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Viruses Feb 2022Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically,... (Review)
Review
Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases.
Topics: Animals; Colony-Forming Units Assay; Defective Viruses; Genome, Viral; Humans; Microscopy, Electron, Transmission; Viral Plaque Assay; Virion; Virus Diseases; Virus Replication
PubMed: 35215979
DOI: 10.3390/v14020383 -
Biology Jul 2022Metabolic rate and its covariation with body mass vary substantially within and among species in little understood ways. Here, I critically review explanations (and... (Review)
Review
Metabolic rate and its covariation with body mass vary substantially within and among species in little understood ways. Here, I critically review explanations (and supporting data) concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic rate and its scaling with body mass. Cell size and growth may affect size-specific metabolic rate, as well as the vertical elevation (metabolic level) and slope (exponent) of metabolic scaling relationships. Mechanistic causes of negative correlations between cell size and metabolic rate may involve reduced resource supply and/or demand in larger cells, related to decreased surface area per volume, larger intracellular resource-transport distances, lower metabolic costs of ionic regulation, slower cell multiplication and somatic growth, and larger intracellular deposits of metabolically inert materials in some tissues. A cell-size perspective helps to explain some (but not all) variation in metabolic rate and its body-mass scaling and thus should be included in any multi-mechanistic theory attempting to explain the full diversity of metabolic scaling. A cell-size approach may also help conceptually integrate studies of the biological regulation of cellular growth and metabolism with those concerning major transitions in ontogenetic development and associated shifts in metabolic scaling.
PubMed: 35892962
DOI: 10.3390/biology11081106 -
Virus Evolution Jan 2019Many organisms disperse in groups, yet this process is understudied in viruses. Recent work, however, has uncovered different types of collective infectious units, all... (Review)
Review
Many organisms disperse in groups, yet this process is understudied in viruses. Recent work, however, has uncovered different types of collective infectious units, all of which lead to the joint delivery of multiple viral genome copies to target cells, favoring co-infections. Collective spread of viruses can occur through widely different mechanisms, including virion aggregation driven by specific extracellular components, cloaking inside lipid vesicles, encasement in protein matrices, or binding to cell surfaces. Cell-to-cell viral spread, which allows the transmission of individual virions in a confined environment, is yet another mode of clustered virus dissemination. Nevertheless, the selective advantages of dispersing in groups remain poorly understood in most cases. Collective dispersal might have emerged as a means of sharing efficacious viral transmission vehicles. Alternatively, increasing the cellular multiplicity of infection may confer certain short-term benefits to viruses, such as overwhelming antiviral responses, avoiding early stochastic loss of viral components required for initiating infection, or complementing genetic defects present in different viral genomes. However, increasing infection multiplicity may also entail long-term costs, such as mutation accumulation and the evolution of defective particles or other types of cheater viruses. These costs and benefits, in turn, should depend on the genetic relatedness among collective infectious unit members. Establishing the genetic basis of collective viral dispersal and performing controlled experiments to pinpoint fitness effects at different spatial and temporal scales should help us clarify the implications of these spread modes for viral fitness, pathogenicity, and evolution.
PubMed: 31249695
DOI: 10.1093/ve/vez014 -
Journal of Neurochemistry May 2020Synucleinopathies are a group of disorders characterized by the accumulation of inclusions rich in the a-synuclein (aSyn) protein. This group of disorders includes... (Review)
Review
Synucleinopathies are a group of disorders characterized by the accumulation of inclusions rich in the a-synuclein (aSyn) protein. This group of disorders includes Parkinson's disease, dementia with Lewy bodies (DLB), multiple systems atrophy, and pure autonomic failure (PAF). In addition, genetic alterations (point mutations and multiplications) in the gene encoding for aSyn (SNCA) are associated with familial forms of Parkinson's disease, the most common synucleinopathy. The Synuclein Meetings are a series that has been taking place every 2 years for about 12 years. The Synuclein Meetings bring together leading experts in the field of Synuclein and related human conditions with the goal of discussing and advancing the research. In 2019, the Synuclein meeting took place in Ofir, a city in the outskirts of Porto, Portugal. The meeting, entitled "Synuclein Meeting 2019: Where we are and where we need to go", brought together >300 scientists studying both clinical and molecular aspects of synucleinopathies. The meeting covered a many of the open questions in the field, in a format that prompted open discussions between the participants, and underscored the need for additional research that, hopefully, will lead to future therapies for a group of as of yet incurable disorders. Here, we provide a summary of the topics discussed in each session and highlight what we know, what we do not know, and what progress needs to be made in order to enable the field to continue to advance. We are confident this systematic assessment of where we stand will be useful to steer the field and contribute to filling knowledge gaps that may form the foundations for future therapeutic strategies, which is where we need to go.
Topics: Animals; Biomarkers; Congresses as Topic; Humans; Inclusion Bodies; Mutation; Portugal; Synucleinopathies; alpha-Synuclein
PubMed: 31957016
DOI: 10.1111/jnc.14965 -
Osteoarthritis and Cartilage May 2016
Topics: Biomedical Research; Data Interpretation, Statistical; Endpoint Determination; Humans; Periodicals as Topic; Rheumatology
PubMed: 26802548
DOI: 10.1016/j.joca.2016.01.008 -
Frontiers in Microbiology 2014Salmonella enterica species are Gram-negative bacteria, which are responsible for a wide range of food- and water-borne diseases in both humans and animals, thereby... (Review)
Review
Salmonella enterica species are Gram-negative bacteria, which are responsible for a wide range of food- and water-borne diseases in both humans and animals, thereby posing a major threat to public health. Recently, there has been an increasing number of reports, linking Salmonella contaminated raw vegetables and fruits with food poisoning. Many studies have shown that an essential feature of the pathogenicity of Salmonella is its capacity to cross a number of barriers requiring invasion of a large variety of cells and that the extent of internalization may be influenced by numerous factors. However, it is poorly understood how Salmonella successfully infects hosts as diversified as animals or plants. The aim of this review is to describe the different stages required for Salmonella interaction with its hosts: (i) attachment to host surfaces; (ii) entry processes; (iii) multiplication; (iv) suppression of host defense mechanisms; and to point out similarities and differences between animal and plant infections.
PubMed: 25653644
DOI: 10.3389/fmicb.2014.00791 -
Journal of International Relations and... 2022Resilience has become an oft-invoked concept in development and security policy circles and the subject of much debate in the literature. Yet, one aspect that needs to...
Resilience has become an oft-invoked concept in development and security policy circles and the subject of much debate in the literature. Yet, one aspect that needs to be further theorised is the complex relationship between resilience, conflict and gender. This introduction identifies the gradual congruence between the programmatic agendas of the United Nations Security Council Resolution 1325 (UNSCR 1325) and resilience-building approaches in peacebuilding and argues that this convergence needs to be further scrutinised. Our main argument is that it is time for the scholarship to go beyond the simple categorisation of resilience as being either the new paradigmatic solution to international interventions, conflicts and crises or a meaningless and useless governmental buzzword. Instead, the contributions found in this Special Issue see resilience in terms of multiplicity. Resilience, understood in terms of multiplicity and in a multidimensional way, appears a valuable analytical concept to study both the systemic nature of gendered power relations and their prevalence and adaptation over time, as well as the responses of individuals, communities and institutions to the gendered effects of conflict. To add empirical richness to the Special Issue, these conceptual connections are analysed in multiple geographical case studies, including Bosnia and Herzegovina, Sierra Leone, Cote d'Ivoire, Iraq, Liberia, Palestine and Rwanda.
PubMed: 36275638
DOI: 10.1057/s41268-022-00279-7 -
Malaria Journal Apr 2018Multiplicity of infection (MOI), also termed complexity of infection (COI), is defined as the number of genetically distinct parasite strains co-infecting a single host,... (Review)
Review
Multiplicity of infection (MOI), also termed complexity of infection (COI), is defined as the number of genetically distinct parasite strains co-infecting a single host, which is an important indicator of malaria epidemiology. PCR-based genotyping often underestimates MOI. Next generation sequencing technologies provide much more accurate and genome-wide characterization of polyclonal infections. However, complete haplotype characterization of multiclonal infections remains a challenge due to PCR artifacts and sequencing errors, and requires efficient computational tools. In this review, the advantages and limitations of current molecular approaches to determine multiplicity of malaria parasite infection are discussed.
Topics: Genotype; High-Throughput Nucleotide Sequencing; Humans; Malaria; Plasmodium
PubMed: 29685152
DOI: 10.1186/s12936-018-2322-5 -
G3 (Bethesda, Md.) Jun 2020The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact....
The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals. MoBPS utilizes a highly efficient implementation with bit-wise data storage and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. Individual haplotypes are not stored but instead automatically derived based on points of recombination and mutations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays' complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.
Topics: Breeding; Humans; Models, Genetic; Myelin Proteins
PubMed: 32229505
DOI: 10.1534/g3.120.401193 -
Light, Science & Applications Feb 2022Matrix computation, as a fundamental building block of information processing in science and technology, contributes most of the computational overheads in modern signal... (Review)
Review
Matrix computation, as a fundamental building block of information processing in science and technology, contributes most of the computational overheads in modern signal processing and artificial intelligence algorithms. Photonic accelerators are designed to accelerate specific categories of computing in the optical domain, especially matrix multiplication, to address the growing demand for computing resources and capacity. Photonic matrix multiplication has much potential to expand the domain of telecommunication, and artificial intelligence benefiting from its superior performance. Recent research in photonic matrix multiplication has flourished and may provide opportunities to develop applications that are unachievable at present by conventional electronic processors. In this review, we first introduce the methods of photonic matrix multiplication, mainly including the plane light conversion method, Mach-Zehnder interferometer method and wavelength division multiplexing method. We also summarize the developmental milestones of photonic matrix multiplication and the related applications. Then, we review their detailed advances in applications to optical signal processing and artificial neural networks in recent years. Finally, we comment on the challenges and perspectives of photonic matrix multiplication and photonic acceleration.
PubMed: 35115497
DOI: 10.1038/s41377-022-00717-8