A cell spot microarray method for high-throughput biology

High-throughput screening of cellular effects of RNA interference (RNAi) libraries is now being increasingly applied to explore the role of genes in specific cell biological processes and disease states. However, the technology is still limited to specialty laboratories, due to the requirements for robotic infrastructure, access to expensive reagent libraries, expertise in high-throughput screening assay development, standardization, data analysis and applications. In the future, alternative screening platforms will be required to expand functional large-scale experiments to include more RNAi constructs, allow combinatorial loss-of-function analyses (e.g. genegene or gene-drug interaction), gain-of-function screens, multi-parametric phenotypic readouts or comparative analysis of many different cell types. Such comprehensive perturbation of gene networks in cells will require a major increase in the flexibility of the screening platforms, throughput and reduction of costs. As an alternative for the conventional multi-well based high-throughput screening -platforms, here the development of a novel cell spot microarray method for production of high density siRNA reverse transfection arrays is described. The cell spot microarray platform is distinguished from the majority of other transfection cell microarray techniques by the spatially confined array layout that allow highly parallel screening of large-scale RNAi reagent libraries with assays otherwise difficult or not applicable to high-throughput screening. This study depicts the development of the cell spot microarray method along with biological application examples of high-content immunofluorescence and phenotype based cancer cell biological analyses focusing on the regulation of prostate cancer cell growth, maintenance of genomic integrity in breast cancer cells, and functional analysis of integrin protein-protein interactions in situ.RNA-interferenssin (RNAi) käyttö geenituotteiden toimintojen tutkimuksessa on vuosikymmenessä kehittynyt solubiologisen tutkimuksen merkittävimpien teknologioiden joukkoon. RNAi-menetelmät ovat mahdollistaneet myös eri solubiologisten signaalivälitysreittien kartoittamisen koko perimänlaajuisten geenitoimintojen suurtehoseulonnan avulla. Teknologian nopeasta kehityksestä ja laajamittaisesta hyödyntämisestä huolimatta, RNAi-menetelmien käyttö suurtehoseulontaan rajoittuu edelleen erikoislaboratorioihin huomattavien laite-, reagenssi- sekä tietotaitovaatimusten johdosta. Lisäksi yleisimmin käytetyt kuoppalevypohjaiset seulonta-menetelmät rajoittavat seulontatutkimusten laajuutta, eri analyysimenetelmien käyttöä sekä useiden mallisolulinjojen rinnakkaista seulontaa suuren reagenssikulutuksen takia. RNAi-suurtehoseulonnan kustannuksien ja laiteriippuvuuden alentamiseksi sekä monipuolisuuden lisäämiseksi tulevaisuudessa tarvitaan uusia vaihtoehtoisia seulontamenetelmiä. Tämän väitöskirjatyön lähtökohtana oli uuden kuoppalevyillä tehtäviä seulontamenetelmiä edullisemman ja monipuolisemman RNAi-suurtehoseulontamenetelmän kehittäminen. Tutkimuksessa kehitettiin solujen siRNA käänteistransfektioon perustuva solumikrosirumenetelmä, joka tarkasti rajattujen siRNA näytepisteiden avulla mahdollistaa jopa koko ihmisen perimänlaajuisten siRNA näytekirjastojen seulonnan yksittäisellä mittasirulla. Menetelmän suuri näytetiheys sekä sirujen pieni pinta-ala mahdollistavat myös erikoismittamenetelmien käytön suurtehoseulonnassa, jotka teknisistä tai kustannussyistä eivät sovellu käytettäväksi suurtehoseulontaan kuoppalevyillä. Väitöskirjan ensimmäinen osatyö kuvaa menetelmän kehittämistyön. Väitöskirjan toisessa, kolmannessa ja neljännessä osatyössä menetelmää on hyödynnetty syöpäbiologisissa seulontatutkimuksissa selvitettäessä geenejä jotka vaikuttavat eturauhassyöpäsolujen kasvuun, rintasyöpäsolujen solunjakautumiseen sekä integriini tarttumisreseptorien aktiivisuuden säätelyyn.Siirretty Doriast

Impacts of land cover data selection and trait parameterisation on dynamic modelling of species' range expansion

Peer reviewedPublisher PD

Multiplexed readout of kinetic inductance bolometer arrays

Kinetic inductance bolometer (KIB) technology is a candidate for passive sub-millimeter wave and terahertz imaging systems. Its benefits include scalability into large 2D arrays and operation with intermediate cryogenics in the temperature range of 5 -- 10 K. We have previously demonstrated the scalability in terms of device fabrication, optics integration, and cryogenics. In this article, we address the last missing ingredient, the readout. The concept, serial addressed frequency excitation (SAFE), is an alternative to full frequency-division multiplexing at microwave frequencies conventionally used to read out kinetic inductance detectors. We introduce the concept, and analyze the criteria of the multiplexed readout avoiding the degradation of the signal-to-noise ratio in the presence of a thermal anti-alias filter inherent to thermal detectors. We present a practical scalable realization of a readout system integrated into a prototype imager with 8712 detectors. This is used for demonstrating the noise properties of the readout. Furthermore, we present practical detection experiments with a stand-off laboratory-scale imager.Comment: 7 pages, 6 figure

Effect of xylitol-containing carbohydrate mixtures on acid and ammonia production in suspensions of salivary sediment

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75508/1/j.1600-0722.1987.tb01631.x.pd

Combinatorics on words in information security: Unavoidable regularities in the construction of multicollision attacks on iterated hash functions

Classically in combinatorics on words one studies unavoidable regularities that appear in sufficiently long strings of symbols over a fixed size alphabet. In this paper we take another viewpoint and focus on combinatorial properties of long words in which the number of occurrences of any symbol is restritced by a fixed constant. We then demonstrate the connection of these properties to constructing multicollision attacks on so called generalized iterated hash functions.Comment: In Proceedings WORDS 2011, arXiv:1108.341

Impacts of different climate change regimes and extreme climatic events on an alpine meadow community

Climate variability is expected to increase in future but there exist very few experimental studies that apply different warming regimes on plant communities over several years. We studied an alpine meadow community under three warming regimes over three years. Treatments consisted of (a) a constant level of warming with open-top chambers (ca. 1.9 °C above ambient), (b) yearly stepwise increases in warming (increases of ca. 1.0, 1.9 and 3.5 °C), and (c) pulse warming, a single first-year pulse event of warming (increase of ca. 3.5 °C). Pulse warming and stepwise warming was hypothesised to cause distinct first-year and third-year effects, respectively. We found support for both hypotheses; however, the responses varied among measurement levels (whole community, canopy, bottom layer, and plant functional groups), treatments, and time. Our study revealed complex responses of the alpine plant community to the different experimentally imposed climate warming regimes. Plant cover, height and biomass frequently responded distinctly to the constant level of warming, the stepwise increase in warming and the extreme pulse-warming event. Notably, we found that stepwise warming had an accumulating effect on biomass, the responses to the different warming regimes varied among functional groups, and the short-term perturbations had negative effect on species richness and diversityNFR grant (B-AA/BU 08424) to UM

Impact of the automated dose dispensing with medication review on geriatric primary care patients drug use in Finland : a nationwide cohort study with matched controls

Objective: In an automated dose dispensing (ADD) service, medicines are dispensed in unit-dose bags according to administration times. When the service is initiated, the patient’s medication list is reconciled and a prescription review is conducted. The service is expected to reduce drug use. The aim of this national controlled study was to investigate whether the ADD service with medication review reduces drug use among geriatric primary care patients. Design, setting and patients: This is a nationwide cohort study with matched controls. The study group consisted of all primary care patients ≥65 years enrolled in the ADD service in Finland during 2007 (n = 2073). Control patients (n = 2073) were matched by gender, age, area of patient’s residence and number of the prescription drugs reimbursed. The data on all prescription drugs reimbursed during the 1 year periods before and after the ADD service enrollment were extracted from the Finnish National Prescription Register. Drug use was calculated as defined daily doses (DDD) per day. Results: The studied 20 most used drugs covered 86% of all reimbursed drug use (in DDD) of the study group. The use of 11 out of these 20 active substances studied was reduced significantly (p < .001–.041) when the drug use was adjusted by the number of chronic diseases. Two of these drugs were hypnotics and six were cardiovascular system drugs. Conclusions: Drug use was decreased after initiation of the ADD service in primary care patients ≥65 years compared to matched controls in this 1 year cohort study. Further studies should be conducted in order to explore the causality, assess the ADD service’s impact on drug use quality and costs, as well as impact of accompanied prescription review on positive outcomes.Peer reviewe

Quantum circuits with uniformly controlled one-qubit gates

Uniformly controlled one-qubit gates are quantum gates which can be represented as direct sums of two-dimensional unitary operators acting on a single qubit. We present a quantum gate array which implements any n-qubit gate of this type using at most 2^{n-1} - 1 controlled-NOT gates, 2^{n-1} one-qubit gates and a single diagonal n-qubit gate. The circuit is based on the so-called quantum multiplexor, for which we provide a modified construction. We illustrate the versatility of these gates by applying them to the decomposition of a general n-qubit gate and a local state preparation procedure. Moreover, we study their implementation using only nearest-neighbor gates. We give upper bounds for the one-qubit and controlled-NOT gate counts for all the aforementioned applications. In all four cases, the proposed circuit topologies either improve on or achieve the previously reported upper bounds for the gate counts. Thus, they provide the most efficient method for general gate decompositions currently known.Comment: 8 pages, 10 figures. v2 has simpler notation and sharpens some result