Methods for reducing the number of sequences in molecular evolutionary analyses

Publication date: Available online 31 October 2019Source: Meta GeneAuthor(s): Yoshiyuki Suzuki, Maho Nishimura, Tatsuya Inoue, Yuki KobayashiAbstractDue to the progress in the sequencing technology, the number of nucleotide sequences for pathogens deposited in the public databases has been increasing rapidly. Consequently, in the molecular evolutionary analyses of pathogens, it may occasionally be difficult to include all the available sequences and necessary to reduce the number of sequences to accomplish computation within a realistic time frame. Here several methods for reducing the number of sequences were evaluated using the amount of evolutionary information contained in the retained sequences, which was measured as the total branch length of the phylogenetic tree (L). In the REA (random elimination in alignment) method, each of sequences was eliminated with equal probability. In the phylogenetic tree-based methods, the sequences associated with short exterior branches were eliminated; the sequences to be eliminated were required to constitute neighbors with another sequence in the CNT (closest neighbor in tree) method, whereas no such restriction was imposed in the SET (shortest exterior branch in tree) method. In the distance matrix-based methods, the sequences with small average distances to other sequences were eliminated; the sequences to be eliminated were required to be closely related to another sequence in the CPM (closest pair in matrix) method, whereas no suc...
Source: Meta Gene - Category: Genetics & Stem Cells Source Type: research

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ConclusionsLocal GXP testing compared to centralized multiplex PCR testing for IF, NV and CD, demonstrated sensitivities, specificities and NPV between 95% and 100%. Turnaround times were faster, enabling quicker infection prevention and control decision making. In our local setting (WCUH), the GXP demonstrated the potential to reduce NV and IFA/B outbreaks.
Source: Journal of Hospital Infection - Category: Infectious Diseases Source Type: research
ConclusionsLocal GXP testing compared to centralised multiplex PCR testing for IF, NV and CD, demonstrated sensitivities, specificities and NPV between 95% - 100%. Turnaround times were faster, enabling quicker infection prevention and control decision making. In our local setting (WCUH), the GXP demonstrated the potential to reduce NV and IFA/B outbreaks.
Source: Journal of Hospital Infection - Category: Infectious Diseases Source Type: research
Abstract Studies of vertebrate immunity have traditionally focused on professional cells, including circulating and tissue-resident leukocytes. Evidence that non-professional cells are also intrinsically essential (i.e. not via their effect on leukocytes) for protective immunity in natural conditions of infection has emerged from three lines of research in human genetics. First, studies of Mendelian resistance to infection have revealed an essential role of DARC-expressing erythrocytes in protection against Plasmodium vivax infection, and an essential role of FUT2-expressing intestinal epithelial cells for protect...
Source: Current Opinion in Immunology - Category: Allergy & Immunology Authors: Tags: Curr Opin Immunol Source Type: research
Conclusions and Perspectives It is interesting that watershed events, such as the loss of Neu5Gc from the glycocalyx of human cells have occurred numerous times in many mammalian and other vertebrate species. These cases of convergent evolution represent precious opportunities for increased understanding of evolutionary processes. In some respects, Neu5Gc is an ideal self-molecule as it is “private” to vertebrates and, based on current data, has yet to be successfully mimicked by microbes. Against the background of this benefit, the loss of Neu5Gc appears paradoxical and may implicate strong selective regimes,...
Source: Frontiers in Immunology - Category: Allergy & Immunology Source Type: research
CONCLUSION: Our analysis of our ED experience will aid arrangements for medical services in future Winter Games. Additionally, given our new experience, we will now be able to provide better medical services for future winter sports events. PMID: 31016910 [PubMed - in process]
Source: Yonsei Medical Journal - Category: Universities & Medical Training Authors: Tags: Yonsei Med J Source Type: research
Research ArticlesS. INAIDA, Y. SHOBUGAWA, S. MATSUNO, R. SAITO, H. SUZUKI,Epidemiology&Infection,Volume 144 Issue 12, pp 2561-2567Abstract
Source: Epidemiology and Infection - Category: Epidemiology Source Type: research
(University of Toronto - Leslie Dan Faculty of Pharmacy) Healthcare-associated infections are the fourth leading cause of death in Canada, predicted to move up to second place by 2050. Scientists at the Leslie Dan Faculty of Pharmacy, University of Toronto received $1.5 million in funding from Genome Canada to develop a new nanoparticle sensor technology that will allow hospitals and long-term care facilities to rapidly detect and visually identify highly infectious pathogens including C. difficile, methicillin-resistant S aureus (MRSA), Norovirus and influenza.
Source: EurekAlert! - Medicine and Health - Category: International Medicine & Public Health Source Type: news
Purpose: A common thread among most emerging infectious diseases is Hand Hygiene. So why isn ’t more being done to introduce, educate and bring awareness of this improtant topic among our youngest members in the community. We created a fun scientific experiment with second and third grade students to see if education and intervention will bring about a positive behavioral change that will subsequently decrease the rate of illness during peak influenza and norovirus season.
Source: International Journal of Infectious Diseases - Category: Infectious Diseases Authors: Tags: 20.130 Source Type: research
In this study, we investigated the cross-subtype protective efficacy of pc4-LAIV in conjunction with M2eP using single vaccination, combined treatment, and prime-boost approaches. Chickens vaccinated with pc4-LAIV showed significant reduction of tracheal shedding of a low pathogenicity H5N2 challenge virus. This cross-subtype protective efficacy was further enhanced, during the initial stages of challenge virus replication, in chickens that received a vaccination regimen consisting of priming with pc4-LAIV at 1 day of age and boosting with M2eP. Further, H5N2-specific serum IgG and pc4-LAIV-specific hemagglutination-inhi...
Source: Vaccine - Category: Allergy & Immunology Authors: Tags: Vaccine Source Type: research
Norovirus is a highly contagious viral infection that is commonly referred to as "stomach flu." However, it is not related to the flu, which is caused by the influenza virus. "Norovirus is a virus that causes gastroenteritis," says Dr. Nipunie Rajapakse, a pediatric infectious diseases specialist at Mayo Clinic. "Someone who is infected with norovirus [...]
Source: News from Mayo Clinic - Category: Databases & Libraries Source Type: news
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