Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis

We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence information of multiple binding sites in the upstream region of a gene and that in the upstream regions of its orthologues in related genomes. A probabilistic model was developed for the evaluation of prediction reliability so that the prediction false positive rate could be well controlled. Using this method, we have predicted multiple new members of the NtcA regulons in nine sequenced cyanobacterial genomes, and showed that the false positive rates of the predictions have been reduced on an average of 40-fold compared to the conventional methods. A detailed analysis of the predictions in each genome showed that a significant portion of our predictions are consistent with previously published results about individual genes. Intriguingly, NtcA promoters are found for many genes involved in various stages of photosynthesis. Although photosynthesis is known to be tightly coordinated with nitrogen assimilation, very little is known about the underlying mechanism. We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell

Rate-Splitting for Multi-Antenna Non-Orthogonal Unicast and Multicast Transmission

In a superimposed unicast and multicast transmission system, one layer of Successive Interference Cancellation (SIC) is required at each receiver to remove the multicast stream before decoding the unicast stream. In this paper, we show that a linearly-precoded Rate-Splitting (RS) strategy at the transmitter can efficiently exploit this existing SIC receiver architecture. By splitting the unicast message into common and private parts and encoding the common parts along with the multicast message into a super-common stream decoded by all users, the SIC is used for the dual purpose of separating the unicast and multicast streams as well as better managing the multi-user interference between the unicast streams. The precoders are designed with the objective of maximizing the Weighted Sum Rate (WSR) of the unicast messages subject to a Quality of Service (QoS) requirement of the multicast message and a sum power constraint. Numerical results show that RS outperforms existing Multi-User Linear-Precoding (MU-LP) and power-domain Non-Orthogonal Multiple Access (NOMA) in a wide range of user deployments (with a diversity of channel directions and channel strengths). Moreover, since one layer of SIC is required to separate the unicast and multicast streams, the performance gain of RS comes without any increase in the receiver complexity compared with MU-LP. Hence, in such non-orthogonal unicast and multicast transmissions, RS provides rate and QoS enhancements at no extra cost for the receivers.Comment: arXiv admin note: text overlap with arXiv:1710.1101

Energy Efficiency of Rate-Splitting Multiple Access, and Performance Benefits over SDMA and NOMA

Rate-Splitting Multiple Access (RSMA) is a general and powerful multiple access framework for downlink multi-antenna systems, and contains Space-Division Multiple Access (SDMA) and Non-Orthogonal Multiple Access (NOMA) as special cases. RSMA relies on linearly precoded rate-splitting with Successive Interference Cancellation (SIC) to decode part of the interference and treat the remaining part of the interference as noise. Recently, RSMA has been shown to outperform both SDMA and NOMA rate-wise in a wide range of network loads (underloaded and overloaded regimes) and user deployments (with a diversity of channel directions, channel strengths and qualities of Channel State Information at the Transmitter). Moreover, RSMA was shown to provide spectral efficiency and QoS enhancements over NOMA at a lower computational complexity for the transmit scheduler and the receivers. In this paper, we build upon those results and investigate the energy efficiency of RSMA compared to SDMA and NOMA. Considering a multiple-input single-output broadcast channel, we show that RSMA is more energy-efficient than SDMA and NOMA in a wide range of user deployments (with a diversity of channel directions and channel strengths). We conclude that RSMA is more spectrally and energy-efficient than SDMA and NOMA.Comment: 6 pages, 5 figure

Prediction of functional modules based on comparative genome analysis and Gene Ontology application

We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. We first evaluate the functional relationship between two genes from three different perspectives—phylogenetic profile analysis, gene neighborhood analysis and Gene Ontology assignments. We then combine the three different sources of information in the framework of Bayesian inference, and we use the combined information to measure the strength of gene functional relationship. Finally, we apply a threshold-based method to predict functional modules. By applying this method to Escherichia coli K12, we have predicted 185 functional modules. Our predictions are highly consistent with the previously known functional modules in E.coli. The application results have demonstrated that our approach is highly promising for the prediction of functional modules encoded in a microbial genome

Computational prediction of the osmoregulation network in Synechococcus sp. WH8102

<p>Abstract</p> <p>Background</p> <p>Osmotic stress is caused by sudden changes in the impermeable solute concentration around a cell, which induces instantaneous water flow in or out of the cell to balance the concentration. Very little is known about the detailed response mechanism to osmotic stress in marine <it>Synechococcus</it>, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO₂fixation.</p> <p>Results</p> <p>We present here a computational study of the osmoregulation network in response to hyperosmotic stress of <it>Synechococcus sp </it>strain <it>WH8102 </it>using comparative genome analyses and computational prediction. In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress.</p> <p>Conclusions</p> <p>From the predicted network model, we have made a number of interesting observations about <it>WH8102</it>. Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) σ³⁸, one of the seven types of σ factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.</p