76 research outputs found
jaredhomola/InlandCisco: First release of InlandCisco research compendium
No full text<p>InlandCisco is a research compendium that brings together the data and analyses associated with Homola et al. (in press), Coalescent methods reconstruct contributions of natural colonization and stocking to origins of Michigan inland Cisco (Coregonus artedi), Journal of Great Lakes Research</p>
Biomolekulární interakce a jejich studium metodou rezonance povrchových plasmonů
No full textNázev práce: Biomolekularní interakce a jejich studium metodou rezonance povrchových plasmonů Autor: Markéta Bocková Katedra / Ústav: Katedra Biochemie, PřF UK Vedoucí diplomové práce: Prof. Ing. Jiří Homola, CSc., DSc., Ústav fotoniky a elektroniky Akademie věd České Republiky Abstrakt: Diplomová práce se zabývá využitím metody rezonance povrchových plazmonů (SPR) pro studium dvou typů biomolekulárních interakcí: hybridizace částečně komplementárních oligonukleotidů (ON) a interakcí enzymů a peptidů, které hraji roli v patogenezi Alzheimerovy nemoci (AD). Studium interakcí ON se konkrétně zaměřuje na určení kinetických parametrů procesu hybridizace. Z výsledků vyplývá, že rovnovážná asociační konstanta klesá se zvyšující se hustotou ON na povrchu senzoru. V rámci studia interakcí molekul souvisejících s patogenezí AD je navržena a vyvinuta metoda pro rychlou a citlivou detekci enzymu 17-HSD10 a jeho komplexu s peptidy amyloidu β (Aβ). Zároveň je ukázáno, že navržená metoda umožňuje detekci komplexu 17-HSD10/Aβ v klinických vzorcích mozkomíšního moku (MM) a že vzorky MM pacientů trpících AD obsahují vetší množství komplexu 17-HSD10/Aβ než kontrolní vzorky. Výsledky prezentované v této diplomové práci byly publikovány ve dvou mezinárodních vědeckých časopisech. Klíčová slova: rezonance povrchových...Title: Study of biomolecular interactions by the method of surface plasmon resonance Author: Markéta Bocková Department: Department of Biochemistry, Faculty of Science Supervisor: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics of the Czech Academy of Sciences Abstract: In this diploma work, a surface plasmon resonance (SPR) biosensor technology was exploited to study two different classes of molecular interactions: hybridization of partially complementary oligonucleotides (ONs) and interactions between enzymes and peptides involved in pathogenesis of Alzheimer disease (AD). In particular, the study of interactions between ONs was focused on determining kinetic parameters of the hybridization proces. It was found that the association equilibrium constant decreases with the increasing surface probe density. An SPR biosensor-based method for rapid and sensitive detection of the 17-HSD10 enzyme and its complex with amyloid β (Aβ) peptides was designed and developed. It was demonstrated that the developed method is capable of detecting 17β-HSD10/Aβs complex in real cerebrospinal fluid (CSF) samples and that CSF samples from AD patients exhibited elavated levels of 17β- HSD10/Aβs complex compared to the control groups. The research reported in this thesis resulted in two publications in...Katedra makromolekulární fyzikyDepartment of Macromolecular PhysicsFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult
Study of biomolecular interactions by the method of surface plasmon resonance
No full textTitle: Study of biomolecular interactions by the method of surface plasmon resonance Author: Markéta Bocková Department: Department of Biochemistry, Faculty of Science Supervisor: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics of the Czech Academy of Sciences Abstract: In this diploma work, a surface plasmon resonance (SPR) biosensor technology was exploited to study two different classes of molecular interactions: hybridization of partially complementary oligonucleotides (ONs) and interactions between enzymes and peptides involved in pathogenesis of Alzheimer disease (AD). In particular, the study of interactions between ONs was focused on determining kinetic parameters of the hybridization proces. It was found that the association equilibrium constant decreases with the increasing surface probe density. An SPR biosensor-based method for rapid and sensitive detection of the 17-HSD10 enzyme and its complex with amyloid β (Aβ) peptides was designed and developed. It was demonstrated that the developed method is capable of detecting 17β-HSD10/Aβs complex in real cerebrospinal fluid (CSF) samples and that CSF samples from AD patients exhibited elavated levels of 17β- HSD10/Aβs complex compared to the control groups. The research reported in this thesis resulted in two publications in..
Advancing broodstock selection to optimize brook trout stocking in Wisconsin
No full textAbstract - Brook trout Salvelinus fontinalis is the only native stream-dwelling salmonid to many parts of central and eastern North America and has been intensively stocked across its native range. As wild brook trout stocking programs gain momentum, information is needed detailing patterns of spatial genetic structure, diversity, and stocking influence to aid in the conservation of endemic wild strains. The Wisconsin Department of Natural Resources utilizes a wild trout stocking program, stocking first-filial generation fish (F1; wild parents) or second-filial generation fish (F2; wild grandparents) rather than domestic strain brook trout in many waterbodies. Accurate expectations of post-stocking fitness are needed to help fisheries managers make cost-effective brook trout stocking decisions. The objectives of Chapter I were to determine how measures of genetic diversity, inbreeding, and effective population size vary for wild brook trout populations across Wisconsin. Moreover, I aimed to identify and characterize patterns in genetic structure on the landscape and quantify the influence of domestic strain stocking for each survey population. Brook trout were genotyped from 63 wild populations across Wisconsin and one domesticated hatchery strain at 68 microsatellite loci. Genetic diversity and effective population size showed positive relationships with latitude, and overall levels of domestic strain introgression were low. Six major groups were resolved on a neighbor-joining tree. Distinct groups of genetically similar populations were identified in central and northeastern Wisconsin, but spatial clustering was weak elsewhere. In summary, Chapter I demonstrated higher levels of genetic diversity and effective population size in northern Wisconsin, low overall levels of domestic strain introgression that generally coincide with available stocking records, and some evidence of spatial genetic structure, particularly in central and northeastern Wisconsin. In Chapter II, genetic analyses were used following three years of experimental stocking to estimate relative measures of post-stocking fitness among F1, F2, and domestic strain brook trout. Wild-born brook trout collected in electrofishing surveys were assigned as offspring of F1, F2, or domestic stocked fish using parentage analyses. F1 fish were superior to F2 fish and domestic strain fish, as they were more likely to survive, naturally reproduce, and produce multiple offspring. An overall decline in natural reproduction was observed in each consecutive year of sampling. Collectively, this thesis provides information on genetic diversity, spatial genetic structure, and hatchery influence for wild populations across Wisconsin, in addition to measures of relative fitness of stocked brook trout that were of varying degrees of wildness. These findings may help inform future conservation, management, and stocking practices of brook trout in Wisconsin and beyond
SPATIOTEMPORAL PATTERNS OF GENETIC STOCK MIXING AND THEIR APPLICATION IN MIXTURE-INFORMED CATCH-AT-AGE MODELS FOR LAKE WHITEFISH IN LAKE MICHIGAN
No full textLake Michigan lake whitefish (Coregonus clupeaformis) support the lake’s largest commercial fishery and is comprised of multiple stocks managed across a series of geopolitical management zones (MZs). Limited movement among MZs is an underlying assumption of current lake whitefish management and lake whitefish stock assessment models, yet previous research suggests stock mixing occurs to varying degrees across MZs. This can create challenges when estimating stock-specific harvest and dynamic rates in stock assessment models. In Lake Michigan, statistical catch-at-age models (SCAA) are used to estimate recruitment, abundance, and mortality for lake whitefish MZs to inform harvest quotas and management. Understanding stock compositions of the mixed-stock lake whitefish fishery can aid in allocating fishing effort on spatial and temporal scales to avoid overharvest of vulnerable stocks evaluated by the SCAA models. My research objectives were to: 1) determine spatiotemporal patterns of lake whitefish stock mixing throughout Lake Michigan, 2) determine appropriate sample sizes required to accurately conduct mixed stock analyses, and to 3) evaluate model performance of a newly developed mixture-informed SCAA model that incorporates genetic stock identification mixture compositions for the purpose of understating changes in lake whitefish recruitment. I applied a newly developed genotyping-in-thousands (GT-seq) panel containing 472 single nucleotide polymorphisms to conduct genetic stock identification (GSI) of Lake Michigan lake whitefish. Using GSI, I quantified contributions from each of five genetically distinct reporting units for 39 mixed stock lake whitefish samples collected throughout Lake Michigan from 1977-2022 and evaluated the sensitivity of SCAA model recruitment estimates adjusted to the determined mixture compositions. GSI results demonstrated that the lake whitefish fishery in Lake Michigan is a mixed stock fishery throughout much of the year and that stock compositions vary across seasons and, to a lesser extent, years. In general, the mixture-informed SCAA model was able to converge upon an estimated set of parameters and demonstrated good fit to observed gill and trap net harvest in most MZ models. This thesis provides information on the presence of genetic stocks in different MZs throughout the non-spawning period, further delineation on the genetic structure of lake whitefish in Lake Michigan, as well as initial developments of a mixture-informed SCAA model which inform recruitment estimates valuable to the management of lake whitefish
jaredhomola/VPLandscapeGenetics: First release of VPLandscapeGenetics
No full text<p>First release to enable Zenodo archiving of data.</p>
Study of new catalytic materials for proton exchange membrane fuel cells
No full textTitle: Study of new catalytic materials for proton exchange membrane fuel cells Author: Petr Homola Department: Department of Surface and Plasma Science Supervisor: Prof. RNDr. Vladimír Matolín, DrSc. Abstract: Submitted thesis deals with study of thin layers based on platinum and cerium oxides in order to use them in fuel cells with polymer membrane (PEM- FC). A set of samples with different amount of platinum was prepared by means of magnetron sputtering. Samples were investigated by X - ray Photoelectron Spectroscopy (XPS) and results were confronted with sputtering parameters. It was found out that chemical state of platinum is related to its amount in thin layer. The less platinum was contained in thin layer, the less amount of Pt0 state was observed and amounts of Pt2+ and Pt4+ states increased. Furthermore the temperature stability of prepared layers in the interval from room temperature to 250 ◦ C was studied by means of XPS. The adsorption of carbon monoxide was measured by infrared absorption spectroscopy (IRAS). Increasing degree of adsorption on sample probably related to platinum reduction with increased tem- perature was observed. Measurements of other samples were devaluated by strong contamination with nickel carbonyls. Keywords: PEMFC, cerium oxide, magnetron sputtering, XPS, CO adsorptio
Delineation and Spatial Distribution of Lake Superior's Walleye Stocks
No full textUnderstanding spatial genetic variation within and among wild populations is a key factor for informing conservation. In fishes, reductions in abundance often result in losses of genetic diversity that can lead to declines in resiliency. In populations where isolation or reduced abundance have occurred, maintaining connectivity can help offset some of these negative consequences. Lake Superior walleye (Sander vitreus; Ojibwe: Ogaa) are a native fish species with cultural, recreational, and commercial importance that have experienced widespread declines in abundance throughout the last century. In recent decades, numerous efforts to restore walleye via habitat improvement, regulation modifications, and stocking have been attempted with mixed success. My objectives were to inform Lake Superior walleye rehabilitation efforts by 1) identifying factors associated with variation in genetic diversity among spawning aggregations, 2) characterizing genetic structure and assessing if influences from stocking exist, and 3) identifying environmental correlates of genetic connectivity. Despite widespread declines, walleye spawning aggregations in Lake Superior have maintained a high degree of genetic diversity, are spatially structured into distinct patterns of diverged populations, but have been influenced by stocking. While geographic distance is likely the most influential environmental factor on connectivity, other factors such as water temperature, relative shoreline exposure to wind and waves, and water currents may also influence gene flow and connectivity among Lake Superior walleye spawning aggregations. The results provided here may serve as a useful guide for identifying walleye spawning aggregations harboring endemic genetic variation, habitats that influence gene flow, and potential broodstock sources suitable for conserving genetic diversity.
In mixed-stock fisheries, knowledge of stock-specific movement patterns, spatial distribution, and the factors that influence them can inform adaptive management strategies. Understanding proportional contributions of distinct stocks to harvest-oriented mixed fisheries allows for regulation that decreases risks from overfishing vulnerable stocks and shifts harvest toward more sustainable stocks. Genomic techniques such as genetic stock identification and mixed stock analysis (MSA) can be used to delineate genetic fish stocks and determine mixing rates across space and time. In walleye fisheries like Lake Superior where subsistence, recreational, and commercial fishing exist, MSA monitoring may help inform strategies for maintaining and restoring once abundant genetic stocks. Walleye movement and genetic structure in Lake Superior has been studied at local geographic scales, but no lake-wide analysis has been conducted. My objectives were to delineate genetically distinct walleye stocks in Lake Superior and characterize genetic stock-specific movement patterns using MSA. I used a recently developed genotyping-in-thousands by sequencing panel for Great Lakes walleye to develop genetic stock assignment baselines from 32 Lake Superior walleye spawning aggregations and broodstock sources to estimate stock-specific contributions to 68 samples representing over 1300 individuals collected during non-spawning times. Self-assignment testing using leave-one-out cross-validation of spawning aggregations resulted in highly accurate genetic stock delineations for MSA (82.7–100%). My results indicate genetic stock mixing rates were variable by region, with greater mixing rates detected in southwestern and southcentral Lake Superior. Measures of alpha-diversity varied regionally, with higher Shannon diversity indices estimated in northwest Lake Superior, and greater genetic stock richness in the southeast. These results may provide useful insights to guide genetic stock-specific management actions that aim to achieve restoration of walleye throughout Lake Superior
Povrchové plasmony v optických mikrostrukturách a jejich senzorové aplikace
No full textNázev práce: Povrchové plasmony v optických mikrostrukturách a jejich senzorové aplikace Autor: Pavel Adam Ústav: Ústav fotoniky a elektroniky AV ČR, v.v.i., Oddělení optických senzorů Vedoucí doktorské práce: doc. Ing. Jiří Homola, CSc., DSc. Abstrakt: Práce se zabývá studiem senzorů s povrchovými plazmony (SPR senzory), které umožňují využít techniku multiplexování v oboru vlnových délek (WDM), tj. současně excitovat několik různých povrchových plasmonů (SP). Tyto senzory používají mřížkový vazební člen, který excituje buď běžné nebo Braggovsky rozštěpené SP. Problematika SP na difrakčních mřížkách je studována analyticky a srovnána s numerickými metodami (diferenciální a integrální). Poté je studována metoda WDM dvou a tří SP. WDM senzory se dvěma SP jsou analyzovány s ohledem na rozlišení, šum a přeslechy odezev senzoru. Výsledky analýz slouží k optimalizaci senzorů se dvěma SP s ohledem na schopnost separace odezvy senzoru na povrchovou a objemovou změnu indexu lomu. V rámci dizertační práce byly připraveny difrakční mřížky (metodou interferenční holografie) a jejich repliky (metodou měkké litografie), které byly následně charakterizovány a využity pro konstrukci nových typů SPR senzorů. Schopnosti WDM SPR senzorů byly demonstrovány v modelovém experimentu, v kterém byl sledován růst vrstev proteinů. V...Title: Surface plasmons in optical microstructures and their sensor applications Author: Pavel Adam Institute: Institute of Photonics and Electronics AS CR, v.v.i., Department of Optical Sensors Supervisor of the doctoral thesis: doc. Ing. Jiří Homola, CSc., DSc. Abstract: This work is focused on the study of surface plasmon resonance (SPR) sensor platforms based on wavelength division multiplexing (WDM) of multiple surface plasmons (SPs). These sensors are based on advanced diffraction gratings supporting either conventional or Bragg-scattered SPs, which are simultaneously excited at different wavelengths. These SPs are studied both analytically and numerically using rigorous coupled-wave analysis and an integral approach. WDM of two and three SPs is presented and followed by the method for the analysis of the resolution, noise and cross-sensitivity. This method is employed to analyze the ability of different SPR sensor platforms (supporting WDM of two SPs) to discriminate refractive index (RI) changes in a thin layer at the sensor surface from background RI changes. The WDM SPR sensors based on advanced diffraction gratings prepared by interferometric holography are developed and tested in a model biosensing experiment consisting of the layer-by-layer growth of protein multilayers. The linear WDM of two...Matematicko-fyzikální fakultaFaculty of Mathematics and Physic
Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions
No full textTitle: Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions Author: Markéta Bocková Department / Institute: Institute of Physics, Charles University Supervisor of the doctoral thesis: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics, The Czech Academy of Sciences Abstract: Surface plasmon resonance (SPR) biosensors represent the most advanced optical method for the direct, real-time monitoring of biomolecular interactions without the need for labelling. This doctoral thesis aims to advance the SPR biosensor method and to expand its utility in the investigation of biomolecular interactions. This encompasses activities on two major fronts of SPR biosensor research - immobilization methods and biosensing methodologies. Methods for the immobilization of biomolecules were researched with the aim of enabling the immobilization of a broad range of biomolecules on the SPR biosensor surface in a spatially controlled manner. The development of novel biosensing methodologies was pursued in order to address the current limitations of SPR biosensors associated with non-specific adsorption and limited analyte transport, and thus to improve the accuracy and robustness of SPR biosensor measurements. Finally, advances in the development of immobilization..
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