University of Colorado Boulder

About: University of Colorado Boulder is a education organization based out in Boulder, Colorado, United States. It is known for research contribution in the topics: Population & Galaxy. The organization has 48794 authors who have published 115151 publications receiving 5387328 citations. The organization is also known as: CU Boulder & UCB.

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

Abstract: We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.

Normalization and microbial differential abundance strategies depend upon data characteristics

Abstract: Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets ( 20 samples per group) but also critically the only method tested that has a good control of false discovery rate. These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.

Structure and function of intercellular junctions.

Abstract: Publisher Summary Intercellular junctions are specialized regions of contact between the apposed plasma membranes of adjacent cells, and recent evidence suggests that they are essential for the development of multicellular organisms. They provide the structural means for groups of cells to interact in certain defined ways, and thereby enable them to create structures of higher order. This chapter reviews the morphological information on intercellular junctions derived from thin-sectioning, negative staining and freeze-cleave techniques, as well as from x-ray diffraction and biochemical investigations, and correlates the structural parameters with known or proposed physiological functions. The membrane structure of intercellular junctions is described. Membrane proteins can be divided into two groups: peripheral and integral. Peripheral membrane proteins are believed to be associated with the membrane surface, based on the observation that they are held to the membrane by rather weak noncovalent interactions, and are not strongly associated with membrane lipids. Only mild treatments, such as an increase in ionic strength of the medium or the addition of a chelating agent, are needed to dissociate them molecularly intact from the membrane. Furthermore, in the dissociated state they are relatively soluble in neutral aqueous buffers. In contrast, integral membrane proteins appear much more strongly bound to the lipid matrix, since they can be dissociated from the latter only by drastic treatments with chemicals such as detergents, protein denaturants, and organic solvents. The diversity in structure and function of intercellular junctions offers an exciting field for future research in which morphologists, physiologists, and biochemists should be able to make significant contributions to the knowledge of how individual cells interact to form structures of higher order.

Human bone marrow colony growth in agar-gel.

Abstract: A technique for growing human bone marrow cell colonies in agar-gel medium is described. “Feeder layers” containing 1 × 106 normal human peripheral white blood cells are used as the stimulus for colony growth. Human bone marrow aspirates are collected in heparinized syringes and plated as 2 × 105 cells on “feeder layers.” Normal human bone marrow yields 32–102 colonies per 2 × 105 cells plated. Colonies are almost exclusively granulocytic. Growth rate of colonies is slower than with mouse bone marrow but colonies reach a comparable size (500–1500 cells) at days 12–16.

Carvedilol Produces Dose-Related Improvements in Left Ventricular Function and Survival in Subjects With Chronic Heart Failure

Abstract: Background We conducted a multicenter, placebo-controlled trial designed to establish the efficacy and safety of carvedilol, a “third-generation” β-blocking agent with vasodilator properties, in chronic heart failure. Methods and Results Three hundred forty-five subjects with mild to moderate, stable chronic heart failure were randomized to receive treatment with placebo, 6.25 mg BID carvedilol (low-dose group), 12.5 mg BID carvedilol (medium-dose group), or 25 mg BID carvedilol (high-dose group). After a 2- to 4-week up-titration period, subjects remained on study medication for a period of 6 months. The primary efficacy parameter was submaximal exercise measured by two different techniques, the 6-minute corridor walk test and the 9-minute self-powered treadmill test. Carvedilol had no detectable effect on submaximal exercise as measured by either technique. However, carvedilol was associated with dose-related improvements in LV function (by 5, 6, and 8 ejection fraction [EF] units in the low-, medium-, ...