scholarly journals CRISPR-PN2: a flexible and genome-aware platform for diverse CRISPR experiments in parasitic nematodes

BioTechniques ◽  
2021 ◽  
Author(s):  
Damien M O'Halloran
Keyword(s):  
Human Health ◽  
Host Specificity ◽  
Immune Suppression ◽  
Automated Design ◽  
Parasitic Nematodes ◽  
Web Based ◽  
Genetic Tool ◽  
Parasite Biology ◽  
Molecular Picture

Parasitic nematodes represent a significant threat to human health, causing diseases of major socioeconomic importance worldwide. Central to controlling infections of parasitic nematodes is a more detailed molecular picture of host specificity, parasite activation and immune suppression. CRISPR technology holds huge potential for researchers in the field of parasitic nematology, as it provides a powerful genetic tool to dissect questions in parasite biology. To expedite the development of CRISPR technology in parasitic nematodes, software is required to facilitate the design of effective and specific sgRNA sequences. Here, the author introduces CRISPR-PN2, a comprehensive web-based platform that provides flexible use control over the automated design of specific gRNA sequences for CRISPR experiments in parasitic nematodes.

scholarly journals Automated design of CRISPR prime editors for thousands of human pathogenic variants

2020 ◽  
Author(s):  
John A. Morris ◽  
Jahan A. Rahman ◽  
Xinyi Guo ◽  
Neville E. Sanjana
Keyword(s):  
Genetic Variants ◽  
Gene Editing ◽  
Genome Engineering ◽  
Disease Modeling ◽  
Automated Design ◽  
Common Variants ◽  
Therapeutic Gene ◽  
Web Based ◽  
Pathogenic Variants ◽  
Automated Pipeline

AbstractPrime editors (PEs) are CRISPR-based genome engineering tools that can introduce precise base-pair edits at specific locations in the genome. These programmable gene editors have been predicted to repair 89% of known human pathogenic variants in the ClinVar database, although these PE constructs do not presently exist. Towards this end, we developed an automated pipeline to correct (therapeutic editing) or introduce (disease modeling) human pathogenic variants that optimizes the design of several RNA constructs required for prime editing and avoids predicted off-targets in the human genome. However, using optimal PE design criteria, we find that only a small fraction of these pathogenic variants can be targeted. Through the use of alternative Cas9 enzymes and extended templates, we increase the number of targetable pathogenic variants to >50,000 variants and make these pre-designed PE constructs accessible through a web-based portal (http://primeedit.nygenome.org). Given the tremendous potential for therapeutic gene editing, we also assessed the possibility of developing universal PE constructs. By examining the overlap of different PE components with common human genetic variants in dbSNP, we find that common variants affect only a small minority of designed PEs.

Identification of Helminth Parasites from Selar crumenophthalmus in Grenada, West Indies

2019 ◽  
Vol 82 (7) ◽  
pp. 1244-1248 ◽  
Author(s):  
NAUDIA S. DUNDAS ◽  
DANIEL M. FITZPATRICK ◽  
JOHN S. McKIBBEN ◽  
VICTOR A. AMADI ◽  
RHONDA D. PINCKNEY
Keyword(s):  
Human Health ◽  
Fragment Length Polymorphism ◽  
Companion Animals ◽  
Infected Fish ◽  
Parasitic Nematodes ◽  
Polymorphism Analysis ◽  
Helminth Parasites ◽  
Internal Organs ◽  
Future Studies

ABSTRACT Grenada is a tropical island country reliant on local fish for food and export. Specifically, Selar crumenophthalmus, known locally as jacks or bigeye scad, is commonly consumed by residents and visitors to the island. To date, there are no data about the prevalence of different helminths in S. crumenophthalmus in Grenada. In particular, it was unknown if Anisakis, a genus containing parasitic nematodes, implicated in both fish and human disease, is of concern for local fish and human health. In this study, 39 samples of S. crumenophthalmus were dissected and assessed for helminth infection. Of these fish, 26 (67%) contained helminths in and around the internal organs (mean, 3.6 helminths per infected fish). DNA was extracted from each helminth, followed by PCR, restriction fragment length polymorphism analysis, or Sanger sequencing or a combination of them to identify the parasites. Results confirmed that 89 (96%) of 93 helminths identified were Anisakis typica, and the remaining four helminths were likely acanthocephalans. Neither is considered pathogenic to humans, livestock, or companion animals. To our knowledge, this is the first report of either type of helminth in fish in Grenada. Future studies are needed to ascertain the role of A. typica and acanthocephalans in fish health in Grenada, including any association with observed fish kills. Additional studies are also needed to identify other helminths found in S. crumenophtalamus, which may be of importance to its health and also human health. HIGHLIGHTS

scholarly journals What determines host specificity in hyperspecialized plant parasitic nematodes?

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Michael Sabeh ◽  
Etienne Lord ◽  
Éric Grenier ◽  
Marc St-Arnaud ◽  
Benjamin Mimee
Keyword(s):  
Host Specificity ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Plant Parasitic

scholarly journals The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes

2021 ◽  
Author(s):  
Astra S Bryant ◽  
Elissa A Hallem
Keyword(s):  
Dna Sequences ◽  
Codon Bias ◽  
Codon Optimization ◽  
Nematode Species ◽  
Parasitic Nematodes ◽  
Web Tool ◽  
Nematode Caenorhabditis Elegans ◽  
Free Living ◽  
Web Based ◽  
Genome Wide

Abstract Advances in genomics techniques are expanding the range of nematode species that are amenable to transgenesis. Due to divergent codon usage biases across species, codon optimization is often a critical step for the successful expression of exogenous transgenes in nematodes. Platforms for generating DNA sequences codon-optimized for the free-living model nematode Caenorhabditis elegans are broadly available. However, until now such tools did not exist for non-Caenorhabditis nematodes. We therefore developed the Wild Worm Codon Adapter, a tool for rapid transgene codon optimization for expression in non-Caenorhabditis nematodes. The app includes built-in optimization for parasitic nematodes in the Strongyloides, Nippostrongylus, and Brugia genera as well as the predatory nematode Pristionchus pacificus. The app also supports custom optimization for any species using user-provided optimization rules. In addition, the app supports automated insertion of synthetic or native introns, as well as the analysis of codon bias in transgene and native sequences. Here, we describe this web-based tool and demonstrate how it may be used to analyze genome-wide codon bias in Strongyloides species.

scholarly journals Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species

2021 ◽  
Author(s):  
Astra S Bryant ◽  
Stephanie F DeMarco ◽  
Elissa A Hallem
Keyword(s):  
Strongyloides Stercoralis ◽  
Gastrointestinal Nematodes ◽  
Model Systems ◽  
Parasitic Nematodes ◽  
Rna Seq ◽  
Bioinformatics Analyses ◽  
Web Based ◽  
Genomic Expression ◽  
On Demand ◽  
Genomics Tools

Abstract Soil-transmitted gastrointestinal parasitic nematodes infect approximately 1 billion people worldwide, predominantly in low-resource communities. Skin-penetrating gastrointestinal nematodes in the genus Strongyloides are emerging as model systems for mechanistic studies of soil-transmitted helminths due to the growing availability of functional genomics tools for these species. To facilitate future genomics studies of Strongyloides species, we have designed a web-based application, the Strongyloides RNA-seq Browser, that provides an open source, user-friendly portal for accessing and analyzing Strongyloides genomic expression data. Specifically, the Strongyloides RNA-seq Browser takes advantage of alignment-free read mapping tools and R-based transcriptomics tools to re-analyze publicly available RNA sequencing datasets from four Strongyloides species: Strongyloides stercoralis, Strongyloides ratti, Strongyloides papillosus, and Strongyloides venezuelensis. This application permits on-demand exploration and quantification of gene expression across life stages without requiring previous coding experience. Here, we describe this interactive application and demonstrate how it may be used by nematode researchers to conduct a standard set of bioinformatics queries.

scholarly journals Web based Approach to overcome the Market Information Gap between poultry farmers and potential buyers in Tanzania.

2018 ◽  
Author(s):  
Cesilia Mambile ◽  
Dina Machuve
Keyword(s):  
Human Health ◽  
Market Information ◽  
Information Requirements ◽  
Web Based ◽  
Informal Market ◽  
Poultry Products ◽  
Information Gap ◽  
Poultry Farmers ◽  
The Web ◽  
Poultry Farming

Poultry farming is very important sector in Tanzania because it improves the human health and when sold provides income, it supports the livelihoods of 3.7 million households in Tanzania. Poultry farming sector is facing a challenge of lack of market information, also absence of well-coordinated system which is harmonized between stakeholders. Both poultry farmers and buyers rely on informal market information. The findings form this study shows that key market information required by poultry farmers and buyers are price, buyer or farmer location, Poultry kilograms, amount of poultry needed by buyers, amount of poultry products needed by buyers, types of poultry needed by buyers and kind of poultry products needed by buyers. This paper discusses this key market information required by poultry farmers and buyers, also the challenges faced due to lack of market information. In order to disseminate the identified market information requirements and to overcome the mentioned challenges the web based platform has been proposed as a solution to overcome the market information gap.

scholarly journals Lipids in ultraviolet radiation-induced immune modulation

2020 ◽  
Vol 19 (7) ◽  
pp. 870-878
Author(s):  
Benita C. Y. Tse ◽  
Scott N. Byrne
Keyword(s):  
Ultraviolet Radiation ◽  
Human Health ◽  
Uv Radiation ◽  
Immune Suppression ◽  
Immune Modulation ◽  
Sun Exposure ◽  
Radiation Induced

Ultraviolet (UV) radiation modulates cutaneous lipids which in turn mediates immune suppression – a key mechanism conferring both detrimental and beneficial impacts of sun exposure on human health.

scholarly journals Study of PH and Electrical Conductivity in Soil of Barnala District (Punjab, India): Deleterious Effects on Human Lives

2019 ◽  
Vol 7 (6) ◽  
pp. 17-26
Author(s):  
Dr. Kamalpreet Kaur
Keyword(s):  
Adverse Effect ◽  
Electrical Conductivity ◽  
Human Health ◽  
Underground Water ◽  
Parasitic Nematodes ◽  
Agricultural Fields ◽  
Plant Parasitic Nematodes ◽  
Industrial Sites ◽  
Harmful Effects ◽  
Plant Parasitic

The purpose of this study was to determine the pH and electrical conductivity in soil of different villages of   barnala district (Punjab,India ) and their harmful effects on human health. Samples of soil were collected from agricultural fields of four different villages of barnala region such as Rure ke kalan, Gunas, Handiaya and cheema from five different layers(0-10 cm; 10-20 cm; 20-30 cm; 30-40 cm and 40-50 cm depth).There are three industrial sites in barnala district and these four villages are located near to these industial sites. In this study, adverse effect of different industries on fields of these four villages were investigated. Handiaya village has high values of pH and electrical conductivity while Gunas and Cheema villages have lowest value of electrical conductivity and pH respectively. when textile effluent reaches the soil or underground water it causes bad effect on human health such as people may suffer from alkalosis which is due to high pH and can lead to arrhythmia which means irregular heartbeat. Alkalosis can induce a coma, it may cause seizures and malfunctioning of kidneys. Due to large value of Electrical conductivity activity of soil micro-organism declines so, the important microbial processes, such as nitrogen cycling, production of nitrous and other N oxide gases, respiration, and decomposition; populations of plant-parasitic nematodes can increase; and increased nitrogen losses.

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