scholarly journals Revisiting rustrela virus - new cases of encephalitis and a solution to the capsid enigma

2021 ◽  
Author(s):  
Florian Pfaff ◽  
Angele Breithaupt ◽  
Dennis Rubbenstroth ◽  
Sina Nippert ◽  
Christina Baumbach ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Intergenic Region ◽  
Rna Binding ◽  
Sequence Data ◽  
Wide Spectrum ◽  
Sequence Coverage ◽  
Protein Amino Acid ◽  
Nasua Nasua ◽  
Standard Procedures ◽  
History Of

Rustrela virus (RusV, species Rubivirus strelense) is a recently discovered relative of rubella virus (RuV) that has been detected in cases of encephalitis across a wide spectrum of mammals, including placental and marsupial animals. Here we diagnosed two additional cases of fatal RusV-associated meningoencephalitis in a South American coati (Nasua nasua) and a Eurasian otter (Lutra lutra) that were detected in a zoological garden with history of prior RusV infections. Both animals showed abnormal movement or unusual behaviour and their brains tested positive for RusV using specific RT-qPCR and RNA in situ hybridization. As previous sequencing of RusV proved to be very challenging, we employed a sophisticated target-specific capture enrichment with specifically designed RNA baits to generate complete RusV genome sequences from both detected encephalitic animals and apparently healthy wild yellow-necked field mice (Apodemus flavicollis). Furthermore, the technique was used to revise three previously published RusV genomes from two encephalitic animals and a wild yellow-necked field mouse. Virus-to-host sequence ratio and thereby sequence coverage improved markedly using the enrichment method as compared to standard procedures. When comparing the newly generated RusV sequences to the previously published RusV genomes, we identified a previously undetected stretch of 309 nucleotides predicted to represent the intergenic region and the sequence encoding the N-terminus of the capsid protein. This indicated that the original RusV sequence was likely incomplete due to misassembly of the genome at a region with an exceptionally high G+C content of >80 mol%, which could not be resolved even by enormous sequencing efforts with standard methods. The updated capsid protein amino acid sequence now resembles those of RuV and ruhugu virus in size and harbours a predicted RNA binding domain that was not encoded in the original RusV genome version. The new sequence data indicate that RusV has the largest overall genome (9,631 nucleotides), intergenic region (290 nucleotides) and capsid protein-encoding sequence (331 codons) within the genus Rubivirus.

scholarly journals Polymeric Nanocarriers: A Transformation in Doxorubicin Therapies

Materials ◽  
2021 ◽  
Vol 14 (9) ◽  
pp. 2135
Author(s):  
Kamila Butowska ◽  
Anna Woziwodzka ◽  
Agnieszka Borowik ◽  
Jacek Piosik
Keyword(s):  
Drug Delivery ◽  
Wide Spectrum ◽  
Stimuli Responsive ◽  
First Line ◽  
Medical Expenses ◽  
Polymeric Nanocarriers ◽  
Essential Properties ◽  
Life Threatening ◽  
History Of ◽  
Cancerous Cells

Doxorubicin, a member of the anthracycline family, is a common anticancer agent often used as a first line treatment for the wide spectrum of cancers. Doxorubicin-based chemotherapy, although effective, is associated with serious side effects, such as irreversible cardiotoxicity or nephrotoxicity. Those often life-threatening adverse risks, responsible for the elongation of the patients’ recuperation period and increasing medical expenses, have prompted the need for creating novel and safer drug delivery systems. Among many proposed concepts, polymeric nanocarriers are shown to be a promising approach, allowing for controlled and selective drug delivery, simultaneously enhancing its activity towards cancerous cells and reducing toxic effects on healthy tissues. This article is a chronological examination of the history of the work progress on polymeric nanostructures, designed as efficient doxorubicin nanocarriers, with the emphasis on the main achievements of 2010–2020. Numerous publications have been reviewed to provide an essential summation of the nanopolymer types and their essential properties, mechanisms towards efficient drug delivery, as well as active targeting stimuli-responsive strategies that are currently utilized in the doxorubicin transportation field.

scholarly journals Life History of the Tamarind Weevil, Sitophilus linearis (Herbst) (Coleoptera: Curculionidae), on Tamarind Seed

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
James Adebayo Ojo ◽  
Adebayo Amos Omoloye
Keyword(s):  
Life History ◽  
Management Strategy ◽  
Head Capsule ◽  
Developmental Period ◽  
Growth Ratio ◽  
Egg Incubation ◽  
Tamarind Seed ◽  
Standard Procedures ◽  
Important Pest ◽  
History Of

The tamarind weevil, Sitophilus linearis Herbst (Coleoptera: Curculionidae), is an important pest of tamarind and other Caesalpinioideae. Investigating its life history is important in the implementation of management strategy. Its life history was monitored daily to understand its developmental biology on tamarind seed following standard procedures under laboratory conditions of 24–30°C temperature, 60–70% relative humidity, and 12L : 12D photoperiod. The egg incubation period lasted 3.17 ± 0.07 days. A mated female of S. linearis laid an average of 165 ± 5.78 eggs during an oviposition period of 86.8 ± 2.47 days. There were four larval instars, with a total larval developmental period of 16 days. The pupal period lasted 8 days, and adult lived 108.5 ± 3.61 days. The overall growth ratio for the four instars was 1.33. There was a regular relationship and significant correlation (r=0.94) between the stages of larval development and head capsule width.

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.

Abstract MP048: Partner Violence is Associated with Higher Blood Pressure in Men and Women

Circulation ◽  
2012 ◽  
Vol 125 (suppl_10) ◽  
Author(s):  
Cari J Clark ◽  
Susan A Everson-Rose ◽  
Resnick Michael ◽  
Iris Borowsky ◽  
Sonya S Brady ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Partner Violence ◽  
Male Victims ◽  
Men And Women ◽  
Standard Procedures ◽  
Conflict Tactics Scales ◽  
History Of ◽  
Conflict Tactics ◽  
The Relationship ◽  
Revised Conflict Tactics Scales

Introduction: Women are more likely to experience distress and injury from intimate partner violence (IPV), and may also be at greater risk of higher blood pressure than male victims. However, most prior epidemiologic research has not included men and has not examined perpetation, despite the predominance of mutually violent relationships. Therefore, this study investigates sex differences in the relationship between exposure to IPV victimization and perpetration and systolic blood pressure (SB). Methods: The study included 3447 (52% female; mean(sd) age=22(3)) participants of Waves 3 (2001–2002) and 4 (2007) of the publically-available subset of the National Longitudinal Study of Adolescent Health. Frequency of psychological, physical, sexual IPV and IPV-related injury were ascertained with the Revised Conflict Tactics Scales at Wave 3. Exposure to IPV was categorized as no IPV victimization or perpetration (ref), only low victimization and / or perpetration, high victimization and low/no perpetration, high perpetration and low/no victimization, and both high victimization and perpetration. SBP was measured at Wave 4 using standard procedures. Potential confounders (age, educational attainment, race, history of child abuse) and mediators (depressive symptoms, breakfast consumption, moderate physical exercise, BMI, smoking, alcohol consumption) were recorded at Wave 3. Multivariable weighted linear regression was used to test the relationship between SBP and IPV by adjusting for confounders then by adjusting for the proposed mediators. Analyses were stratified by sex and a multiplicative term was tested. Results: Approximately 30% of the sample reported IPV exposure (n=2050), of which 23% (n=831) experienced low victimization and or perpetration, 5% (n=157) high victimization, 6% (N=203) high perpetration, 6% (n=206) both high victimization and perpetration. Women were slightly more likely to report high perpetration and both high victimization and high perpetration (p<0.01). In separate models controlling for confounders, experiencing both high victimization and perpetration was associated with 4.02 mmHg SBP higher in men (95% CI: 0.32, 7.72) and 2.51 mmHg SBP higher in women (95% CI: 0.18, 4.84) compared to those with no IPV. In addition, reporting high perpetration was associated with 3.83 mmHg higher SBP in men (95% CI: –0.72, 8.38), while high victimization was associated with 2.94 mmHg higher SBP for women (95% CI: –0.61, 6.49). Further adjustment for the hypothesized mediators slightly attenuated the findings. The multiplicative term (IPV X sex) was marginally significant (p=0.09). Conclusions: Exposure to high levels of victimization and perpetration is associated with higher levels of SBP for men and women. High victimization alone is related to higher SBP for women while high perpetration is related to higher SBP for men.

scholarly journals Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

2021 ◽  
Author(s):  
Ryan O Schenck ◽  
Gabriel Brosula ◽  
Jeffrey West ◽  
Simon Leedham ◽  
Darryl Shibata ◽  
...  
Keyword(s):  
Base Pair ◽  
In Silico ◽  
Sequence Data ◽  
Agent Based Modeling ◽  
Sequence Coverage ◽  
Agent Based ◽  
Coverage Error ◽  
Somatic Evolution ◽  
User Friendly ◽  
Mutation Spectra

Gattaca provides the first base-pair resolution artificial genomes for tracking somatic mutations within agent based modeling. Through the incorporation of human reference genomes, mutational context, sequence coverage/error information Gattaca is able to realistically provide comparable sequence data for in-silico comparative evolution studies with human somatic evolution studies. This user-friendly method, incorporated into each in-silico cell, allows us to fully capture somatic mutation spectra and evolution.

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 SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes

2020 ◽  
Author(s):  
Qingzhen Hou ◽  
Bas Stringer ◽  
Katharina Waury ◽  
Henriette Capel ◽  
Reza Haydarlou ◽  
...  
Keyword(s):  
Rna Binding ◽  
Sequence Data ◽  
Conformational Epitope ◽  
Test Set ◽  
Epitope Region ◽  
Protein Protein Interaction ◽  
Wide Range ◽  
Single Antigen ◽  
Wet Lab ◽  
Antigen Structure

AbstractMotivationAntibodies play an important role in clinical research and biotechnology, with their specificity determined by the interaction with the antigen’s epitope region, as a special type of protein-protein interaction (PPI) interface. The ubiquitous availability of sequence data, allows us to predicting epitopes from sequence in order to focus time-consuming wet-lab experiments onto the most promising epitope regions. Here, we extend our previously developed sequence-based predictors for homodimer and heterodimer PPI interfaces to predict epitope residues that have the potential to bind an antibody.ResultsWe collected and curated a high quality epitope dataset from the SAbDaB database. Our generic PPI heterodimer predictor obtained an AUC-ROC of 0.666 when evaluated on the epitope test set. We then trained a random forest model specifically on the epitope dataset, reaching AUC 0.694. Further training on the combined heterodimer and epitope datasets, improves our final predictor to AUC 0.703 on the epitope test set. This is better than the best state-of-the-art sequence-based epitope predictor BepiPred-2.0. On one solved antibody-antigen structure of the COVID19 virus spike RNA binding domain, our predictor reaches AUC 0.778. We added the SeRenDIP-CE Conformational Epitope predictors to our webserver, which is simple to use and only requires a single antigen sequence as input, which will help make the method immediately applicable in a wide range of biomedical and biomolecular research.AvailabilityWebserver, source code and datasets are available at www.ibi.vu.nl/programs/serendipwww/[email protected]

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 Prioritizing variants in complete Hereditary Breast and Ovarian Cancer (HBOC) genes in patients lacking known BRCA mutations

2016 ◽  
Author(s):  
Natasha G Caminsky ◽  
Eliseos J Mucaki ◽  
Ami M. Perri ◽  
Ruipeng Lu ◽  
Joan H.M. Knoll ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Wide Spectrum ◽  
Pedigree Information ◽  
Brca Mutations ◽  
Pathogenic Variants ◽  
Uncertain Significance ◽  
Common Framework ◽  
Flanking Sequences ◽  
Coding Variants

BRCA1andBRCA2testing for HBOC does not identify all pathogenic variants. Sequencing of 20 complete genes in HBOC patients with uninformative test results (N=287), including non-coding and flanking sequences ofATM,BARD1,BRCA1,BRCA2,CDH1,CHEK2,EPCAM,MLH1,MRE11A,MSH2,MSH6,MUTYH,NBN,PALB2,PMS2,PTEN,RAD51B,STK11,TP53, andXRCC2, identified 38,372 unique variants. We apply information theory (IT) to predict novel functions for and prioritize non-coding variants of uncertain significance (VUS) in throughout regulatory, coding, and intronic regions based on changes in binding sites in these genesof these genes. Besides mRNA splicing, IT provides a common framework to evaluate potential affinity changes inin transcription factor (TFBSs), splicing regulatory (SRBSs), and RNA-binding protein (RBBSs) protein binding sites following mutationat mutated binding sites. We prioritized variants affecting the strengths of 10 variants affecting splice sites (4 natural, 6 cryptic), 148 SRBS, 36 TFBS, and 31 RBBS binding strength-affecting variantss. Three variants were also prioritized based on their predicted effects on mRNA secondary (2°) structure, and 17 for pseudoexon activation. Additionally, 4 frameshift, 2 in-frame deletions, and 5 stop-gain mutations were identified. When combined with pedigree information, complete gene sequence analysis can focus attention on a limited set of variants in a wide spectrum of functional mutation types for downstream functional and co-segregation analysis.

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