Rotational Tuning of Transmembrane Helix Properties Based on the Precise Placements of Aromatic and Charged Residues

Designed model transmembrane peptides and oriented 2H and 15N solid-state nuclear magnetic resonance (NMR) spectroscopy were used to analyze how simple sequence modifications can influence peptide structure, behavior and dynamics as well as for determining the pKa of glutamic acid at the membrane interface. The GW5,19ALP23 (acetyl-GGALW(LA)6LWLAGA-amide) peptide framework adopts a well-defined tilted orientation in lipid bilayers (DLPC, DMPC and DOPC) and undergoes low amounts of dynamic motion. The sequence was initially modified by moving the Trp residues outwards to positions 4 and 20. This new sequence GW4,20ALP23 (acetyl-GGAW(AL)7AWAGA-amide) displays high amounts of signal averaging of NMR observables caused by extensive dynamic motion about its average azimuthal rotation. The high dynamics are due to side chain competition induced by the opposing radial locations of the interfacial Trp(W) residues. The GW4,20ALP23 sequence was subsequently modified by introducing Arg(R) residues at either position 14 or 12. The R14 peptide adopts a well-defined tilt in lipid bilayers while completely arresting the high dynamics of the parent framework. In response, the C-terminal Trp causes partial unwinding of the core helix, while the N-terminal residues tighten into the core helix to compensate. R12 pulls the peptide to the membrane surface. A helix discontinuity is observed beginning at residue 11 as well as the formation of a partial N-terminal 310-helix. Modifying the core sequence of GW4,20ALP23 with Leu residues at positions 5 and 19 does not significantly affect the high dynamics, yet causes the peptide to adopt the same tilt as the original GW5,19ALP23 sequence. Removing W4 and replacing it with two Phe residues at positions 4 and 5 not only reduces the dynamics but also causes C-terminal helix distortion. Moving away from helix dynamics, 2H NMR was used to determine the side chain pKa of an interfacial Glu residue in the GW5,19ALP23 framework will oriented in the three lipid bilayers. The pKa increases with lipid bilayer thickness ranging from 4.3 to 11.0. Together, these experiments with model membrane peptides and solid-state NMR can be used to help our understanding of the basic principles that govern protein-lipid interactions

Performance Analysis of MIMO-MRC in Double-Correlated Rayleigh Environments

We consider multiple-input multiple-output (MIMO) transmit beamforming systems with maximum ratio combining (MRC) receivers. The operating environment is Rayleigh-fading with both transmit and receive spatial correlation. We present exact expressions for the probability density function (p.d.f.) of the output signal-to-noise ratio (SNR), as well as the system outage probability. The results are based on explicit closed-form expressions which we derive for the p.d.f. and c.d.f. of the maximum eigenvalue of double-correlated complex Wishart matrices. For systems with two antennas at either the transmitter or the receiver, we also derive exact closed-form expressions for the symbol error rate (SER). The new expressions are used to prove that MIMO-MRC achieves the maximum available spatial diversity order, and to demonstrate the effect of spatial correlation. The analysis is validated through comparison with Monte-Carlo simulations.Comment: 25 pages. Submitted to the IEEE Transactions on Communication

On the Mutual Information Distribution of OFDM-Based Spatial Multiplexing: Exact Variance and Outage Approximation

This paper considers the distribution of the mutual information of frequency-selective spatially-uncorrelated Rayleigh fading MIMO channels. Results are presented for OFDM-based spatial multiplexing. New exact closed-form expressions are derived for the variance of the mutual information. In contrast to previous results, our new expressions apply for systems with both arbitrary numbers of antennas and arbitrary-length channels. Simplified expressions are also presented for high and low SNR regimes. The analytical variance results are used to provide accurate analytical approximations for the distribution of the mutual information and the outage capacity.Comment: 18 pages, 10 figures, accepted for publication in IEEE Transactions on Information Theor

Within-species trade-offs in plant-stimulated soil enzyme activity and growth, flowering, and seed size

Soil microbial communities affect species demographic rates of plants. In turn, plants influence the composition and function of the soil microbiome, potentially resulting in beneficial feedbacks that alter their fitness and establishment. For example, differences in the ability to stimulate soil enzyme activity among plant lineages may affect plant growth and reproduction. We used a common garden study to test differences in plant-stimulated soil enzyme activity between lineages of the same species across developmental stages. Lineages employed different strategies whereby growth, days to flowering and seed size traded-off with plant-stimulated soil enzyme activity. Specifically, the smaller seeded lineage stimulated more enzyme activity at the early stage of development and flowered earlier while the larger seeded lineage sustained lower but consistent enzyme activity through development. We suggest that these lineages, which are both successful invaders, employ distinct strategies (a colonizer and a competitor) and differ in their influence on soil microbial activity. Synthesis. The ability to influence the soil microbial community by plants may be an important trait that trades off with growth, flowering, and seed size for promoting plant establishment, reproduction, and invasion

Plasticity of Total and Intracellular Phosphorus Quotas in Microcystis aeruginosa Cultures and Lake Erie Algal Assemblages

Blooms of the potentially toxic cyanobacterium Microcystis are common events globally, and as a result significant resources continue to be dedicated to monitoring and controlling these events. Recent studies have shown that a significant proportion of total cell-associated phosphorus (P) in marine phytoplankton can be surface adsorbed; as a result studies completed to date do not accurately report the P demands of these organisms. In this study we measure the total cell-associated and intracellular P as well as growth rates of two toxic strains of Microcystis aeruginosa Kütz grown under a range of P concentrations. The results show that the intracellular P pool in Microcystis represents a percentage of total cell-associated P (50–90%) similar to what has been reported for actively growing algae in marine systems. Intracellular P concentrations (39–147 fg cell−1) generally increased with increasing P concentrations in the growth medium, but growth rate and the ratio of total cell-associated to intracellular P remained generally stable. Intracellular P quotas and growth rates in cells grown under the different P treatments illustrate the ability of this organism to successfully respond to changes in ambient P loads, and thus have implications for ecosystem scale productivity models employing P concentrations to predict algal bloom events

Hormone-dependent control of developmental timing through regulation of chromatin accessibility

Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory transcription factors are required to control tissue-specific gene expression programs. However, the mechanisms controlling how tissue-specific gene expression changes over time are less well understood. Here, we show that hormone-induced transcription factors control temporal gene expression by regulating the accessibility of DNA regulatory elements. Using the Drosophila wing, we demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. We also uncover a temporal cascade of transcription factors following a pulse of the steroid hormone ecdysone such that different times in wing development can be defined by distinct combinations of hormone-induced transcription factors. Finally, we show that the ecdysone-induced transcription factor E93 controls temporal identity by directly regulating chromatin accessibility across the genome. Notably, we found that E93 controls enhancer activity through three different modalities, including promoting accessibility of late-acting enhancers and decreasing accessibility of early-acting enhancers. Together, this work supports a model in which an extrinsic signal triggers an intrinsic transcription factor cascade that drives development forward in time through regulation of chromatin accessibility

The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories

Highlights • Archaeal community composition reflects locally specific environmental challenges • Biogeochemical properties do not predict archaeal community structure • Environmental history controls subseafloor archaeal populations Summary We explore archaeal distributions in sedimentary subseafloor habitats of Guaymas Basin and the adjacent Sonora Margin, located in the Gulf of California, México. Sampling locations include (1) control sediments without hydrothermal or seep influence, (2) Sonora Margin sediments underlying oxygen minimum zone water, (3) compacted, highly reduced sediments from a pressure ridge with numerous seeps at the base of the Sonora Margin, and (4) sediments impacted by hydrothermal circulation at the off-axis Ringvent site. Generally, archaeal communities largely comprise Bathyarchaeal lineages, members of the Hadesarchaea, MBG-D, TMEG, and ANME-1 groups. Variations in archaeal community composition reflect locally specific environmental challenges. Background sediments are divided into surface and subsurface niches. Overall, the environmental setting and history of a particular site, not isolated biogeochemical properties out of context, control the subseafloor archaeal communities in Guaymas Basin and Sonora Margin sediments

ArborZ: Photometric Redshifts Using Boosted Decision Trees

Precision photometric redshifts will be essential for extracting cosmological parameters from the next generation of wide-area imaging surveys. In this paper we introduce a photometric redshift algorithm, ArborZ, based on the machine-learning technique of Boosted Decision Trees. We study the algorithm using galaxies from the Sloan Digital Sky Survey and from mock catalogs intended to simulate both the SDSS and the upcoming Dark Energy Survey. We show that it improves upon the performance of existing algorithms. Moreover, the method naturally leads to the reconstruction of a full probability density function (PDF) for the photometric redshift of each galaxy, not merely a single "best estimate" and error, and also provides a photo-z quality figure-of-merit for each galaxy that can be used to reject outliers. We show that the stacked PDFs yield a more accurate reconstruction of the redshift distribution N(z). We discuss limitations of the current algorithm and ideas for future work.Comment: 10 pages, 13 figures, submitted to Ap