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Search Results: 1 - 10 of 178 matches for " Jenni Hultman "
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Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere  [PDF]
Malin Bomberg, Mari Nyyss?nen, Aura Nousiainen, Jenni Hultman, Lars Paulin, Petri Auvinen, Merja It?vaara
Open Journal of Ecology (OJE) , 2014, DOI: 10.4236/oje.2014.48040
Abstract:

A suite of molecular methods targeting 16S rRNA genes (i.e., DGGE, clone and high-throughput [HTP] amplicon library sequencing) was used to profile the microbial communities in deep Fennoscandian crystalline bedrock fracture fluids. Variation among bacterial 16S rRNA genes was examined with two commonly used primer pairs: P1/P2 and U968f/U1401r. DGGE using U968f/ U1401r mostly detected β-, γ-proteobacteria and Firmicutes, while P1/P2 primers additionally detected other proteobacterial clades and candidate divisions. However, in combination with clone libraries the U968f/U1401r primers detected a higher bacterial diversity than DGGE alone. HTP amplicon sequencing with P1/P2 revealed an abundance of the DGGE bacterial groups as well as many other bacterial taxa likely representing minor components of these communities. Archaeal diversity was investigated via DGGE or HTP amplicon sequencingusing primers A344F/ 519RP. The majority of archaea detected with HTP amplicon sequencing belonged to uncultured Thermoplasmatales and Pendant 33/DHVE3, 4, 6 groups. DGGE of the same samples detected mostly SAGMEG and Methanosarcinales archaea, but almost none of those were revealed by HTP amplicon sequencing. Overall, our results show that the inferred diversity and composition of microbial communities in deep fracture fluids is highly dependent on analytical technique and that the method should be carefully selected with this in mind.

Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
Jarmo Ritari, Lars Paulin, Jenni Hultman, Petri Auvinen
BMC Research Notes , 2009, DOI: 10.1186/1756-0500-2-249
Abstract: Here we demonstrate the application of a per-spot hybridization control oligonucleotide probe and a novel way of computing normalization for tag array data. The method takes into account the absolute value of the detection probe signal and the variability in the control probe signal to significantly alleviate problems caused by artefacts and noise on low quality microarrays.Diagnostic microarray platforms require experimental and computational tools to enable efficient correction of array artefacts. The techniques presented here improve the signal to noise ratio and help in determining true positives with better statistical significance and in allowing the use of arrays with poor quality that would otherwise be discarded.Nucleic acid detection by ligation and single-nucleotide extension minisequencing techniques take advantage of the catalytic selectivity of DNA ligase and polymerase enzymes, respectively, to recognize a unique position in a target DNA strand. In ligation assays, two specific ssDNA oligonucleotide detection probes are designed to hybridize adjacently on target DNA strand so that the 3' end of the label-carrying probe recognizes a discriminating position and is ligated to the phosphorylated 5' end of the other probe in the presence of a matching target molecule (figure 1A) [1,2]. Ligation detection can also be implemented as a single probe which is circularized upon ligation [3]. In minisequencing, the target is recognized through the addition of a specific labeled dideoxynucleotide to the 3' end of the oligonucleotide detection primer annealed immediately upstream of a discriminating position in the target (figure 1B) [4,5]. Both methods allow tagging of the probes for detection on a microarray platform containing complementary tag sequences providing uniform thermodynamic hybridization properties for all probes. The relatively high throughput and superior accuracy over traditional microarray and PCR based methods have motivated the application of l
Universal ligation-detection-reaction microarray applied for compost microbes
Jenni Hultman, Jarmo Ritari, Martin Romantschuk, Lars Paulin, Petri Auvinen
BMC Microbiology , 2008, DOI: 10.1186/1471-2180-8-237
Abstract: Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS) area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array.This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.Composting is one of the principal methods to treat separately collected biodegradable waste. In composting, organic material is aerobically decomposed into humus-like material by bacteria, fungi and, to a lesser extent, other larger organisms [1]. To understand the composting process and the ecological processes of composting, the microbes present in the process need to be tracked. The compost microbiota have been characterised with a variety of molecular and cultivation based methods in both laboratory and full-scale processes (e.g. [2-6]. In order to follow the industrial composting process and to confirm the hygienisation of the compost, the microbiology needs to be understood and followed. Several approaches has been used to resolve compost microbiology, such as single-stranded conformational polymorphism (SSCP) [7], automated rRNA intergenic spacer analysis (ARISA) [5] denaturing gradient gel electrophoresis (DGGE) [3,4] and cloning and sequencing (Hultman et al. unpublished, Partanen et al. unpublished). Common to the technologies mentioned above is that they are rather time consuming and not suitable for routine determination of compost
Bacterial diversity at different stages of the composting process
Pasi Partanen, Jenni Hultman, Lars Paulin, Petri Auvinen, Martin Romantschuk
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-94
Abstract: Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts.Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.Composting is an aerobic process, during which organic waste is biologically degraded by micro-organisms to humus-like material. The end product should not contain pathogens or viable seeds, and it should be stable and suitable for use as a soil amendment [1]. Many factors such as oxygen content, moisture, composition of the feed, pH, and temperature, affect the composting process and ultimately the end product. Furthermore, these parameters are strongly connected.The source of separated biowaste, as collected and treated in the Nordic countries and other cold climate areas, primarily consists of food waste which in itself has a low pH and contains high quantities of carbohydrates that form organic acids upon degradation. The low initial pH limits microbial activity and delays the increase in temperature [2,3].In recent years, composting has attracted much attention as a viable and environmentally sensible alternative for treatment of or
Detection of Human Papillomaviruses by Polymerase Chain Reaction and Ligation Reaction on Universal Microarray
Jarmo Ritari, Jenni Hultman, Rita Fingerroos, Jussi Tarkkanen, Janne Pullat, Lars Paulin, Niina Kivi, Petri Auvinen, Eeva Auvinen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034211
Abstract: Sensitive and specific detection of human papillomaviruses (HPV) in cervical samples is a useful tool for the early diagnosis of epithelial neoplasia and anogenital lesions. Recent studies support the feasibility of HPV DNA testing instead of cytology (Pap smear) as a primary test in population screening for cervical cancer. This is likely to be an option in the near future in many countries, and it would increase the efficiency of screening for cervical abnormalities. We present here a microarray test for the detection and typing of 15 most important high-risk HPV types and two low risk types. The method is based on type specific multiplex PCR amplification of the L1 viral genomic region followed by ligation detection reaction where two specific ssDNA probes, one containing a fluorescent label and the other a flanking ZipCode sequence, are joined by enzymatic ligation in the presence of the correct HPV PCR product. Human beta-globin is amplified in the same reaction to control for sample quality and adequacy. The genotyping capacity of our approach was evaluated against Linear Array test using cervical samples collected in transport medium. Altogether 14 out of 15 valid samples (93%) gave concordant results between our test and Linear Array. One sample was HPV56 positive in our test and high-risk positive in Hybrid Capture 2 but remained negative in Linear Array. The preliminary results suggest that our test has accurate multiple HPV genotyping capability with the additional advantages of generic detection format, and potential for high-throughput screening.
Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation
Jarmo Ritari, Kaisa Koskinen, Jenni Hultman, Jukka M Kurola, Maritta Kym?l?inen, Martin Romantschuk, Lars Paulin, Petri Auvinen
BMC Microbiology , 2012, DOI: 10.1186/1471-2180-12-121
Abstract: The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%.The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.
Criteria for rational smoothness of some symmetric orbit closures
Axel Hultman
Mathematics , 2009,
Abstract: Let $G$ be a connected reductive linear algebraic group over $\C$ with an involution $\theta$. Denote by $K$ the subgroup of fixed points. In certain cases, the $K$-orbits in the flag variety $G/B$ are indexed by the twisted identities $\iot = \{\theta(w^{-1})w\mid w\in W\}$ in the Weyl group $W$. Under this assumption, we establish a criterion for rational smoothness of orbit closures which generalises classical results of Carrell and Peterson for Schubert varieties. That is, whether an orbit closure is rationally smooth at a given point can be determined by examining the degrees in a ``Bruhat graph'' whose vertices form a subset of $\iot$. Moreover, an orbit closure is rationally smooth everywhere if and only if its corresponding interval in the Bruhat order on $\iot$ is rank symmetric. In the special case $K=\Sp_{2n}(\C)$, $G=\SL_{2n}(\C)$, we strengthen our criterion by showing that only the degree of a single vertex, the ``bottom one'', needs to be examined. This generalises a result of Deodhar for type $A$ Schubert varieties.
Inversion arrangements and Bruhat intervals
Axel Hultman
Mathematics , 2010,
Abstract: Let $W$ be a finite reflection group. For a given $w \in W$, the following assertion may or may not be satisfied: (*) The principal Bruhat order ideal of $w$ contains as many elements as there are regions in the inversion hyperplane arrangement of $w$. We present a type independent combinatorial criterion which characterises the elements $w\in W$ that satisfy (*). A couple of immediate consequences are derived: (1) The criterion only involves the order ideal of $w$ as an abstract poset. In this sense, (*) is a poset-theoretic property. (2) For $W$ of type $A$, another characterisation of (*), in terms of pattern avoidance, was previously given in collaboration with Linusson, Shareshian and Sj\"ostrand. We obtain a short and simple proof of that result. (3) If $W$ is a Weyl group and the Schubert variety indexed by $w \in W$ is rationally smooth, then $w$ satisfies (*).
Permutation statistics of products of random permutations
Axel Hultman
Mathematics , 2013,
Abstract: Given a permutation statistic $s : S_n \to \mathbb{R}$, define the mean statistic $\bar{s}$ as the statistic which computes the mean of $s$ over conjugacy classes. We describe a way to calculate the expected value of $s$ on a product of $t$ independently chosen elements from the uniform distribution on a union of conjugacy classes $\Gamma \subseteq S_n$. In order to apply the formula, one needs to express the class function $\bar{s}$ as a linear combination of irreducible $S_n$-characters. We provide such expressions for several commonly studied permutation statistics, including the excedance number, inversion number, descent number, major index and $k$-cycle number. In particular, this leads to formulae for the expected values of said statistics.
Link complexes of subspace arrangements
Axel Hultman
Mathematics , 2005,
Abstract: Given a simplicial hyperplane arrangement H and a subspace arrangement A embedded in H, we define a simplicial complex Delta_{A,H} as the subdivision of the link of A induced by H. In particular, this generalizes Steingrimsson's coloring complex of a graph. We do the following: (1) When A is a hyperplane arrangement, Delta_{A,H} is shown to be shellable. As a special case, we answer affirmatively a question of Steingrimsson on coloring complexes. (2) For H being a Coxeter arrangement of type A or B we obtain a close connection between the Hilbert series of the Stanley-Reisner ring of Delta_{A,H} and the characteristic polynomial of A. This extends results of Steingrimsson and provides an interpretation of chromatic polynomials of hypergraphs and signed graphs in terms of Hilbert polynomials.
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