Matemaattis-luonnontieteellinen tiedekuntahttps://jyx.jyu.fi/handle/123456789/255972024-03-28T18:19:05Z2024-03-28T18:19:05ZVitroJet : new features and case studiesHenderikx, Rene J. M.Mann, DanielDomanska, AušraDong, JingShahzad, SabaLak, BehnamFilopoulou, AikateriniLudig, DamianGrininger, MartinMomoh, JeffreyLaanto, ElinaOksanen, Hanna M.Bisikalo, KyryloWilliams, Pamela A.Butcher, Sarah J.Peters, Peter J.Beulen, Bart W. A. M. M.https://jyx.jyu.fi/handle/123456789/941112024-03-28T14:20:25Z2024-03-28T10:06:39ZVitroJet : new features and case studies
Henderikx, Rene J. M.; Mann, Daniel; Domanska, Aušra; Dong, Jing; Shahzad, Saba; Lak, Behnam; Filopoulou, Aikaterini; Ludig, Damian; Grininger, Martin; Momoh, Jeffrey; Laanto, Elina; Oksanen, Hanna M.; Bisikalo, Kyrylo; Williams, Pamela A.; Butcher, Sarah J.; Peters, Peter J.; Beulen, Bart W. A. M. M.
Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tickborne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.
2024-03-28T10:06:39ZSobolev, BV and perimeter extensions in metric measure spacesCaputo, EmanueleKoivu, JesseRajala, Tapiohttps://jyx.jyu.fi/handle/123456789/940932024-03-27T14:19:09Z2024-03-27T12:27:18ZSobolev, BV and perimeter extensions in metric measure spaces
Caputo, Emanuele; Koivu, Jesse; Rajala, Tapio
We study extensions of sets and functions in general metric measure spaces. We show that an open set has the strong BV-extension property if and only if it has the strong extension property for sets of finite perimeter. We also prove several implications between the strong BV-extension property and extendability of two different non-equivalent versions of Sobolev W 1,1 -spaces and show via examples that the remaining implications fail.; Tutkimme joukkojen ja funktioiden laajennuksia yleisissä metrisissä mitta-avaruuksissa. Osoitamme, että avoimella joukolla on vahva BV-laajennusominaisuus jos ja vain jos sillä on vahva laajennusominaisuus äärellisperimetrisille joukoille. Tutkimme myös vahvan BV-laajennuksen yhteyttä kahteen eri versioon Sobolev W1,1-laajennuksista todistaen ne tapaukset missä yksi laajennusominaisuus antaa toisen sekä antamalla vastaesimerkit jäljelle jääviin tapauksiin
2024-03-27T12:27:18ZA quantitative second order estimate for (weighted) p-harmonic functions in manifolds under curvature-dimension conditionLiu, JiayinZhang, ShijinZhou, Yuanhttps://jyx.jyu.fi/handle/123456789/940922024-03-27T14:18:39Z2024-03-27T11:49:41ZA quantitative second order estimate for (weighted) p-harmonic functions in manifolds under curvature-dimension condition
Liu, Jiayin; Zhang, Shijin; Zhou, Yuan
We build up a quantitative second-order Sobolev estimate of lnw for positive p-harmonic functions w in Riemannian manifolds under Ricci curvature bounded from below and also for positive weighted p-harmonic functions w in weighted manifolds under the Bakry-Émery curvature-dimension condition.
2024-03-27T11:49:41ZLuonnontieteiden ja matematiikan uramahdollisuuksia avattava nuorille paremminNissinen, Maijahttps://jyx.jyu.fi/handle/123456789/940722024-03-25T14:19:55Z2024-03-25T11:29:01ZLuonnontieteiden ja matematiikan uramahdollisuuksia avattava nuorille paremmin
Nissinen, Maija
Jyväskylän yliopisto avasi tänä syksynä pienten ja keskisuurten lukioiden kanssa LUMA-linjapilotin innostaakseen nuoria matematiikan ja luonnontieteiden pariin. Juuri nämä ovat aloja, joilla aikamme suuria globaaleja ongelmia ratkaistaan monitieteisessä yhteistyössä, kirjoittaa varadekaani Maija Nissinen.
2024-03-25T11:29:01ZInfluence of Reaction Parameters on Nanogold-Catalyzed Glucose and Xylose Oxidation : A Joint Experimental and DFT StudyOña, Jay PeeLaverdure, LauraLatonen, Rose MarieKumar, NarendraPeurla, MarkusAngervo, IlariHonkala, KaroliinaGrénman, Henrikhttps://jyx.jyu.fi/handle/123456789/940452024-03-22T14:20:43Z2024-03-22T11:59:27ZInfluence of Reaction Parameters on Nanogold-Catalyzed Glucose and Xylose Oxidation : A Joint Experimental and DFT Study
Oña, Jay Pee; Laverdure, Laura; Latonen, Rose Marie; Kumar, Narendra; Peurla, Markus; Angervo, Ilari; Honkala, Karoliina; Grénman, Henrik
The electrocatalytic oxidation (ECO) of glucose on gold requires alkaline conditions and relatively high potentials (>0.3 VRHE). Although the adsorption of hydroxide ions (OHads) is also known to occur under these conditions, the generally accepted proton-coupled electron transfer mechanism for sugar ECO does not explicitly state the role of OHads in the sugar adsorption or oxidation steps. To investigate this, we carried out a combined experimental and density functional theory (DFT) study on the ECO of glucose and xylose over a nanogold catalyst under temperature and pH control. Grand canonical DFT (GC-DFT) was used to identify the preferred reaction mechanism in which OHads facilitates the thermodynamically feasible formation of gluconic and xylonic acid. Calculated results also showed that OHads plays a role in improving the acid selectivity. Constant-potential electrolyses in sugar solutions were performed using mesoporous (Sibunit) carbon-supported Au nanoparticles (AuNPs) with an average cluster size of 4.7 nm. Experimental results showed that the highest conversions for glucose (57.7%) and xylose (49.4%) were obtained at 25 °C and pH 12.5, with gluconic and xylonic acid selectivity of 81.5 and 87.8%, respectively. The catalytic activities were high considering the low Au loading (∼0.1% wt). Higher pH led to a decrease in the ECO rate possibly due to excess hydroxide ions blocking active sites for sugar adsorption. Our results highlight the importance of computational studies in elucidating reaction mechanisms for sugar ECO where sugar acids are the main oxidation products. This is crucial in designing reaction systems for the viable production of these value-added chemicals from biomass.
2024-03-22T11:59:27ZHamilton-Jacobi flows and characterization of solutions of Aronsson equationsJuutinen, PetriSaksman, Eerohttps://jyx.jyu.fi/handle/123456789/940432024-03-22T14:15:27Z2024-03-22T11:39:56ZHamilton-Jacobi flows and characterization of solutions of Aronsson equations
Juutinen, Petri; Saksman, Eero
2024-03-22T11:39:56ZEffects of past and present habitat on the gut microbiota of a wild rodentScholier, TiffanyLavrinienko, AntonKallio, Eva R.Watts, Phillip C.Mappes, Tapiohttps://jyx.jyu.fi/handle/123456789/940422024-03-22T14:19:03Z2024-03-22T11:32:21ZEffects of past and present habitat on the gut microbiota of a wild rodent
Scholier, Tiffany; Lavrinienko, Anton; Kallio, Eva R.; Watts, Phillip C.; Mappes, Tapio
The response of the gut microbiota to changes in the host environment can be influenced by both the host's past and present habitats. To quantify their contributions for two different life stages, we studied the gut microbiota of wild bank voles (Clethrionomys glareolus) by performing a reciprocal transfer experiment with adults and their newborn offspring between urban and rural forests in a boreal ecosystem. Here, we show that the post-transfer gut microbiota in adults did not shift to resemble the post-transfer gut microbiota of animals 'native' to the present habitat. Instead, their gut microbiota appear to be structured by both their past and present habitat, with some features of the adult gut microbiota still determined by the past living environment (e.g. alpha diversity, compositional turnover). By contrast, we did not find evidence of the maternal past habitat (maternal effects) affecting the post-transfer gut microbiota of the juvenile offspring, and only a weak effect of the present habitat. Our results show that both the contemporary living environment and the past environment of the host organism can structure the gut microbiota communities, especially in adult individuals. These data are relevant for decision-making in the field of conservation and wildlife translocations.
2024-03-22T11:32:21ZGene expression centroids that link with low intrinsic aerobic exercise capacity and complex disease riskKivelä, RiikkaSilvennoinen, MikaLehti, MaaritRinnankoski, RitaPurhonen, TatjaKetola, TarmoPullinen, KatriVuento, MeriMutanen, NiinaSartor, MaureenReunanen, HilkkaKoch, LaurenBritton, StevenKainulainen, Heikkihttps://jyx.jyu.fi/handle/123456789/940312024-03-22T14:17:19Z2024-03-22T10:35:04ZGene expression centroids that link with low intrinsic aerobic exercise capacity and complex disease risk
Kivelä, Riikka; Silvennoinen, Mika; Lehti, Maarit; Rinnankoski, Rita; Purhonen, Tatja; Ketola, Tarmo; Pullinen, Katri; Vuento, Meri; Mutanen, Niina; Sartor, Maureen; Reunanen, Hilkka; Koch, Lauren; Britton, Steven; Kainulainen, Heikki
2024-03-22T10:35:04ZSpodium bonding in bis(alkynyl)mecurialsOnn, Chee S.Hill, Anthony F.Ward, Jas S.https://jyx.jyu.fi/handle/123456789/940302024-03-22T14:19:33Z2024-03-22T09:47:01ZSpodium bonding in bis(alkynyl)mecurials
Onn, Chee S.; Hill, Anthony F.; Ward, Jas S.
The new bis(alkynyl)mercurial Hg{C[triple bond, length as m-dash]CSeC[triple bond, length as m-dash]W(CO)2(Tp*)}2 (Tp* = tris(dimethylpyrazolyl)borate) forms adducts with fluoride and phenathroline, the structures of which are interpreted in the context of two-coordinate mercury presenting a σ-torroid for spodium bonding.
2024-03-22T09:47:01ZFitness as the organismal performance measure guiding adaptive evolutionFromhage, LutzJennions, Michael D.Myllymaa, LauriHenshaw, Jonathan M.https://jyx.jyu.fi/handle/123456789/940142024-03-25T06:11:14Z2024-03-21T13:35:29ZFitness as the organismal performance measure guiding adaptive evolution
Fromhage, Lutz; Jennions, Michael D.; Myllymaa, Lauri; Henshaw, Jonathan M.
A long-standing problem in evolutionary theory is to clarify in what sense (if any) natural selection cumulatively improves the design of organisms. Various concepts, such as fitness and inclusive fitness, have been proposed to resolve this problem. In addition, there have been attempts to replace the original problem with more tractable questions such as whether a given gene or trait is favoured by selection. Here we ask what theoretical properties the concept fitness should possess to encapsulate the improvement criterion required to talk meaningfully about adaptive evolution. We argue that natural selection tends to shape phenotypes based on the causal properties of individuals, and that this tendency is therefore best captured by a fitness concept that focusses on these properties. We highlight a fitness concept which meets this role under broad conditions, but requires adjustments in our conceptual understanding of adaptive evolution. These adjustments combine elements of Dawkinsian gene selectionism and Egbert Leigh’s “parliament of genes”.
2024-03-21T13:35:29Z