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Rare Ones (rare + ones)
Selected AbstractsThe structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genesENVIRONMENTAL MICROBIOLOGY, Issue 5 2010David L. Kirchman Summary Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the ,seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones. [source] The lognormal distribution is not an appropriate null hypothesis for the species,abundance distributionJOURNAL OF ANIMAL ECOLOGY, Issue 3 2005MARK WILLIAMSON Summary 1Of the many models for species,abundance distributions (SADs), the lognormal has been the most popular and has been put forward as an appropriate null model for testing against theoretical SADs. In this paper we explore a number of reasons why the lognormal is not an appropriate null model, or indeed an appropriate model of any sort, for a SAD. 2We use three empirical examples, based on published data sets, to illustrate features of SADs in general and of the lognormal in particular: the abundance of British breeding birds, the number of trees > 1 cm diameter at breast height (d.b.h.) on a 50 ha Panamanian plot, and the abundance of certain butterflies trapped at Jatun Sacha, Ecuador. The first two are complete enumerations and show left skew under logarithmic transformation, the third is an incomplete enumeration and shows right skew. 3Fitting SADs by ,2 test is less efficient and less informative than fitting probability plots. The left skewness of complete enumerations seems to arise from a lack of extremely abundant species rather than from a surplus of rare ones. One consequence is that the logit-normal, which stretches the right-hand end of the distribution, consistently gives a slightly better fit. 4The central limit theorem predicts lognormality of abundances within species but not between them, and so is not a basis for the lognormal SAD. Niche breakage and population dynamical models can predict a lognormal SAD but equally can predict many other SADs. 5The lognormal sits uncomfortably between distributions with infinite variance and the log-binomial. The latter removes the absurdity of the invisible highly abundant half of the individuals abundance curve predicted by the lognormal SAD. The veil line is a misunderstanding of the sampling properties of the SAD and fitting the Poisson lognormal is not satisfactory. A satisfactory SAD should have a thinner right-hand tail than the lognormal, as is observed empirically. 6The SAD for logarithmic abundance cannot be Gaussian. [source] Protein EqualizerÔ Technology, : The quest for a "democratic proteome"PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2006Pier Giorgio Righetti Professor Abstract No proteome can be considered "democratic", but rather "oligarchic", since a few proteins dominate the landscape and often obliterate the signal of the rare ones. This is the reason why most scientists lament that, in proteome analysis, the same set of abundant proteins is seen again and again. A host of pre-fractionation techniques have been described, but all of them, one way or another, are besieged by problems, in that they are based on a "depletion principle", i.e. getting rid of the unwanted species. Yet "democracy" calls not for killing the enemy, but for giving "equal rights" to all people. One way to achieve that would be the use of "Protein Equalizer Technology" for reducing protein concentration differences. This comprises a diverse library of combinatorial ligands coupled to spherical porous beads. When these beads come into contact with complex proteomes (e.g. human urine and serum, egg white, and any cell lysate, for that matter) of widely differing protein composition and relative abundances, they are able to "equalize" the protein population, by sharply reducing the concentration of the most abundant components, while simultaneously enhancing the concentration of the most dilute species. It is felt that this novel method could offer a strong step forward in bringing the "unseen proteome" (due to either low abundance and/or presence of interference) within the detection capabilities of current proteomics detection methods. Examples are given of equalization of human urine and serum samples, resulting in the discovery of a host of proteins never reported before. Additionally, these beads can be used to remove host cell proteins from purified recombinant proteins or protein purified from natural sources that are intended for human consumption. These proteins typically reach purities of the order of 98%: higher purities often become prohibitively expensive. Yet, if incubated with "equalizer beads", these last impurities can be effectively removed at a small cost and with minute losses of the main, valuable product. [source] Morphological and molecular analysis of bromeliad-inhabiting ciliates in EcuadorTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005MICAH SAUL DUNTHORN The microbial inhabitants of Neotropical forests are poorly known. According to Finlay (2002, Science, 296:1061,1063) the majority of taxa in tropical forests should be previously described elsewhere. Conversely, Foissner (1999, Protist, 150:363,368) points to examples of endemic protists, and states that while we can identify the common species there are few trained taxonomists to identify the rare ones in large sampling investigations. To test these hypotheses, I am following up on an initial study of Foissner et al. (2003, Europ. J. Protistol., 39:365,372) of the ciliates inhabiting waters in canopy, sub-canopy and terrestrial bromeliad tanks in two Ecuadorian forests. Using morphological (protargol, silver nitrate, and silver carbonate stains; scanning electron micrographs) and molecular methods (SSU and ITS sequencing) I will concentrate my investigations on the colpodid taxa found free-living in the bromeliad tanks in two Ecuadorian forests. If I find many new taxa, Finlay's hypothesis may not be applicable to atleast bromeliad-inhabiting ciliates. [source] Prospective application of a multiplex reverse transcription-polymerase chain reaction assay for the detection of balanced translocations in leukaemia: a single-laboratory study of 390 paediatric and adult patientsBRITISH JOURNAL OF HAEMATOLOGY, Issue 1 2004Lene Hyldahl Olesen Summary The upfront application of molecular methods for identifying the fusion transcripts arising from balanced translocations in haematopoietic malignancies has several advantages: sensitivity is independent of its frequency, i.e. rare ones are not missed, cytogenetically cryptic aberrations are identified and it provides a platform for minimal residual disease (MRD) detection. Employing a multiplex reverse transcription polymerase chain reaction (RT-PCR) assay identifying 27 fusion transcripts we prospectively analysed blood and/or bone marrow samples from 390 patients referred for diagnosis and treatment for acute leukaemia and chronic myeloproliferative disorders (CMPD) from a geographically well-defined region in Denmark. A total of 233 patients were diagnosed with acute myeloid leukaemia (AML), 95 with acute lymphoblastic leukaemia (ALL) origin and 62 patients were recorded as CMPD. Twenty-three percent AML, 32% ALL and 55% CMPD patients exhibited chromosomal aberrations detected by the multiplex RT-PCR. Cytogenetically cryptic translocations were seen in 15% of the cases. Conversely, the cytogenetic analysis identified chromosomal aberrations other than translocations in 45% of AML cases and 63% of ALL cases. We conclude that, while the fraction of translocation positive leukaemia patients in an unselected cohort is lower than hitherto believed, a molecular approach to their diagnosis is worthwhile, partly for identifying cryptic and rare translocations, partly for monitoring MRD. [source] | ||||||||||