Homologous Codes for Multiple Access Channels

Building on recent development by Padakandla and Pradhan, and by Lim, Feng, Pastore, Nazer, and Gastpar, this paper studies the potential of structured nested coset coding as a complete replacement for random coding in network information theory. The roles of two techniques used in nested coset coding to generate nonuniform codewords, namely, shaping and channel transformation, are clarified and illustrated via the simple example of the two-sender multiple access channel. While individually deficient, the optimal combination of shaping and channel transformation is shown to achieve the same performance as traditional random codes for the general two-sender multiple access channel. The achievability proof of the capacity region is extended to the multiple access channels with more than two senders, and with one or more receivers. A quantization argument consistent with the construction of nested coset codes is presented to prove achievability for their Gaussian counterparts. These results open up new possibilities of utilizing nested coset codes with the same generator matrix for a broader class of applications

Characterization of Expression of the KCNE Gene Family in Zebrafish, Danio rerio

The KCNE gene family codes for five transmembrane accessory proteins, minK related peptides or Mirps, involved in the modification of voltage-gated potassium (Kv) channels, K+ selective pores vital in the regulation of membrane potential and repolarization in all organisms. In mammals, all five KCNE gene members are conserved and active in the heart. In the zebrafish Danio rerio, there are no apparent orthologs for KCNE2 or KCNE5, yet they contain Kv channels with homologous structure, function, and Mirp regulatory behavior to other organisms. Sequence analysis of wildtype zebrafish KCNE1, 3 and 4, and rtPCR on RNA from zebrafish tissues to assess adult expression led to the identification of the Mirps in zebrafish and a depiction of their expression patterns. Specifically, zebrafish were phylogenetically identified as homologs to KCNE1 and KCNE4 from other species and KCNE1 and KCNE3 cDNA showed expression in wildtype adult zebrafish heart tissue, implicating that MinK, Mirp2, and Mirp3 play active roles in the regulation of voltage-gated potassium channels in zebrafish, Danio rerio

Shape: A 3D Modeling Tool for Astrophysics

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a-priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.Comment: 13 pages, 11 figures, accepted for publication in the "IEEE Transactions on Visualization and Computer Graphics

Modulator Therapy for Cystic Fibrosis: An Exploration of Current Research

Developing a drug therapy that addresses the root cause of cystic fibrosis (CF) by increasing CFTR protein levels has long been a research challenge. After genetic therapy failed because a suitable delivery system could not be found, researchers began searching for small organic molecules that could act as chaperones for CFTR. These molecules, known as modulators, allowed CFTR to be assembled correctly and function similarly to wild type CFTR. Since 2012, four modulator drugs have been developed, tested, and approved by the FDA. In October 2019, Trikafta was approved as the first triple-combination modulator drug and has completely revolutionized CF therapy. This paper details the research challenges, successes, and failures that led to the development of modulator therapies

Genes for Membrane Transport Proteins: Not So Rare in Viruses

Some viruses have genes encoding proteins with membrane transport functions. It is unknown if these types of proteins are rare or are common in viruses. In particular, the evolutionary origin of some of the viral genes is obscure, where other viral proteins have homologs in prokaryotic and eukaryotic organisms. We searched virus genomes in databases looking for transmembrane proteins with possible transport function. This effort led to the detection of 18 different types of putative membrane transport proteins indicating that they are not a rarity in viral genomes. The most abundant proteins are K+ channels. Their predicted structures vary between different viruses. With a few exceptions, the viral proteins differed significantly from homologs in their current hosts. In some cases the data provide evidence for a recent gene transfer between host and virus, but in other cases the evidence indicates a more complex evolutionary history

Structural insights on TRPV5 gating by endogenous modulators.

TRPV5 is a transient receptor potential channel involved in calcium reabsorption. Here we investigate the interaction of two endogenous modulators with TRPV5. Both phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and calmodulin (CaM) have been shown to directly bind to TRPV5 and activate or inactivate the channel, respectively. Using cryo-electron microscopy (cryo-EM), we determined TRPV5 structures in the presence of dioctanoyl PI(4,5)P2 and CaM. The PI(4,5)P2 structure reveals a binding site between the N-linker, S4-S5 linker and S6 helix of TRPV5. These interactions with PI(4,5)P2 induce conformational rearrangements in the lower gate, opening the channel. The CaM structure reveals two TRPV5 C-terminal peptides anchoring a single CaM molecule and that calcium inhibition is mediated through a cation-π interaction between Lys116 on the C-lobe of calcium-activated CaM and Trp583 at the intracellular gate of TRPV5. Overall, this investigation provides insight into the endogenous modulation of TRPV5, which has the potential to guide drug discovery

CAV-2 Vector Development and Gene Transfer in the Central and Peripheral Nervous Systems

The options available for genetic modification of cells of the central nervous system (CNS) have greatly increased in the last decade. The current panoply of viral and nonviral vectors provides multifunctional platforms to deliver expression cassettes to many structures and nuclei. These cassettes can replace defective genes, modify a given pathway perturbed by diseases, or express proteins that can be selectively activated by drugs or light to extinguish or excite neurons. This review focuses on the use of canine adenovirus type 2 (CAV-2) vectors for gene transfer to neurons in the brain, spinal cord, and peripheral nervous system. We discuss (1) recent advances in vector production, (2) why CAV-2 vectors preferentially transduce neurons, (3) the mechanism underlying their widespread distribution via retrograde axonal transport, (4) how CAV-2 vectors have been used to address structure/function, and (5) their therapeutic applications

The antibiotic sensitivity patterns and plasmid DNA content of gram-negative anaerobic bacteria isolated in Palmerston North, New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Masters in Science at Massey University

One hundred and seven Gram-negative bacteria, including 65 Bacteroides species, 28 fusobacteria and 14 veillonellae were isolated from 17 oral infections treated in two dental surgeries in Palmerston North. These bacteria, plus 37 isolates belonging to the B. fragilis group received from Palmerston North hospital, were surveyed for their antibiotic sensitivity levels, and their plasmid DNA content. The hospital isolates of the B. fragilis group were found to have sensitivity levels comparable with those of B. fragilis group isolates reported in the literature recently. The oral isolates were more sensitive to penicillin, cefoxitin, and tetracycline than isolates of the same species reported in the literature. Half the hospital isolates had plasmids, which were all between 8.5 and 2.7 kilobases (kb) in size except for one 60, and one 43 kb plasmid. Comparatively few of the oral anaerobes had plasmids. One Fusobacterium russii isolate had four plasmids, and five Bacteroides isolates had one plasmid each. These five Bacteroides isolates came from two specimens, R5 and R6. Restriction enzyme analysis of all plasmids revealed that the three 5.6 kb plasmids from sample R5 may be related to a group of 5.8 kb plasmids harboured by four of the hospital isolates. Two different species of Bacteroides isolated from sample R5 harboured the 5.6 kb plasmid, and two species of the B. fragilis group bacteria harboured the 5.8 kb plasmid. Plasmid DNA isolated from two tetracycline resistant hospital isolates was used to transform restriction negative E. coli to a low level of tetracycline resistance