgingival Gram-positive bacteria were associated with increasing periodontal stage. Serum LPS showed no significant association with either staging or grading. Gram-negative bacteria increased significantly with staging only when all stages were combined. Both Gram-negative and Gram-positive bacterial levels were higher in grade C patients compared with grade A patients.
Conclusions: Saliva LPS was associated with periodontal staging, while subgingival bacteria, particularly Gram-positive species, were linked to both staging and grading, supporting their potential use in periodontal diagnostics.Tutkielman tavoitteena oli selvittää, ovatko syljen ja seerumin lipopolysakkaridi (LPS) sekä subgingivaaliset Gram-positiiviset ja Gram-negatiiviset bakteerit yhteydessä parodontiitin nykyluokitukseen, joka määritettiin vuonna 2017 järjestetyssä World Workshop on the Classification of Periodontal and Peri-implant Diseases and Conditions -työpajassa. Tässä luokituksessa potilaan parodontiittidiagnoosin jälkeen määritetään taudin vaihe eli vaikeusaste (staging) ja riskiluokka eli taudin etenemisnopeus (grading).
Tutkimuspopulaatio koostui Corogene-tutkimukseen kuuluvasta Parogene-kohortista, joka sisälsi 505 potilasta. Näille potilaille oli sepelvaltimoiden angiografian lisäksi tehty myös suun kliininen sekä radiologinen tutkimus. Potilaiden syljen ja seerumin LPS-aktiivisuus määritettiin Limulus amebocyte lysate -kokeella kromogeenista substraattia käyttäen. Subgingivaalibakteerinäytteet kerättiin jokaisen leukaneljänneksen syvimmästä ientaskusta, ja niistä analysoitiin 29 lajia (18 Gram-negatiivista ja 11 Gram-positiivista bakteeria). Näiden bakteeribiomarkkerien yhteyttä parodontiitin vaikeusasteeseen ja riskiluokkaan tutkittiin regressioanalyysillä.
Tuloksena havaittiin, että kohonnut syljen LPS-pitoisuus ja subgingivaalisten Gram-positiivisten bakteerien määrä olivat yhteydessä vaikeampaan parodontiitin vaiheeseen. Seerumin LPS ei ollut merkitsevästi yhteydessä vaikeusasteeseen tai riskiluokkaan. Gram-negatiivisten bakteerien määrä kasvoi merkitsevästi parodontiitin vaikeutuessa vain silloin, kun taudin kaikki vaiheet yhdistettiin analyysiin. Sekä Gram-negatiivisia että Gram-positiivisia bakteereja esiintyi enemmän C-riskiluokan potilailla verrattuna A-luokan potilaisiin.
Tutkimuksen tulokset viittaavat siihen, että syljen LPS ja subgingivaaliset bakteerit, erityisesti Gram-positiiviset lajit, ovat yhteydessä parodontiitin vaikeusasteeseen. Lisäksi subgingivaalisilla bakteereilla todettiin positiivinen yhteys riskiluokitukseen. Yhdessä nämä biomarkkerit voivat toimia mahdollisina työvälineinä parodontiitin diagnostiikassa
3D Digital exoscope is safe tool in the surgery of olfactory groove meningiomas
No full textBackground Digital 3D exoscopes have been introduced as alternatives for operating microscopes in microneurosurgery. It has been hypothesized that exoscope may provide benefits especially at the most anterior skull base, where surgical trajectories often require heavy tilting of the magnification device. We evaluated the safety and practicality of the digital 3D exoscopes in surgery of olfactory groove meningiomas (OGM) during the transition from using a microscope to an exoscope.
Methods In this retrospective cohort study, we included all consecutive adult patients who underwent surgery for OGM (n=22) by a single senior neurosurgeon between 2016 and 2024 either with a microscope (n=13) or an exoscope (n=9). We reviewed the pre- and postoperative MRIs, patient records (including Modified Rankin Scale (mRS)), and surgical videos of all the patients. The surgical approach was unilateral fronto-temporal in all the cases.
Results The patients in the exoscope group had larger tumors (median 61cm³ (IQR 49) vs. 17cm³ (IQR 32)), more clinical symptoms and required more help in their daily activities preoperatively (mRS ≥3: n=3 (33%) vs n=1 (8%)). Gross-total or near total resection was achieved in all the patients. The exoscopic surgeries took longer (165 min (IQR 106) vs. 121 min (IQR 27)), probably due to the larger tumor sizes. Two severe complications occurred, one in each group (post-op hematoma and blindness of ipsilateral eye). Clinical outcomes were nearly the same in both groups. At the 3-month follow-up, eight (89%, exoscope) and 12 (92%, microscope) patients were independent (mRS 0-2).
Conclusion The surgical outcomes for OGMs remained consistent during the transition from using a microscope to an exoscope. The exoscope is a safe tool in the surgery of OGMs, even when operating on large tumors. The wider range of angular movement of the camera head is particularly advantageous when accessing the anterior skull base