AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

High throughput sequencing (HTSeq) of small ribosomal subunit amplicons has the potential for a comprehensive characterization of microbial community compositions, down to rare species. However, the error-prone nature of the multi-step experimental process requires that the resulting raw sequences are subjected to quality control procedures. These procedures often involve an abundance cutoff for rare sequences or clustering of sequences, both of which limit genetic resolution. Here we propose a simple experimental protocol that retains the high genetic resolution granted by HTSeq methods while effectively removing many low abundance sequences that are likely due to PCR and sequencing errors. According to this protocol, we split samples and submit both halves to independent PCR and sequencing runs. The resulting sequence data is graphically and quantitatively characterized by the discordance between the two experimental branches, allowing for a quick identification of problematic samples. Further, we discard sequences that are not found in both branches (“AmpliconDuo filter”). We show that the majority of sequences removed in this way, mostly low abundance but also some higher abundance sequences, show features expected from random modifications of true sequences as introduced by PCR and sequencing errors. On the other hand, the filter retains many low abundance sequences observed in both branches and thus provides a more reliable census of the rare biosphere. We find that the AmpliconDuo filter increases biological resolution as it increases apparent community similarity between biologically similar communities, while it does not affect apparent community similarities between biologically dissimilar communities. The filter does not distort overall apparent community compositions. Finally, we quantitatively explain the effect of the AmpliconDuo filter by a simple mathematical model.     

Photosynthesis of the cyanobacterial soil-crust lichen Collema tenax from arid lands in southern Utah, USA: role of water content on light and temperature responses of CO2 exchange

1. The gelatinous cyanobacterial Collema tenax is a dominant lichen of biotic soil crusts in the western United States. In laboratory experiments, we studied CO₂ exchange of this species as dependent on water content (WC), light and temperature. Results are compared with performance of green-algal lichens of the same site investigated earlier.
2. As compared with published data, photosynthetic capacity of C. tenax is higher than that of other cyanobacterial and green-algal soil-crust species studied. At all temperatures and photon flux densities of ecological relevance, net photosynthesis (NP) shows a strong depression at high degrees of hydration; maximal apparent quantum-use efficiency of CO₂ fixation is also reduced. Water requirements (moisture compensation point, WC for maximal NP) are higher than that of the green-algal lichens. Collema tenax exhibits extreme 'sun plant' features and is adapted to high thallus temperatures.
3. Erratic rain showers are the main source of moisture for soil crusts on the Colorado Plateau, quickly saturating the lichens with liquid water. High water-holding capacity of C. tenax ensures extended phases of favourable hydration at conditions of high light and temperature after the rain for substantial photosynthetic production. Under such conditions the cyanobacterial lichen appears superior over its green-algal competitors, which seem better adapted to habitats with high air humidity, dew or fog as prevailing source of moisture.     

Metabolic control of the cell cycle

Cell division is a metabolically demanding process, requiring the production of large amounts of energy and biomass. Not surprisingly therefore, a cell''s decision to initiate division is co-determined by its metabolic status and the availability of nutrients. Emerging evidence reveals that metabolism is not only undergoing substantial changes during the cell cycle, but it is becoming equally clear that metabolism regulates cell cycle progression. Here, we overview the emerging role of those metabolic pathways that have been best characterized to change during or influence cell cycle progression. We then studied how Notch signaling, a key angiogenic pathway that inhibits endothelial cell (EC) proliferation, controls EC metabolism (glycolysis) during the cell cycle.     

Bayesian approximations and extensions: Optimal decisions for small brains and possibly big ones too

We compared the performance of Bayesian learning strategies and approximations to such strategies, which are far less computationally demanding, in a setting requiring individuals to make binary decisions based on experience. Extending Bayesian updating schemes, we compared the different strategies while allowing for various implementations of memory and knowledge about the environment. The dynamics of the observable variables was modeled through basic probability distributions and convolution. This theoretical framework was applied to the problem of male fruit flies who have to decide which females they should court. Computer simulations indicated that, for most parameter values, approximations to the Bayesian strategy performed as well as the full Bayesian one. The linear approximation, reminiscent of the linear operator, was notably successful, and, without innate knowledge, the only successful learning strategy. Besides being less demanding in computation and thus realistic for small brains, the linear approximation was also successful at limited memory, which would translate into robustness in rapidly changing environments. Knowledge about the environment boosted the performance of the various learning strategies with maximal performance at large utilization of memory. Only for limited memory capacities, intermediate knowledge was most successful. We conclude that many animals may rely on algorithms that involve approximations rather than full Bayesian calculations because such approximations achieve high levels of performance with only a fraction of the computational requirements, in particular for extensions of Bayesian updating schemes, which can represent universal and realistic environments.     

Accurate and superaccurate gene mapping.

Highly accurate gene mapping techniques need to be developed to clone disease genes with unknown defective products. The classical pedigree method and methods based on cytologically observable chromosome aberrations share definite limits in resolution. We quantify the limits in resolution for the pedigree method. We also discuss a technique for gene localization that exploits the possible presence of minute depletions overlapping the disease locus. One can search for such submicroscopic deletions by aiming random probes at them. We show quantitatively that relatively few probes may suffice to hit a target deletion. Choosing which probes to aim should be guided by pedigree studies and by close examination of relevant cytologically observable translocations and deletions.     

Genetic analysis of eight linked polymorphisms within the human immunoglobulin heavy-chain region.

Genetic analyses of multiple restriction fragment length polymorphisms, revealed by a single DNA probe containing the switch region of the immunoglobulin constant heavy-chain (IgCH) mu gene, are presented here in detail. Five of the polymorphic loci segregate in complete linkage with IgCH allotypic markers, while one appears to be located at more than 10 centimorgans from the IgCH region. A study of over 100 random haplotypes typed at eight linked loci, including the Ig switch polymorphisms and the classical Gm-Am allotypes, allowed us to construct an evolutionary tree by which each haplotypic variant can be derived one from the other either by single-step mutation or by recombination. A few of the recombinant haplotypes appeared to carry large DNA duplications that could be explained by unequal crossing over; others might postulate gene-conversion events. Linkage disequilibria observed between the IgCH-linked loci were compared with expected ones. A heterogeneous distribution of recombination rates is clearly documented, a "hot" region of recombination being present between the gamma 2 and switch alpha 2 loci.     

Degradation of the Isoflavone Biochanin A and Its Glucoside Conjugates by Ascochyta rabiei

Strains of Ascochyta rabiei which are pathogenic to chickpea (Cicer arietinum L.) readily catabolized the main chickpea isoflavone biochanin A (5,7-dihydroxy-4′-methoxyisoflavone). 3′-Hydroxylation and O-demethylation reactions led to the isoflavones pratensein, genistein, and orobol, which were rapidly further degraded. Dihydrogenistein and p-hydroxyphenylacetic acid were also identified as catabolites. Biochanin A-7-O-glucoside was degraded, leading to aglycone and pratensein. Biochanin A-7-O-glucoside-6″-O-malonate, the main phenolic constituent of chickpea, was very slowly degraded without subsequent accumulation of catabolites.     

Loci of catabolism of beta-very low density lipoprotein in vivo delineated with a residualizing label, 125I-dilactitol tyramine

beta-Very low density lipoprotein (beta-VLDL) may be a major atherogenic lipoprotein, and knowledge of the sites of its catabolism should facilitate elucidation of mechanisms important in the regulation of its plasma concentrations. In this study, catabolic sites of beta-VLDL have been delineated in normolipidemic rabbits with a novel, radioiodinated, residualizing label, 125I-dilactitol tyramine (125I-DLT). Comparative studies of beta-VLDL and low density lipoprotein catabolism were performed with 125I-DLT conjugated to each lipoprotein and with lipoproteins iodine-labeled conventionally. Conjugation did not alter size distributions or charge characteristics of lipoprotein particles. The overall processing (binding and degradation) of lipoproteins by cultured rabbit skin fibroblasts was not influenced by 125I-DLT derivatization, suggesting that attachment of the label did not influence cell receptor-lipoprotein interactions. Furthermore, although degradation products of 125I-lipoproteins leaked out of the cells and into the medium, the degradation products of 125I-DLT lipoproteins were retained by the cells. The principal catabolic site of beta-VLDL in normolipidemic rabbits was found to be the liver with 54 +/- 4% of injected 125I retained in this organ 24 h after injection of 125I-DLT-beta-VLDL. When catabolism was normalized to tissue weight, the liver and adrenals were found to be approximately equally active in the metabolism of beta-VLDL. In agreement with results of other studies with residualizing labels, the principal organ of catabolism of 125I-DLT-LDL in vivo was the liver. The adrenals were the most highly catabolizing organ when results were normalized for tissue weight. The quantitative differences observed in the tissue distributions of injected 125I-DLT-beta-VLDL and 125I-DLT-low density lipoprotein suggested that a significant proportion of beta-VLDL is removed by tissues before conversion to low density lipoprotein.