Problem areas in the use of the firefly luciferase assay for bacterial detection

By purifying the firefly luciferase extract and adding all necessary chemicals but ATP in excess, an assay for ATP was performed by measuring the amount of light produced when a sample containing soluble ATP is added to the luciferase reaction mixture. Instrumentation, applications, and basic characteristics of the luciferase assay are presented. Effect of the growth medium and length of time grown in this medium on ATP per viable E. coli values is shown in graphic form, along with an ATP concentration curve showing relative light units versus ATP injected. Reagent functions and concentration methods are explored. Efforts to develop a fast automatable system to detect the presence of bacteria in biological fluids, especially urine, resulted in the optimization of procedures for use with different types of samples

High-Throughput Method for Automated Colony and Cell Counting by Digital Image Analysis Based on Edge Detection

Counting cells and colonies is an integral part of high-throughput screens and quantitative cellular assays. Due to its subjective and time-intensive nature, manual counting has hindered the adoption of cellular assays such as tumor spheroid formation in high-throughput screens. The objective of this study was to develop an automated method for quick and reliable counting of cells and colonies from digital images. For this purpose, I developed an ImageJ macro Cell Colony Edge and a CellProfiler Pipeline Cell Colony Counting, and compared them to other open-source digital methods and manual counts. The ImageJ macro Cell Colony Edge is valuable in counting cells and colonies, and measuring their area, volume, morphology, and intensity. In this study, I demonstrate that Cell Colony Edge is superior to other open-source methods, in speed, accuracy and applicability to diverse cellular assays. It can fulfill the need to automate colony/cell counting in high-throughput screens, colony forming assays, and cellular assays

Analytical Applications of Bioluminescence and Chemiluminescence

Bioluminescence and chemiluminescence studies were used to measure the amount of adenosine triphosphate and therefore the amount of energy available. Firefly luciferase - luciferin enzyme system was emphasized. Photometer designs are also considered

Guidelines for the use of cell lines in biomedical research

Cell-line misidentification and contamination with microorganisms, such as mycoplasma, together with instability, both genetic and phenotypic, are among the problems that continue to affect cell culture. Many of these problems are avoidable with the necessary foresight, and these Guidelines have been prepared to provide those new to the field and others engaged in teaching and instruction with the information necessary to increase their awareness of the problems and to enable them to deal with them effectively. The Guidelines cover areas such as development, acquisition, authentication, cryopreservation, transfer of cell lines between laboratories, microbial contamination, characterisation, instability and misidentification. Advice is also given on complying with current legal and ethical requirements when deriving cell lines from human and animal tissues, the selection and maintenance of equipment and how to deal with problems that may arise

Storage Problems of Poplar Chips from Short Rotation Plantations with Special Emphasis on Fungal Development = Rövid vágásfordulójú nyár apríték tárolási problémái, különös tekintettel a kifejlődő gombákra

There are several problems in storing wood chips freshly harvested from short rotation plantations, which result in quality losses as well as in dry matter and energy losses. The factors influencing the degradation of raw material are examined in this paper with special focus on fungal development. An excessive growth of fungi is connected to dry matter losses and also to an increased health risk during raw material handling. The following factors were measured during 6 months storage of poplar wood chips depending on particle size: box temperature, moisture content, pH-value, appearance of fungi in the storage and the concentration of fungal particles in the air. The results show a close connection between particle size, temperature and attack of fungi. During the storage mesophilic and termophilic species of the genera Alternaria, Aspergillus, Cladosporium, Mucor and Penicillium appeared. The concentration of fungal particles is the highest for fine chips and decreases in bigger particles. There was a special focus on the investigation of the properties of coarse chips (G 50), which represent a good compromise between handling, storage losses and health risk due to fungal development. | Frissen kitermelt rövid vágásfordulójú fafajokból előállított apríték tárolása során számos probléma merül fel, melyek eredménye minőség-, szárazanyag- és energiaveszteség. Ebben a tanulmányban a nyersanyag-degradációt befolyásoló tényezők kerültek vizsgálatra, különös tekintettel a kifejlődő gombákra. Ezek rendkívüli elszaporodásának köszönhető a szárazanyag-veszteség mellett a nyersanyag kezelése során fellépő, megnövekedett egészségügyi kockázat is. Nyár faapríték hat hónapos tárolása folyamán az aprítékméret függvényében a következő tényezők mérése zajlott: a tárolón belüli hőmérséklet, nedvességtartalom, pH, a tárolóban megjelenő gombák és azok száma a levegőben. Az eredmények szoros összefüggést mutatnak, különösen az aprítékméret, a hőmérséklet és a gombák száma közt. A tárolás során mezofil és termofil gombák fejlődtek. A következő nemzetségekhez tartozó fajok voltak megfigyelhetők: Alternaria, Aspergillus, Cladosporium, Mucor, Penicillium. A gombák száma a finom aprítéknál volt a legmagasabb, ami az aprítékméret növekedésével csökkent. A kutatás folyamán különös szerepet kapott a középfinom apríték tulajdonságainak vizsgálata (G 50), mely kompromisszumos megoldást jelent a kezelés, tárolási veszteségek és a kifejlődő gombáknak köszönhető egészségügyi kockázatok között

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Antimicrobial activity of carbon-based fillers

Diplomová práce se zabývá vlivem uhlíkatého plniva na životaschopnost a produkci extracelulárních látek vybrané bakterie Bacillus subtilis (CCM 1999) a kvasinky Yarrowia lipolytica (CCY 29-26-52). Antimikrobiální aktivita těchto částic, přítomných v kultivačním mediu, byla sledována pomocí následujících parametrů: růst daného mikroorganismu, produkce extracelulárních proteinů a v poslední řadě byla monitorována produkce extracelulárních polymerních substancí, které mají úzkou souvislost s tvorbou biofilmu. Suspenze materiálů (0,135 mg/mL) byly připraveny ve dvou rozdílných kultivačních mediích; tzn. živné medium s obsahem glukózy pro Bacillus subtilis a bazální medium s přídavkem Tweenu 80 pro Yarrowia lipolytica, a media byla inokulována příslušným typem mikroorganismu. Experimenty probíhaly po dobu 6 dnů při rychlosti třepání 160 rpm a teplotě 30 °C pro Bacillus subtilis a 28 °C pro Yarrowia lipolytica. Testovány byly celkem tři typy uhlíkatého nanomateriálu, získané z Katedry anorganické chemie, Vysoké školy chemicko-technologické v Praze. Tyto materiály specifikované jako materiál “A”, “B” a “C” se navzájem lišily velikostí částic a stupněm oxidace. Na základě skríningových studií byla vybrána koncentrace testovaného materiálu 0,135 mg/mL a rychlost třepání 160 rpm. Metodou měření optické hustoty vzorku při 600 nm byly sestaveny a porovnány růstové křivky obou mikroorganismů v přítomnosti testovaných nanočástic po dobu 5 dní. Tímto způsobem bylo zjištěno, že přítomnost nanočástic v mediu nemá velký vliv na růst zkoumaného mikroorganismu. Tato metoda, je však pouze orientační, protože se nevyhneme chybě díky přítomnosti mrtvých buněk. Dále byla testována produkce celkových a extracelulárních proteinů daným mikroorganismem v přítomnosti testovaných nanočástic. Nebyla však pozorována výrazná odchylka hodnot od hodnot kontrolního vzorku, který neobsahoval testovaný materiál. Na základě metod počítání kolonií (Bacillus subtilis) a buněk (Yarrowia lipolytica) byly určeny ztráty životaschopnosti mikroorganismu ve 3 časech (6, 48 a 144 hodin); v kratším časovém intervalu byl růst spíše podporován. Dále byla monitorována produkce extracelulárních polymerních substancí (EPS), tedy proteinů, redukujících substancí a polysacharidů. Tyto látky byly vylučovány daným mikroorganismem do prostředí v průběhu 24 hodin. Bacillus subtilis produkoval EPS ve větší míře než Yarrowia lipolytica. Předpokládáme, že produkce EPS by mohla souviset s tvorbou biofilmu, který chrání buňky před toxicitou nanočástic.The aim of this diploma thesis is focused on the impact of carbon-based fillers on viability and extracellular substances production by bacterium Bacillus subtilis (CCM 1999) and yeast Yarrowia lipolytica (CCY 29-26-52). Antimicrobial activity of these particles, present in cultivation nutrient medium was examined using following parameters: growth of mentioned microorganisms, production of extracellular proteins and finally extracellular polymeric substances production, which is strongly connected with biofilm formation. Nanomaterials suspension (0.135 mg/mL) was prepared in two different cultivation media i.e. nutrient medium supplemented with glucose for Bacillus subtilis and basal medium with the addition of 2% (vol.) Tween 80 for Yarrowia lipolytica and media were inoculated by appropriate type of microorganism. Experiments were performed for 6 days under shaking rate at 160 rpm and at temperature of 30 °C for Bacillus subtilis and 28 °C for Yarrowia lipolytica. Three types of carbon nanomaterials obtained from Department of Inorganic Chemistry, Institute of Chemical Technology, Prague were examined. These materials specified as material “A”, “B” and “C” are mutually different by the size of its particles and the degree of oxidation. Based on the screening studies the tested material concentration of 0.135 mg/mL and shaking rate of 160 rpm were chosen. According to the optical density measurement at 600 nm, the growth curves of both microorganisms in the presence of tested nanoparticles during 5 days period were compared. It was find out, that the presence of nanoparticles don’t have a significant influence on tested microorganisms growth, by this technique. However, this method is just wider point of view, due to mistakes caused by presence of dead cells. Further, production of total cells proteins and extracellular proteins by microorganisms in presence of tested nanoparticles was examined. There was not observed any significant deviation from control samples values, where the tested materials were absent. Based on colony counting method (used for Bacillus subtilis) and cells counting in Bürker counting chamber (used for Yarrowia lipolytica), loss of microorganism viability was determined in 3 cultivation periods (6, 48 and 144 hours); there was observed a support of growth of microorganisms rather in shorter incubation period. Thereafter the extracellular polymeric substances (EPS) production that means proteins, reducing substances and polysaccharides was monitored. These substances were secreted into the medium by mentioned microorganisms during 24 hours of incubation. Bacillus subtilis cells produce much more EPS than Yarrowia lipolytica cells. We suppose that the EPS production could be closely associated with production of biofilm, which protects cells against nanoparticles toxicity.

CD8 T-cell induction against vascular endothelial growth factor receptor 2 by Salmonella for vaccination purposes against a murine melanoma.

The Salmonella type III secretion system (T3SS) efficiently translocates heterologous proteins into the cytosol of eukaryotic cells. This leads to an antigen-specific CD8 T-cell induction in mice orally immunized with recombinant Salmonella. Recently, we have used Salmonella's T3SS as a prophylactic and therapeutic intervention against a murine fibrosarcoma. In this study, we constructed a recombinant Salmonella strain translocating the immunogenic H-2D(b)-specific CD8 T-cell epitope VILTNPISM (KDR2) from the murine vascular endothelial growth factor receptor 2 (VEGFR2). VEGFR2 is a member of the tyrosine protein kinase family and is upregulated on proliferating endothelial cells of the tumor vasculature. After single orogastric vaccination, we detected significant numbers of KDR2-tetramer-positive CD8 T cells in the spleens of immunized mice. The efficacy of these cytotoxic T cells was evaluated in a prophylactic setting to protect mice from challenges with B16F10 melanoma cells in a flank tumor model, and to reduce dissemination of spontaneous pulmonary melanoma metastases. Vaccinated mice revealed a reduction of angiogenesis by 62% in the solid tumor and consequently a significant decrease of tumor growth as compared to non-immunized mice. Moreover, in the lung metastasis model, immunization with recombinant Salmonella resulted in a reduction of the metastatic melanoma burden by approximately 60%

Reporting guidelines, review of methodological standards, and challenges toward harmonization in bone marrow adiposity research. Report of the Methodologies Working Group of the International Bone Marrow Adiposity Society

The interest in bone marrow adiposity (BMA) has increased over the last decade due to its association with, and potential role, in a range of diseases (osteoporosis, diabetes, anorexia, cancer) as well as treatments (corticosteroid, radiation, chemotherapy, thiazolidinediones). However, to advance the field of BMA research, standardization of methods is desirable to increase comparability of study outcomes and foster collaboration. Therefore, at the 2017 annual BMA meeting, the International Bone Marrow Adiposity Society (BMAS) founded a working group to evaluate methodologies in BMA research. All BMAS members could volunteer to participate. The working group members, who are all active preclinical or clinical BMA researchers, searched the literature for articles investigating BMA and discussed the results during personal and telephone conferences. According to the consensus opinion, both based on the review of the literature and on expert opinion, we describe existing methodologies and discuss the challenges and future directions for (1) histomorphometry of bone marrow adipocytes, (2