MuLSi-Co: Multilayer Sinks and Cooperation-Based Data Routing Techniques for Underwater Acoustic Wireless Sensor Networks (UA-WSNs)

Designing an efficient, reliable, and stable algorithm for underwater acoustic wireless sensor networks (UA-WSNs) needs immense attention. It is due to their notable and distinctive challenges. To address the difficulties and challenges, the article introduces two algorithms: the multilayer sink (MuLSi) algorithm and its reliable version MuLSi-Co using the cooperation technique. The first algorithm proposes a multilayered network structure instead of a solid single structure and sinks placement at the optimal position, which reduces multiple hops communication. Moreover, the best forwarder selection amongst the nodes based on nodes’ closeness to the sink is a good choice. As a result, it makes the network perform better. Unlike the traditional algorithms, the proposed scheme does not need location information about nodes. However, the MuLSi algorithm does not fulfill the requirement of reliable operation due to a single link. Therefore, the MuLSi-Co algorithm utilizes nodes’collaborative behavior for reliable information. In cooperation, the receiver has multiple copies of the same data. Then, it combines these packets for the purpose of correct data reception. The data forwarding by the relay without any latency eliminates the synchronization problem. Moreover, the overhearing of the data gets rid of duplicate transmissions. The proposed schemes are superior in energy cost and reliable exchanging of data and have more alive and less dead nodes.

Printing and Publishing of Music

This article covers the dissemination of musical scores by technical means. The function of both printing and publication is to produce multiple copies of a work or a group of works and to arrange for the distribution of those copies to many purchasers. This requires diverse skills: on the one hand, the ability to print, involving preparing a copy of the music in a form suitable for the printing press, and then producing the copies; on the other, to make marketing decisions, to handle advertising and distribution of copies to individuals or to music shops, and to budget and plan for profits. Since the first printed music produced by Ottaviano Petrucci at the beginning of the 16th century, printing has been developed in Europe on a broad scale. Its technical requirements have changed from movable type to engraving, lithography, and, most recently, the computer. Entries are arranged to cover these activities separately, and then provide an introduction to bibliography, the scholarly study of both activities. Descriptive bibliography and analytic bibliography are recent in the field of music; they have been primarily devoted to the study of the printers and publishers from the 16th to the 18th centuries established in the main centers in Europe, including Venice, Paris, Antwerp, Frankfurt, London, and Vienna. Specific topics have become of increasing interest in recent years, including patterns of distributing copies and reaching markets and music appearing in general cultural periodicals and magazines. In addition, two subjects have risen to importance, the first, the paratext, or matters of design, which is sparsely discussed in connection with music; and the second, the place of music and its editions in cultural and intellectual history. Use of printed music has changed during the 20th century. Employed as a mean for performing and circulating music among musicians, professionals, and amateurs during four centuries, printed music became a support to produce performing rights when audiovisual media became the main access to music. Another important evolution has been the production of different kind of editions. During a long period, publishers sold the music written day by day for the entertainment of specific groups in society and for a specific purpose—liturgy, concert life, house music. Following a growing interest in the music of the past, they began to produce collected works and critical editions that reconcile mass production to the quality of the publishing.

Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids

Theoretical population genetics has been mostly developed for sexually reproducing diploid and for monoploid (haploid) organisms, focusing on eukaryotes. The evolution of bacteria and archaea is often studied by models for the allele dynamics in monoploid populations. However, many prokaryotic organisms harbor multicopy replicons -- chromosomes and plasmids -- and theory for the allele dynamics in populations of polyploid prokaryotes remains lacking. Here we present a population genetics model for replicons with multiple copies in the cell. Using this model, we characterize the fixation process of a dominant beneficial mutation at two levels: the phenotype and the genotype. Our results show that, depending on the mode of replication and segregation, the fixation time of mutant phenotypes may precede the genotypic fixation time by many generations; we term this time interval the heterozygosity window. We furthermore derive concise analytical expressions for the occurrence and length of the heterozygosity window, showing that it emerges if the copy number is high and selection strong. Replicon ploidy thus allows for the maintenance of genetic variation following phenotypic adaptation and consequently for reversibility in adaptation to fluctuating environmental conditions.

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.

Plant Virus Nanoparticles for Anti-cancer Therapy

Plant virus nanoparticles (VNPs) are inexpensive to produce, safe, biodegradable and efficacious as treatments. The applications of r plant virus nanoparticles range from epitope carriers for vaccines to agents in cancer immunotherapy. Both VNPs and virus-like particles (VLPs) are highly immunogenic and are readily phagocytosed by antigen presenting cells (APCs), which in turn elicit antigen processing and display of pathogenic epitopes on their surfaces. Since the VLPs are composed of multiple copies of their respective capsid proteins, they present repetitive multivalent scaffolds which aid in antigen presentation. Therefore, the VLPs prove to be highly suitable platforms for delivery and presentation of antigenic epitopes, resulting in induction of more robust immune response compared to those of their soluble counterparts. Since the tumor microenvironment poses the challenge of self-antigen tolerance, VLPs are preferrable platforms for delivery and display of self-antigens as well as otherwise weakly immunogenic antigens. These properties, in addition to their diminutive size, enable the VLPs to deliver vaccines to the draining lymph nodes in addition to promoting APC interactions. Furthermore, many plant viral VLPs possess inherent adjuvant properties dispensing with the requirement of additional adjuvants to stimulate immune activity. Some of the highly immunogenic VLPs elicit innate immune activity, which in turn instigate adaptive immunity in tumor micro-environments. Plant viral VLPs are nontoxic, inherently stable, and capable of being mass-produced as well as being modified with antigens and drugs, therefore providing an attractive option for eliciting anti-tumor immunity. The following review explores the use of plant viruses as epitope carrying nanoparticles and as a novel tools in cancer immunotherapy.

Soluble MAC is primarily released from MAC-resistant bacteria that potently convert complement component C5

The Membrane Attack Complex (MAC or C5b-9) is an important effector of the immune system to kill invading microbes. MAC is formed when complement enzymes on the bacterial surface convert complement component C5 into C5b. Although the MAC is a membrane-inserted complex, soluble forms of MAC (sMAC, or terminal complement complex (TCC)) are often detected in sera of patients suffering from infections. Consequently, sMAC has been proposed as a biomarker, but it remains unclear when and how it is formed during infections. Here, we studied mechanisms of MAC formation on bacteria and found that sMAC is primarily formed in human serum by bacteria resistant to MAC-dependent killing. Surprisingly, C5 was converted into C5b more potently by MAC-resistant compared to MAC-sensitive Escherichia coli strains. Both the increase in C5 conversion and sMAC generation were linked to the expression of lipopolysaccharide (LPS) O-Antigen in the bacterial outer membrane. In addition, we found that MAC precursors are released from the surface of MAC-resistant bacteria during MAC assembly. Release of MAC precursors from bacteria induced lysis of bystander human erythrocytes in the absence of other serum components. However, serum regulators vitronectin (Vn) and clusterin (Clu) can prevent this bystander lysis. Combining size exclusion chromatography with mass spectrometry profiling, we show that sMAC released from bacteria in serum is a heterogeneous mixture of complexes composed of C5b-8, up to 3 copies of C9 and multiple copies of Vn and Clu. Altogether, our data provide molecular insight into how sMAC is generated during bacterial infections. This fundamental knowledge could form the basis for exploring the use of sMAC as biomarker.

In Pursuit of Distinctiveness: Transmembrane Nucleoporins and Their Disease Associations

The bi-directional nucleocytoplasmic shuttling of macromolecules like molecular signals, transcription factors, regulatory proteins, and RNAs occurs exclusively through Nuclear Pore Complex (NPC) residing in the nuclear membrane. This magnanimous complex is essentially a congregation of ~32 conserved proteins termed Nucleoporins (Nups) present in multiple copies and mostly arranged as subcomplexes to constitute a functional NPC. Nups participate in ancillary functions such as chromatin organization, transcription regulation, DNA damage repair, genome stabilization, and cell cycle control, apart from their central role as nucleocytoplasmic conduits. Thus, Nups exert a role in the maintenance of cellular homeostasis. In mammals, precisely three nucleoporins traverse the nuclear membrane, are called transmembrane Nups (TM-Nups), and are involved in multiple cellular functions. Owing to their vital roles in cellular processes and homeostasis, dysregulation of nucleoporin function is implicated in various diseases. The deregulated functioning of TM-Nups can thus act as an opportune window for the development of diseases. Indeed, mounting evidence exhibits a strong association of TM-Nups in cancer and numerous other physiological disorders. These findings have provided much-needed insights into the novel mechanisms of disease progression. While nucleoporin’s functions have often been summarized in the disease context, a focus on TM-Nups has always lacked. This review emphasizes the elucidation of distinct canonical and non-canonical functions of mammalian TM-Nups and the underlying mechanisms of their disease association.

Evolution of B Chromosomes: From Dispensable Parasitic Chromosomes to Essential Genomic Players

B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they mostly arise through rearrangements and duplications from standard chromosomes. They can occur in single or multiple copies in a cell and are usually present only in a subset of individuals in the population. Because B chromosomes frequently show unstable inheritance, their maintenance in a population is often associated with meiotic drive or other mechanisms that increase the probability of their transmission to the next generation. For all these reasons, B chromosomes have been commonly considered to be nonessential, selfish, parasitic elements. Although it was originally believed that B chromosomes had little or no effect on an organism’s biology and fitness, a growing number of studies have shown that B chromosomes can play a significant role in processes such as sex determination, pathogenicity and resistance to pathogens. In some cases, B chromosomes became an essential part of the genome, turning into new sex chromosomes or germline-restricted chromosomes with important roles in the organism’s fertility. Here, we review such cases of “cellular domestication” of B chromosomes and show that B chromosomes can be important genomic players with significant evolutionary impact.

Undoing Wh-Movement: On the Need for Multiple Copies

This contribution presents an outline of the current scholarly discussion of reconstruction with wh-movement, focussing on the Lebeaux Effect (LE) and wider aspects of reconstruction with wh-movement. It presents empirical problems for both the proposals based on the LE and the novel account of movement and reconstruction based on the notion of Minimal Copy. It points out that particular copies may differ not only in size (i.e., they do or do not include the adjunct as a relative clause or PP) but also in content. It refers to an analysis, where copies left by movement are levelled with copies left by ellipsis and subject to the mechanism of Vehicle Change. An account of reconstruction including multiple copies and Vehicle Change predicts that the structural complexity of the wh-phrase and its distance from the offending c-commanding pronoun (embedding and obviation effects) should contribute to an amelioration of Condition C in addition to the LE.

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Programmed –1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection.