scholarly journals Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

2021 ◽  
Author(s):  
Kathryn Campbell ◽  
Robert J Gifford ◽  
Joshua Singer ◽  
Verity Hill ◽  
Aine O'Toole ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Sequence Data ◽  
Classification Systems ◽  
Virus Elimination ◽  
Data Resource ◽  
Genomic Tools ◽  
Control Programmes ◽  
History Of ◽  
Virus Sequence ◽  
Globally Distributed

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses.

scholarly journals On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1628
Author(s):  
Kanika D. Nahata ◽  
Nena Bollen ◽  
Mandev S. Gill ◽  
Maylis Layan ◽  
Hervé Bourhy ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Rna Viruses ◽  
Sequence Data ◽  
The Past ◽  
Research Areas ◽  
Research Fields ◽  
History Of ◽  
Review Study ◽  
Global Initiative ◽  
Reservoir Hosts

Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.

scholarly journals Rabies-induced Spongiform Change and Encephalitis in a Heifer

1995 ◽  
Vol 32 (3) ◽  
pp. 309-311 ◽  
Author(s):  
G. L. Foley ◽  
J. F. Zachary
Keyword(s):  
Rabies Virus ◽  
Fluorescent Antibody ◽  
Virus Antigen ◽  
Spongiform Encephalopathy ◽  
Antibody Testing ◽  
Spongiform Change ◽  
The Usa ◽  
History Of ◽  
The Central Nervous System ◽  
The University

A 1-year-old mixed breed heifer was presented to the Veterinary Medical Teaching Hospital at the University of Illinois with a 3-day history of abnormal mentation and aggressive behavior. Based on the history and clinical examination, euthanasia and necropsy were recommended. The differential diagnoses included rabies, pseudorabies, and a brain abscess. The brain was removed within 60 minutes of death, and the section submitted for fluorescent antibody testing was positive for rabies virus antigen. Residual brain tissue was immersion fixed in 10% neutral buffered formalin. Histologic examination revealed a marked perivascular and meningeal lymphocytic meningoencephalitis and locally extensive spongiform change of the gray matter affecting the neuropil and neuron cell bodies. The most severely affected regions with spongiform change were the thalamus and cerebral cortex. No Negri bodies were found in any sections. Since the outbreak of bovine spongiform encephalopathy (BSE) in the United Kingdom, there has been an increased surveillance of bovine neurologic cases in an effort to assess if BSE has occurred in the USA. In areas where rabies virus is endemic, rabies should be included as a possible differential diagnosis in cases of spongiform changes of the central nervous system.

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

The Art of Bread Production in Sardinia: Cultural Aspects and Issues of Classification

2020 ◽  
pp. 169-179
Author(s):  
Армандо Мажиа
Keyword(s):  
Field Research ◽  
Classification Systems ◽  
Traditional Practice ◽  
Cultural Aspects ◽  
History Of ◽  
Bread Production ◽  
Ethnographic Analysis ◽  
Technology Of Production ◽  
Term Field

В настоящей статье автор, преимущественно на материалах собственных многолетних полевых исследований, рассматривает в контексте современности малоизученную традиционную практику хлебопроизводства в Сардинии. Анализ особенностей этого древнейшего сектора локальной культуры он предваряет освещением специфики истории региона и принципов расселения в нем, значительно повлиявших на множественность разнообразных «типажей» хлеба, как повседневных, так и праздничных, показывает специфику их иконографии и декорирования, отличия их рецептуры и технологии производства, их «привязок» к конкретным поводам, событиям, верованиям и ритуалам. Помимо этнографической части, в исследовании присутствуют теоретико-методологические аспекты: автор задается вопросом о несовершенстве существующих систем классификации сардинских хлебов, о нерешенности вопроса их таксономирования и, апеллируя к примеру эмпирического материала Сардинии, предлагает иные пути и подходы к систематизации в антропологическом исследовании в целом, а в частности, переход от «монотетической» классификации к ретикулярной, ризоматической систематизации Based mainly on the author’s long-term field research, this article examines the littlestudied traditional practice of bread production in Sardinia in the context of modernity. The analysis of this, the oldest sector of local culture, is preceded by a history of the region and the nature of its settlement which influenced the multiplicity of various types of bread, both everyday and festive. The article explains the specifics of bread’s iconography and decoration, differences in recipes and technology of production, and its links to specific occasions, events, beliefs and rituals. In addition to ethnographic analysis, the study examines theoretical and methodological issues. The author considers problems with existing classification systems of Sardinian bread, discusses the unresolved issue of their taxonomy, and questions the general approach to systematization in anthropological research, and in particular, the transition from “monotheistic” classification to reticular, rhizomatic systematization. Key words: Sardinia, Mediterranean, bread, cooking technologies, species diversity.

scholarly journals Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification

2019 ◽  
Author(s):  
Daria Koscinski ◽  
Paul Handford ◽  
Pablo L. Tubaro ◽  
Peiwen Li ◽  
Stephen C. Lougheed
Keyword(s):  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Elevational Gradient ◽  
Northwestern Argentina ◽  
Dna Sequence Data ◽  
The Andes ◽  
Common Causes ◽  
History Of ◽  
Historical Range

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species: Pleurodema borellii (Family: Leiuperidae, 130 individuals; 20 sites), and Hypsiboas riojanus (Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However, Pleurodema borellii exhibited markedly deeper temporal divergence (≥4 Ma) than H. riojanus (1-2 Ma). The three main mtDNA lineages of P. borellii were nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specialized H. riojanus than in the more generalist P. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.

scholarly journals A statistical evaluation of the origin of cypress domes in Florida

2020 ◽  
Author(s):  
Eron Raines
Keyword(s):  
Striking Similarity ◽  
Geologic History ◽  
Parameter Spaces ◽  
Surface Areas ◽  
Biological Explanation ◽  
Starting Conditions ◽  
History Of ◽  
Cypress Domes ◽  
Ecological Feedbacks ◽  
Globally Distributed

Two competing explanations exist for the origin of one type of karstic landform found in Florida called the cypress dome. One explanation relies on complex ecological feedbacks stemming from nutrient cycling suggesting biota contribute more significantly to processes of landscape evolution in Florida than anywhere else in the world. The second explanation is that the landforms are sinkholes that completely preclude the biological explanation while fitting more parsimoniously with the surrounding geological narrative. This work puts forward geostatistical analyses and a model linking the landforms to sinkholes, thus bolstering the geological explanation for origin of the landform. Satellite imagery of sinkholes occurring in limestone from locations spanning the planet was analyzed. Measurements of globally distributed limestone sinkhole surface areas are best characterized by an exponential distribution indicating sinkhole formation is robust to starting conditions (i.e., climate, tectonics). This observation is supported by an analysis of sinkhole geometry and geospatial dispersion. This demonstrates the geospatial parameters space for globally distributed groups of sinkholes forming in limestone are statistically indistinguishable despite sinkhole formation in different climates, tectonic regimes, and at different times. Employing this observation as a tool, sinkholes are directly compared to the cypress domes in Florida and are found to be statistically indistinguishable. From the striking similarity in spatial parameter spaces in conjunction with the geologic history of the area, it is interpreted that these landforms originate through geologic, not biologic, processes.

scholarly journals The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

2018 ◽  
Author(s):  
Sandra Oliveira ◽  
Alexander Hübner ◽  
Anne-Maria Fehn ◽  
Teresa Aço ◽  
Fernanda Lages ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sequence Data ◽  
Population History ◽  
Female Population ◽  
Bantu Languages ◽  
Mtdna Sequence ◽  
Population Sizes ◽  
Group Variation ◽  
History Of ◽  
Previous Demonstration

AbstractSouthwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx’a, Khoe-Kwadi and Bantu languages. Although present-day Bantu-speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been though to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the non-recombining Y chromosome (NRY) from 170 individuals with previously reported mitochondrial genomes (mtDNA), to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun) and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu NRY lineages among Bantu-speaking groups, except for small amounts of “Khoisan” introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for NRY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

scholarly journals The data universe of structural biology

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 630-638 ◽  
Author(s):  
Helen M. Berman ◽  
Brinda Vallat ◽  
Catherine L. Lawson
Keyword(s):  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
Small Data ◽  
Complex Structures ◽  
Data Resource ◽  
History Of

The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology. The history of the growth of the PDB and the role that the community has played in developing standards and policies are described. This article also illustrates how other biophysics communities are collaborating with the worldwide PDB to create a network of interoperating data resources. This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.

What Is Diversity?

2020 ◽  
pp. 1-27
Author(s):  
Mona Sue Weissmark
Keyword(s):  
Social Issues ◽  
Brain Size ◽  
Single Species ◽  
Classification Systems ◽  
Human Beings ◽  
Tower Of Babel ◽  
Theory Of Evolution ◽  
The Bible ◽  
History Of ◽  
Physical Attributes

This introductory chapter traces the history of ideas about race and human classification systems, from the bible to the Classical period and on to the first “scientific” attempts to rank differences and ascribe characteristics to races. Starting with the view from the Tower of Babel came the notion that linguistic and cultural diversity was the Supreme Being’s punitive response to such human hubris of reaching for heaven on earth. Following that came a litany of scholars, scientists, and doctors, who established hierarchies that left white Europeans on the top of the intellectual period, and other races lagging behind. Among these was Hippocrates, who wrote that the forms and dispositions of human beings corresponded with the nature of the country, their region’s climate and topography. Meanwhile, the French physician Francois Bernier developed the first post-Classical racial classification system, basing it on physical attributes. Johann Friedrich Blumenbach was the first phrenologist, and although he also classified race, he asserted that all races belonged to a single species. Physician George Morton measured cranial size and then estimated brain size in an effort to rank humans based on intelligence. The chapter then looks at more modern concepts, such as Charles Darwin’s theory of evolution; scientific rejection of the notion that races were biologically different; and UNESCO’s statement that social issues give rise to racism.

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