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Viral evolution

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https://www.readbyqxmd.com/read/28730408/evolution-of-the-hiv-1-transgenic-rat-utility-in-assessing-the-progression-of-hiv-1-associated-neurocognitive-disorders
#1
Kristen A McLaurin, Rosemarie M Booze, Charles F Mactutus
Understanding the progression of HIV-1-associated neurocognitive disorders (HAND) is a critical need as the prevalence of HIV-1 in older individuals (>50 years) is markedly increasing due to the great success of combination antiretroviral therapy (cART). Longitudinal experimental designs, in comparison to cross-sectional studies, provide an opportunity to establish age-related disease progression in HAND. The HIV-1 transgenic (Tg) rat, which has been promoted for investigating the effect of long-term HIV-1 viral protein exposure, was used to examine two interrelated goals...
July 20, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/28730261/post-medication-stevens-johnson-syndrome-in-a-girl-hospitalized-for-a-norovirus-and-rotavirus-infection
#2
Simona Dumitra, LuminiŢa Pilat, Alina Iftode, Ozana Nicoleta Bălan, Carmen Ramona StănculeŢ, Elena Claudia Covaci, Alexandru Fica Mircea Onel, Carmen Nicoleta Crişan
Stevens-Johnson syndrome (SJS) is a cutaneous mucosal disorder characterized by extended necrosis and detachment of the epidermis affecting <10% of the body surface, caused by drugs or infections. The authors report a case of a girl with Depakine resistant epilepsy, who develops a SJS in the third week of introducing lamotrigine. The girl also presents an acute diarrheal disease with double viral etiology - rotavirus and norovirus. The clinical image comprises polymorphic erythematous maculopapular exanthema with vesicular and bullous elements, with ulcerations and desquamations at the level of the eyelids, mouth, anogenital area and tegument denuding at the level of the abdomen and limbs...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#3
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28725230/genetics-and-genomics-of-cotton-leaf-curl-disease-its-viral-causal-agents-and-whitefly-vector-a-way-forward-to-sustain-cotton-fiber-security
#4
REVIEW
Mehboob-Ur- Rahman, Ali Q Khan, Zainab Rahmat, Muhammad A Iqbal, Yusuf Zafar
Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28723886/prolonged-viral-replication-and-longitudinal-viral-dynamic-differences-among-respiratory-syncytial-virus-rsv-infected-infants
#5
Monica E Brint, Joshua M Hughes, Aditya Shah, Chelsea R Miller, Lisa G Harrison, Elizabeth A Meals, Jacqueline Blanch, Charlotte R Thompson, Stephania A Cormier, John P DeVincenzo
BACKGROUND: Longitudinal RSV dynamics have not been well-studied despite existence of factors favoring prolonged RSV replication including: high mutation rates allowing rapid evolution and potential escape from immune control. We therefore measured viral load in previously RSV-naïve infants over prolonged time-spans. METHODS: During 2014-2015, quantitative nasal aspirates were collected from 51 RSV-PCR+ infants. Multiple parallel assessments of viral loads were quantified at each collected time point using a well-validated real-time qRT-PCR assay...
July 19, 2017: Pediatric Research
https://www.readbyqxmd.com/read/28718801/from-variation-of-influenza-viral-proteins-to-vaccine-development
#6
REVIEW
Wandi Zhu, Chao Wang, Bao-Zhong Wang
Recurrent influenza epidemics and occasional pandemics are one of the most important global public health concerns and are major causes of human morbidity and mortality. Influenza viruses can evolve through antigen drift and shift to overcome the barriers of human immunity, leading to host adaption and transmission. Mechanisms underlying this viral evolution are gradually being elucidated. Vaccination is an effective method for the prevention of influenza virus infection. However, the emergence of novel viruses, including the 2009 pandemic influenza A (H1N1), the avian influenza A virus (H7N9), and the highly pathogenic avian influenza A virus (HPAI H5N1), that have infected human populations frequently in recent years reveals the tremendous challenges to the current influenza vaccine strategy...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#7
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28716906/virus-found-in-a-boreal-lake-links-ssdna-and-dsdna-viruses
#8
Elina Laanto, Sari Mäntynen, Luigi De Colibus, Jenni Marjakangas, Ashley Gillum, David I Stuart, Janne J Ravantti, Juha T Huiskonen, Lotta-Riina Sundberg
Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (Flavobacterium-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28715435/spatial-patterns-of-dengue-cases-in-brazil
#9
Fernando Jose Antonio, Andreia Silva Itami, Sergio de Picoli, Jorge Juarez Vieira Teixeira, Renio Dos Santos Mendes
Dengue infection plays a central role in our society, since it is the most prevalent vector-borne viral disease affecting humans. We statistically investigated patterns concerning the spatial spreading of dengue epidemics in Brazil, as well as their temporal evolution in all Brazilian municipalities for a period of 12 years. We showed that the distributions of cases in municipalities follow power laws persistent in time and that the infection scales linearly with the population of the municipalities. We also found that the average number of dengue cases does not have a clear dependence on the longitudinal position of municipalities...
2017: PloS One
https://www.readbyqxmd.com/read/28705717/whole-genome-characterization-of-uruguayan-strains-of-avian-infectious-bronchitis-virus-reveals-extensive-recombination-between-the-two-major-south-american-lineages
#10
Ana Marandino, Gonzalo Tomás, Yanina Panzera, Gonzalo Greif, Adriana Parodi-Talice, Martín Hernández, Claudia Techera, Diego Hernández, Ruben Pérez
Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing...
July 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28705467/sarcoidosis-with-fever-and-a-splenic-infarct-due-to-cmv-or-lymphoma
#11
REVIEW
Burke A Cunha, Thulashie Sivarajah, Ismail Jimada
We present a case of an adult female with a past history of pulmonary sarcoidosis who presented with fever, night sweats, profound fatigue, and LUQ abdominal pain. Sarcoidosis is an afebrile disorder (excluding Lofgren's syndrome, Heerfordt's syndrome or neurosarcoidosis). Therefore, the presence of fever with sarcoidosis should suggest infection, usually viral, or lymphoma. Sarcoidosis-lymphoma syndrome describes the evolution of a lymphoma in long standing sarcoidosis. Fever aside, possible lymphoma is suggested by otherwise unexplained fever, pleural unilateral effusion, highly elevated ESR or ferritin levels...
July 10, 2017: Heart & Lung: the Journal of Critical Care
https://www.readbyqxmd.com/read/28701775/viral-evolution-every-flu-evolves-in-the-same-way
#12
Irene Vacca
No abstract text is available yet for this article.
July 13, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28695291/missing-or-altered-self-human-nk-cell-receptors-that-recognize-hla-c
#13
REVIEW
Hugo G Hilton, Peter Parham
Natural killer (NK) cells are fast-acting and versatile lymphocytes that are critical effectors of innate immunity, adaptive immunity, and placental development. Controlling NK cell function are the interactions between killer-cell immunoglobulin-like receptors (KIRs) and their HLA-A, HLA-B and HLA-C ligands. Due to the extensive polymorphism of both KIR and HLA class I, these interactions are highly diversified and specific combinations correlate with protection or susceptibility to a range of infectious, autoimmune, and reproductive disorders...
July 10, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28694862/primary-hepatic-marginal-zone-lymphoma-in-a-patient-with-chronic-hepatitis-c
#14
George S Gherlan, Razvan Stoia, Mihaly Enyedi, Camelia Dobrea, Petre I Calistru
Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) is a low-grade malignant lymphoma that appears frequently in the stomach, but other sites can also be involved: the intestinal tract, lungs, head, neck, skin, thyroid, breasts and liver. Recently, epidemiological evidences support the idea that there is an association between hepatitis C and B-cell non-Hodgkin lymphomas (that include MALT as a subtype). Primary non-Hodgkin lymphomas confi ned only to the liver are very rare (only 0...
September 2016: Mædica
https://www.readbyqxmd.com/read/28692701/molecular-features-of-influenza-a-h1n1-pdm09-prevalent-in-mexico-during-winter-seasons-2012-2014
#15
Rocío Arellano-Llamas, Luis Alfaro-Ruiz, Cristian Arriaga Canon, Ivan Imaz Rosshandler, Alfredo Cruz-Lagunas, Joaquín Zúñiga, Rosa Rebollar Vega, Christopher W Wong, Sebastian Maurer-Stroh, Sandra Romero Córdoba, Edison T Liu, Alfredo Hidalgo-Miranda, Joel A Vázquez-Pérez
Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011-2012 winter season and finally, during the 2013-2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease...
2017: PloS One
https://www.readbyqxmd.com/read/28690608/phylogenetic-tracings-of-proteome-size-support-the-gradual-accretion-of-protein-structural-domains-and-the-early-origin-of-viruses-from-primordial-cells
#16
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28685417/the-lymph-node-in-hiv-pathogenesis
#17
REVIEW
Yiannis Dimopoulos, Eirini Moysi, Constantinos Petrovas
Lymph nodes play a central role in the development of adaptive immunity against pathogens and particularly the generation of antigen-specific B cell responses in specialized areas called germinal centers (GCs). Lymph node (LN) pathology was recognized as an important consequence of human immunodeficiency virus (HIV) infection since the beginning of the HIV epidemic. Investigation into the structural and functional alterations induced by HIV and Simian immunodeficiency virus (SIV) has further cemented the central role that lymphoid tissue plays in HIV/SIV pathogenesis...
July 7, 2017: Current HIV/AIDS Reports
https://www.readbyqxmd.com/read/28679760/co-operation-between-strain-specific-and-broadly-neutralizing-responses-limited-viral-escape-and-prolonged-exposure-of-the-broadly-neutralizing-epitope
#18
Colin Anthony, Talita York, Valerie Bekker, David Matten, Philippe Selhorst, Roux-Cil Ferreria, Nigel J Garrett, Salim S Abdool Karim, Lynn Morris, Natasha T Wood, Penny L Moore, Carolyn Williamson
V3-glycan targeting broadly neutralizing antibodies (bNAbs) are a focus of HIV-1 vaccine development. Understanding the viral dynamics that stimulate the development of these antibodies can provide insights for immunogen design. We used a deep sequencing approach, together with neutralization phenotyping, to investigate the rate and complexity of escape from V3-glycan directed bNAbs, compared to overlapping early strain-specific neutralizing antibody (ssNAb) responses to the V3/C3 region in donor CAP177. Escape from the ssNAb response occurred rapidly, via a N334 to N332 glycan switch, which took just 7...
July 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28679700/chemostat-culture-for-yeast-experimental-evolution
#19
Celia Payen, Maitreya J Dunham
Experimental evolution is one approach used to address a broad range of questions related to evolution and adaptation to strong selection pressures. Experimental evolution of diverse microbial and viral systems has routinely been used to study new traits and behaviors and also to dissect mechanisms of rapid evolution. This protocol describes the practical aspects of experimental evolution with yeast grown in chemostats, including the setup of the experiment and sampling methods as well as best laboratory and record-keeping practices...
July 5, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28675835/new-insights-into-influenza-a-specificity-an-evolution-of-paradigms
#20
REVIEW
Ye Ji, Yohanna Jb White, Jodi A Hadden, Oliver C Grant, Robert J Woods
Understanding the molecular origin of influenza receptor specificity is complicated by the paucity of quantitative affinity measurements, and the qualitative and variable nature of glycan array data. Further obstacles arise from the varied impact of viral glycosylation and the relatively narrow spectrum of biologically relevant receptors present on glycan arrays. A survey of receptor conformational properties is presented, leading to the conclusion that conformational entropy plays a key role in defining specificity, as does the newly reported ability of biantennary receptors that terminate in Siaα2-6Gal sequences to form bidentate interactions to two binding sites in a hemagglutinin trimer...
July 1, 2017: Current Opinion in Structural Biology
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