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21.
qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data 总被引:14,自引:0,他引:14
Although quantitative PCR (qPCR) is becoming the method of choice for expression profiling of selected genes, accurate and straightforward processing of the raw measurements remains a major hurdle. Here we outline advanced and universally applicable models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track. These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data. 相似文献
22.
Piasecka A Souffreau C Vandepitte K Vanysacker L Bilad RM Bie TD Hellemans B Meester LD Yan X Declerck P Vankelecom IF 《Biofouling》2012,28(2):225-238
Membrane biofouling was investigated during the early stages of filtration in a laboratory-scale membrane bioreactor operated on molasses wastewater. The bacterial diversity and composition of the membrane biofilm and activated sludge were analyzed using terminal restriction fragment length polymorphism coupled with 16S rRNA clone library construction and sequencing. The amount of extracellular polymeric substances produced by bacteria was investigated using spectroscopic methods. The results reveal that the bacterial community of activated sludge differs significantly from that of the membrane biofilm, especially at the initial phase. Phylogenetic analysis based on 16S rRNA gene sequences identified 25 pioneer OTUs responsible for membrane surface colonization. Also, the relationship between the identified bacterial strains and the system specifications was explored. 相似文献
23.
Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north-eastern Atlantic 总被引:1,自引:0,他引:1
Maarten H. D. Larmuseau Jeroen K. J. Van Houdt Jef Guelinckx Bart Hellemans Filip A. M. Volckaert 《Journal of Biogeography》2009,36(6):1138-1151
Aim The Pleistocene glaciations were the most significant historical event during the evolutionary life span of most extant species. However, little is known about the consequences of these climate changes for the distribution and demography of marine animals of the north‐eastern Atlantic. The present study focuses on the phylogeographic and demographic patterns of the sand goby, Pomatoschistus minutus (Teleostei: Gobiidae), a small marine demersal fish. Location North‐eastern Atlantic, Mediterranean, Irish, North and Baltic seas. Methods Analysis was carried out by sequencing the mtDNA cytochrome b gene of sand gobies from 12 localities throughout the species’ range, and using this information in combination with published data of allozyme markers and mtDNA control region sequences. Several phylogenetic methods and a network analysis were used to explore the phylogeographic pattern. The historical demography of P. minutus was studied through a mismatch analysis and a Bayesian skyline plot. Results Reciprocal monophyly was found between a Mediterranean Sea (MS) clade and an Atlantic Ocean (AO) clade, both with a Middle Pleistocene origin. The AO Clade contains two evolutionary significant units (ESUs): the Iberian Peninsula (IB) Group and the North Atlantic (NA) Group. These two groups diverged during Middle Pleistocene glacial cycles. For the NA Group there is evidence for geographic sorting of the ancestral haplotypes with recent radiations in the Baltic Sea, Irish Sea, North Sea and Bay of Biscay. The demographic histories of the Mediterranean Clade and the two Atlantic ESUs were influenced mainly by expansions dated as occurring during the Middle Pleistocene glaciations and post‐Eem, respectively. Main conclusions The pre‐LGM (Last Glacial Maximum) subdivision signals were not erased for P. minutus during the LGM. Middle Pleistocene glaciations yielded isolated and differently evolving sets of populations. In contrast to the case for most other taxa, only the northern Atlantic group contributed to the post‐glacial recolonization. The historical demography of Mediterranean sand gobies was influenced mainly by Middle Pleistocene glaciations, in contrast to that of the Atlantic populations, which was shaped by Late Pleistocene expansions. 相似文献
24.
Karine H. Hellemans Jean-Claude Hannaert Bart Denys Knut R. Steffensen Cindy Raemdonck Geert A. Martens Paul P. Van Veldhoven Jan-?ke Gustafsson Daniel Pipeleers 《PloS one》2009,4(9)
Chronically elevated levels of fatty acids-FA can cause beta cell death in vitro. Beta cells vary in their individual susceptibility to FA-toxicity. Rat beta cells were previously shown to better resist FA-toxicity in conditions that increased triglyceride formation or mitochondrial and peroxisomal FA-oxidation, possibly reducing cytoplasmic levels of toxic FA-moieties. We now show that stearoyl-CoA desaturase-SCD is involved in this cytoprotective mechanism through its ability to transfer saturated FA into monounsaturated FA that are incorporated in lipids. In purified beta cells, SCD expression was induced by LXR- and PPARα-agonists, which were found to protect rat, mouse and human beta cells against palmitate toxicity. When their SCD was inhibited or silenced, the agonist-induced protection was also suppressed. A correlation between beta cell-SCD expression and susceptibility to palmitate was also found in beta cell preparations isolated from different rodent models. In mice with LXR-deletion (LXRβ-/- and LXRαβ-/-), beta cells presented a reduced SCD-expression as well as an increased susceptibility to palmitate-toxicity, which could not be counteracted by LXR or PPARα agonists. In Zucker fatty rats and in rats treated with the LXR-agonist TO1317, beta cells show an increased SCD-expression and lower palmitate-toxicity. In the normal rat beta cell population, the subpopulation with lower metabolic responsiveness to glucose exhibits a lower SCD1 expression and a higher susceptibility to palmitate toxicity. These data demonstrate that the beta cell susceptibility to saturated fatty acids can be reduced by stearoyl-coA desaturase, which upon stimulation by LXR and PPARα agonists favors their desaturation and subsequent incorporation in neutral lipids. 相似文献
25.
Delfien Syx Fransiska Malfait Lut Van Laer Jan Hellemans Trinh Hermanns-Lê Andy Willaert Abdelmajid Benmansour Anne De Paepe Alain Verloes 《Human genetics》2010,128(1):79-88
Defects leading to impaired intracellular trafficking have recently been shown to play an important role in the pathogenesis
of genodermatoses, such as the Ehlers–Danlos and the cutis laxa syndromes. A new genodermatosis, termed macrocephaly, alopecia,
cutis laxa and scoliosis (MACS) syndrome has been described, resulting from a homozygous 1-bp deletion in RIN2. RIN2 encodes the Ras and Rab interactor 2, involved in the regulation of Rab5-mediated early endocytosis. We performed a clinical,
ultrastructural and molecular study in a consanguineous Algerian family with three siblings affected by a distinctive autosomal
recessive genodermatosis, reported in 2005 by Verloes et al. The most striking clinical features include progressive facial
coarsening, gingival hypertrophy, severe scoliosis, sparse hair and skin and joint hyperlaxity. Ultrastructural studies of
the skin revealed important abnormalities in the collagen fibril morphology, and fibroblasts exhibited a dilated endoplasmic
reticulum and an abnormal Golgi apparatus with rarefied and dilated cisternae. Molecular analysis of RIN2 revealed a novel homozygous 2-bp deletion in all affected individuals. The c.1914_1915delGC mutation introduces a frameshift
and creates a premature termination codon, leading to nonsense-mediated mRNA decay. These findings confirm that RIN2 defects are associated with a distinct genodermatosis and underscore the involvement of RIN2 and its associated pathways in the pathogenesis of connective tissue disorders. The current family displays considerable
phenotypic overlap with MACS syndrome. However, our family shows a dermatological and ultrastructural phenotype belonging
to the Ehlers–Danlos rather than the cutis laxa spectrum. Therefore, the MACS acronym is not entirely appropriate for the
current family. 相似文献
26.
Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods 总被引:1,自引:0,他引:1
Louise Vanysacker Steven A. J. Declerck Bart Hellemans Luc De Meester Ivo Vankelecom Priscilla Declerck 《Applied microbiology and biotechnology》2010,88(1):299-307
The effectiveness of three commercially available direct DNA isolation kits (Mobio, Fast, Qiagen) and one published direct
DNA extraction protocol (Bead) for extracting bacterial DNA from different types of activated sludge was investigated and
mutually compared. The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene.
Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. The resulting community
profiles were analyzed with canonical correspondence analysis. Our results clearly demonstrate that direct DNA extraction
methods can significantly influence the DNA quantity, purity, and observed community patterns of microbiota in activated sludge.
Fast and Mobio generated high amounts of good quality DNA compared to Bead and Qiagen. Mobio also resulted in the detection
of the highest number of species while Fast scored the best in discriminating between the community patterns of different
activated sludge types. With respect to the characterization of community profiles, our analyses demonstrated a strong sludge
type dependent variability among methods. Taking into account our results, we recommend Fast as the most suitable DNA extraction
method for activated sludge samples used for bacterial community studies. 相似文献
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29.
Phylogenetic relationships among Palearctic and Nearctic burbot (Lota lota): Pleistocene extinctions and recolonization 总被引:3,自引:0,他引:3
The burbot (Lota lota Linnaeus, 1758) is the only freshwater species from the cod family. Various taxonomic hypotheses were tested against molecular data by sequencing the mitochondrial cytochrome b locus of 120 burbot from 41 populations together with the related species Molva molva (ling) and Brosme brosme (tusk), which represented the other Lotinae genera. Within the genus Lota two distinct phylogroups were observed: one in North America south of the Great Slave Lakes (Lota lota maculosa) and one in Eurasia and the remainder of the Nearctic region (Lota lota lota). The burbot lineage separated 10 Myr BP from the other Lotinae, while the genetic variation within burbot appeared to be approximately 1 Myr old. However, fossil evidence suggested that burbot already existed in the Early Pliocene in Europe, from were it probably colonized North America in the Early Pleistocene. While Nearctic burbot survived climatic oscillations and diverged in several refugia, the Eurasian form became extinct or was reduced to a very small population. In the Late Pleistocene the species recolonized the Palearctic region to establish its present distribution range. 相似文献
30.