A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds. Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.

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Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences

10.1101/042200 ◽

2016 ◽

Author(s):

Alexey M. Kozlov ◽

Jiajie Zhang ◽

Pelin Yilmaz ◽

Frank Oliver Glöckner ◽

Alexandros Stamatakis

Keyword(s):

Phylogenetic Signal ◽

Simulated Data ◽

High Accuracy ◽

Reference Sequence ◽

Manual Curation ◽

Reference Databases ◽

Placement Algorithm ◽

Evolutionary Placement Algorithm ◽

Taxonomic Annotation

AbstractMolecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labour-intensive manual curation process.Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (“mislabels”) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity / 91.7% precision) as well as correction (94.9% sensitivity / 89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria.SATIVA is freely available at https://github.com/amkozlov/sativa.

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A reliable ex vivo invasion assay of human reticulocytes by Plasmodium vivax

Blood ◽

10.1182/blood-2011-04-348748 ◽

2011 ◽

Vol 118 (13) ◽

pp. e74-e81 ◽

Cited By ~ 94

Author(s):

Bruce Russell ◽

Rossarin Suwanarusk ◽

Céline Borlon ◽

Fabio T. M. Costa ◽

Cindy S. Chu ◽

...

Keyword(s):

South America ◽

Cord Blood ◽

Plasmodium Vivax ◽

Malaria Parasite ◽

Ex Vivo ◽

Clinical Isolates ◽

Invasion Assay ◽

Large Panel ◽

Invasion Assays

AbstractCurrently, there are no reliable RBC invasion assays to guide the discovery of vaccines against Plasmodium vivax, the most prevalent malaria parasite in Asia and South America. Here we describe a protocol for an ex vivo P vivax invasion assay that can be easily deployed in laboratories located in endemic countries. The assay is based on mixing enriched cord blood reticulocytes with matured, trypsin-treated P vivax schizonts concentrated from clinical isolates. The reliability of this assay was demonstrated using a large panel of P vivax isolates freshly collected from patients in Thailand.

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An improved mitochondrial reference genome for Arabidopsis thaliana Col-0

10.1101/249086 ◽

2018 ◽

Cited By ~ 3

Author(s):

Daniel B. Sloan ◽

Zhiqiang Wu ◽

Joel Sharbrough

Keyword(s):

Arabidopsis Thaliana ◽

Mitochondrial Genome ◽

Reference Genome ◽

Sequence Data ◽

Error Rates ◽

Reference Sequence ◽

Mitochondrial Mutation ◽

Illumina Sequence ◽

Substantial Progress ◽

Genetics And Genomics

Arabidopsis thaliana remains the foremost model system for plant genetics and genomics, and researchers rely on the accuracy of its genomic resources. The first completely sequenced angiosperm mitochondrial genome was obtained from A. thaliana C24 (Unseld et al., 1997), and more recent efforts have produced additional A. thaliana reference genomes, including one for Col-0, the most widely used ecotype (Davila et al., 2011). These studies were based on older DNA sequencing methods, making them subject to errors associated with lower levels of sequencing coverage or the extremely short read lengths produced by early-generation Illumina technologies. Indeed, although the more recently published A. thaliana mitochondrial reference genome sequences made substantial progress in improving upon earlier versions, they still have high error rates. By comparing publicly available Illumina sequence data to the A. thaliana Col-0 reference genome, we found that it contains a sequence error every 2.4 kb on average, including 57 SNPs, 96 indels (up to 901 bp in size), and a large repeat-mediated rearrangement. Most of these errors appear to have been carried over from the original A. thaliana mitochondrial genome sequence by reference-based assembly approaches, which has misled subsequent studies of plant mitochondrial mutation and molecular evolution by giving the false impression that the errors are naturally occurring variants present in multiple ecotypes. Building on the progress made by previous researchers, we provide a corrected reference sequence that we hope will serve as a useful community resource for future investigations in the field of plant mitochondrial genetics.

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Cytoprotective Agents to Avoid Chemotherapy Induced Sideeffects on Normal Cells: A Review

Current Cancer Drug Targets ◽

10.2174/1568009619666190326120457 ◽

2019 ◽

Vol 19 (10) ◽

pp. 765-781

Author(s):

Seema Rohilla ◽

Harish Dureja ◽

Vinay Chawla

Keyword(s):

Adverse Effects ◽

Anticancer Agents ◽

Therapeutic Index ◽

Chemotherapeutic Agents ◽

Vital Role ◽

Normal Cells ◽

Normal Tissues ◽

Organ Specific ◽

Delay In Treatment

Anticancer agents play a vital role in the cure of patients suffering from malignancy. Though, the chemotherapeutic agents are associated with various adverse effects which produce significant toxic symptoms in the patients. But this therapy affects both the malignant and normal cells and leads to constricted therapeutic index of antimalignant drugs which adversely impacts the quality of patients’ life. Due to these adversities, sufficient dose of drug is not delivered to patients leading to delay in treatment or improper treatment. Chemoprotective agents have been developed either to minimize or to mitigate the toxicity allied with chemotherapeutic agents. Without any concession in the therapeutic efficacy of anticancer drugs, they provide organ specific guard to normal tissues.

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Phamacognostical and Pharmaceutical Evaluation of Chandrashakaladi Vataka - A herbal formulation

Journal of Ayurveda and Integrated Medical Sciences (JAIMS) ◽

10.21760/jaims.v1i3.4414 ◽

2016 ◽

Vol 1 (3) ◽

Author(s):

Dr. Akash S Changole ◽

Mandip Goyal ◽

Harish CR

Keyword(s):

Classical Method ◽

Raw Materials ◽

Herbal Medicines ◽

Vital Role ◽

Published Data ◽

Herbal Formulation ◽

Physico Chemical ◽

Good Manufacturing Practices ◽

Solvent Systems

Background: Quality control and the standardization of herbal medicines involve steps like standard source and quality of raw materials, good manufacturing practices and adequate analytical screening. These practices play a vital role in guaranting the quality and stability of herbal preparations. Chandrashakaladi Vataka is an Ayurvedic herbal formulation mentioned to be beneficial in Kushtha. Till date no published data is available on its analytical profile. Aim: To develop the Pharmacognostical and Phyto-chemical profile of Chandrashakaladi Vataka. Material and Methods: Chandrashakaladi Vataka was prepared as per classical method and analytical findings were recorded. Samples were subjected to organoleptic analysis, physico-chemical analysis and HPTLC examination by optimizing the solvent systems. Results and Conclusions: Pharmacognostical profile of Chandrashakaladi Vataka was established. Loss on drying, Ash value, Acid insoluble extract, Methanol soluble extract, Chandrashakaladi Vataka was found within prescribed limits. HPTLC profile of Chandrashakaladi Vataka revealed 12 spots at 254 nm and 13 spots at 366 nm.

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Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

Microbiome ◽

10.1186/s40168-020-00975-x ◽

2021 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Leeann Klassen ◽

Greta Reintjes ◽

Jeffrey P. Tingley ◽

Darryl R. Jones ◽

Jan-Hendrik Hehemann ◽

...

Keyword(s):

Metabolic Pathways ◽

Ex Vivo ◽

Rapid Assessment ◽

Vital Role ◽

Strain Level ◽

Metabolic Phenotype ◽

Specific Cell ◽

Bacterial Cells ◽

Carbohydrate Utilization

AbstractGut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as “medium grower” and “high grower.” Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and “omics” approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem.

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A Systematic Review of Healthcare Professionals’ Knowledge, Self-Efficacy and Attitudes Towards Working with Autistic People

Review Journal of Autism and Developmental Disorders ◽

10.1007/s40489-021-00263-w ◽

2021 ◽

Author(s):

Kirsten Corden ◽

Rebecca Brewer ◽

Eilidh Cage

Keyword(s):

Health Professionals ◽

Self Efficacy ◽

Healthcare Professionals ◽

Assessment Tool ◽

Vital Role ◽

Narrative Synthesis ◽

Quality Assessment Tool ◽

Professional Background ◽

Autistic People

AbstractHealthcare professionals play a vital role in identifying and supporting autistic people. This study systematically reviewed empirical research examining healthcare professionals’ knowledge, self-efficacy and attitudes towards working with autistic people. Thirty-five studies were included. The included studies sampled a range of countries and professional backgrounds. A modified quality assessment tool found the quality of the included studies was moderately good. Narrative synthesis indicated that healthcare professionals report only moderate levels of autism knowledge and self-efficacy, and often lack training. Variation within and between countries and professional background was not explained by demographic factors. The reviewed evidence suggests health professionals’ limited knowledge and self-efficacy in working with autistic people is a challenge to the provision of healthcare for autistic individuals.

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Evaluation of Quality of Pharmacoeconomic Studies in Asia Pacific and Identification of Influencing Variables

Value in Health ◽

10.1016/j.jval.2016.08.482 ◽

2016 ◽

Vol 19 (7) ◽

pp. A848-A849

Author(s):

R Pandey ◽

P Pandey ◽

Shrivastav ◽

S Mittra ◽

Shah

Keyword(s):

Asia Pacific

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Processes, Challenges and Optimisation of Rum Production from Molasses—A Contemporary Review

Fermentation ◽

10.3390/fermentation7010021 ◽

2021 ◽

Vol 7 (1) ◽

pp. 21

Author(s):

Tinashe Mangwanda ◽

Joel B. Johnson ◽

Janice S. Mani ◽

Steve Jackson ◽

Shaneel Chandra ◽

...

Keyword(s):

Management Practices ◽

Scientific Literature ◽

Asia Pacific ◽

Yeast Strains ◽

Challenges And Opportunities ◽

The Caribbean ◽

The Impact ◽

Production Industry ◽

Stringent Quality

The rum industry is currently worth USD 16 billion, with production concentrated in tropical countries of the Caribbean and Asia-Pacific regions. The primary feedstock for rum production is sugar cane molasses, a by-product of sugar refineries. The main variables known to affect rum quality include the composition of the molasses, the length of fermentation, and the type of barrels and length of time used for aging the rum. The goal of this review is to provide an overview of the impact of these variables on rum quality, and to highlight current challenges and opportunities in the production of rum from molasses. In order to achieve this, we review the relevant contemporary scientific literature on these topics. The major contemporary challenges in the rum production industry include minimising the effects of variability in feedstock quality, ensuring the fermentation process runs to completion, preventing microbial contamination, and the selection and maintenance of yeast strains providing optimum ethanol production. Stringent quality management practices are required to ensure consistency in the quality and organoleptic properties of the rum from batch to batch. Further research is required to fully understand the influences of many of these variables on the final quality of the rum produced.

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Revisiting competences of adult learning facilitators: Perspectives from the Mongolian context

Journal of Adult and Continuing Education ◽

10.1177/14779714211003100 ◽

2021 ◽

pp. 147797142110031

Author(s):

Togtokhmaa Zagir ◽

Helga Dorner

Keyword(s):

Professional Development ◽

Adult Learners ◽

Adult Learning ◽

Needs Assessment ◽

Vital Role ◽

International Studies ◽

Teaching Role ◽

Core Competences ◽

Key Stakeholders

Competent adult learning facilitators play a vital role in improving the quality of adult learning programmes. This article thus explores common and core competences of adult learning facilitators from the perspective of key stakeholders, such as facilitators, adult learners and administrators. By synthesising previous international studies, we developed a survey and collected data in Mongolia ( n = 227). We identified adult learning facilitators’ common and core competences focusing on their teaching role. As found, areas of adult learners’ needs assessment, communication and motivation should be integrated in professional development programmes in order to aim for a better completion rate and higher participation of target audiences in adult learning programmes.

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