Identifying chironomids (Diptera: Chironomidae) for biological monitoring with PCR–RFLP

2003 ◽  
Vol 93 (6) ◽  
pp. 483-490 ◽  
Author(s):  
M.E. Carew ◽  
V. Pettigrove ◽  
A.A. Hoffmann
Keyword(s):  
Molecular Markers ◽  
Large Scale ◽  
Life Stage ◽  
Biological Indicators ◽  
Geographic Area ◽  
Common Species ◽  
Rapid Identification ◽  
Chironomid Species ◽  
Pcr Rflp ◽  
Identification Of Species

AbstractChironomids are excellent biological indicators for the health of aquatic ecosystems, but their use at finer taxonomic levels is hindered by morphological similarity of species at each life stage. Molecular markers have the potential to overcome these problems by facilitating species identification particularly in large-scale surveys. In this study, the potential of the polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach was tested to rapidly distinguish among chironomids within a geographic area, by considering chironomid species from Melbourne, Australia. By comparing molecular markers with diagnostic morphological traits, RFLP profiles of the cytochrome oxidase I (COI) region were identified that were specific to genera and some common species. These profiles were used to develop an RFLP–based key, which was validated by testing the markers on samples from several wetlands and streams. As well as allowing for rapid identification of species that are difficult to separate on morphological grounds, this approach also has the potential to resolve current taxonomic ambiguities.

scholarly journals Technological advancements and their importance for nematode identification

SOIL ◽  
2016 ◽  
Vol 2 (2) ◽  
pp. 257-270 ◽  
Author(s):  
Mohammed Ahmed ◽  
Melanie Sapp ◽  
Thomas Prior ◽  
Gerrit Karssen ◽  
Matthew Alan Back
Keyword(s):  
High Throughput ◽  
Crop Production ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Biological Indicators ◽  
Rapid Identification ◽  
Community Studies ◽  
Terrestrial Environments ◽  
Traditional Taxonomy ◽  
Sequencing Platforms

Abstract. Nematodes represent a species-rich and morphologically diverse group of metazoans known to inhabit both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some plant-parasitic species are also known to cause significant losses to crop production. In spite of this, there still exists a huge gap in our knowledge of their diversity due to the enormity of time and expertise often involved in characterising species using phenotypic features. Molecular methodology provides useful means of complementing the limited number of reliable diagnostic characters available for morphology-based identification. We discuss herein some of the limitations of traditional taxonomy and how molecular methodologies, especially the use of high-throughput sequencing, have assisted in carrying out large-scale nematode community studies and characterisation of phytonematodes through rapid identification of multiple taxa. We also provide brief descriptions of some the current and almost-outdated high-throughput sequencing platforms and their applications in both plant nematology and soil ecology.

scholarly journals Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Strong Support ◽  
Gc Content ◽  
Rapid Identification ◽  
Hairpin Rna ◽  
Rna Sequences ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

scholarly journals Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 982
Author(s):  
Zhiliang Xiao ◽  
Congcong Kong ◽  
Fengqing Han ◽  
Limei Yang ◽  
Mu Zhuang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Brassica Oleracea ◽  
Rapid Identification ◽  
Inbred Lines ◽  
Hybrid Lethality ◽  
Specific Pcr ◽  
Allele Specific ◽  
User Friendly ◽  
Allele Specific Pcr ◽  
Kasp Marker

Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.

Ecological processes maintaining differential tree species distributions in an Australian subtropical rain forest: implications for models of species coexistence

2000 ◽  
Vol 16 (3) ◽  
pp. 387-415 ◽  
Author(s):  
Igor Debski ◽  
David F. R. P. Burslem ◽  
David Lamb
Keyword(s):  
Species Composition ◽  
Tree Species ◽  
Rain Forest ◽  
Large Scale ◽  
Species Coexistence ◽  
Common Species ◽  
Size Class ◽  
Differential Mortality ◽  
Mixed Composition ◽  
Large Scale Disturbance

All stems ≥ 1 cm dbh were measured, tagged, mapped and identified on a 1-ha plot of rain forest at Gambubal State Forest, south-east Queensland, Australia. The spatial patterns and size class distributions of 11 common tree species on the plot were assessed to search for mechanisms determining their distribution and abundance. The forest was species-poor in comparison to many lowland tropical forests and the common species are therefore present at relatively high densities. Despite this, only limited evidence was found for the operation of density-dependent processes at Gambubal. Daphnandra micrantha saplings were clumped towards randomly spaced adults, indicating a shift of distribution over time caused by differential mortality of saplings in these adult associated clumps. Ordination of the species composition in 25-m × 25-m subplots revealed vegetation gradients at that scale, which corresponded to slope across the plot. Adult basal area was dominated by a few large individuals of Sloanea woollsii but the comparative size class distributions and replacement probabilities of the 11 common species suggest that the forest will undergo a transition to a more mixed composition if current conditions persist. The current cohort of large S. woollsii individuals probably established after a large-scale disturbance event and the forest has not attained an equilibrium species composition.

scholarly journals The Costs of Home-Based ART Initiation and Mobile Refill in Uganda

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S436-S436
Author(s):  
D Allen Roberts ◽  
Stephen Asiimwe ◽  
Bosco Turyamureeba ◽  
Ruanne Barnabas
Keyword(s):  
Large Scale ◽  
Viral Suppression ◽  
Geographic Area ◽  
Outreach Worker ◽  
Eligibility Criteria ◽  
Time And Motion Studies ◽  
Art Initiation ◽  
Time And Motion ◽  
Home Based ◽  
Motion Studies

Abstract Background Antiretroviral therapy (ART) is effective at reducing HIV-associated morbidity, mortality, and transmission, but 20 million people who meet WHO eligibility criteria for ART are not in care. While decentralized care is a promising strategy to expand ART access, the costs of implementing a community-based model on a large scale remain unknown. Methods The DO-ART study is a randomized trial of community- vs. clinic-centered ART delivery in South Africa and Uganda using 12-month viral suppression as the primary outcome. We evaluated the costs of home-based ART initiation and refill in southwest Uganda using time-and-motion studies, staff interviews, and budgetary analysis. Costs categories included medications, supplies, personnel, building and utilities, start-up, vehicles, and community mobilization. We used a programmatic perspective with a 3% discount rate and removed research-associated costs. Results The largest cost categories included medications, supplies, and salaries, constituting 41%, 27%, and 17% of the total cost, respectively. Time-and-motion studies revealed that each outreach worker could serve an average of three patients per day in a fully decentralized model. In a scenario of providing home-based ART to 1400 patients aross seven sub-counties, the yearly per-patient cost was estimated to be $304 (2016 USD), which is similar to literature reports of the costs of facility-based ART provision. Conclusion These estimates suggest that home-based ART may be a realistic delivery option, especially if it is found to be effective at improving viral suppression. Further research is needed to evaluate how this intervention can most efficiently scale to provide widespread ART access over a large geographic area. Disclosures All authors: No reported disclosures.

scholarly journals Global biogeographic patterns in bipolar moss species

2017 ◽  
Vol 4 (7) ◽  
pp. 170147 ◽  
Author(s):  
E. M. Biersma ◽  
J. A. Jackson ◽  
J. Hyvönen ◽  
S. Koskinen ◽  
K. Linse ◽  
...  
Keyword(s):  
Large Scale ◽  
Common Species ◽  
Long Distance Dispersal ◽  
Stepping Stones ◽  
Long Distance ◽  
Antarctic Region ◽  
Moss Species ◽  
Biogeographic Patterns ◽  
Biogeographic Pattern ◽  
The Antarctic

A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic ( Polytrichum juniperinum ), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are rare, occurring on multi-million-year timescales. High-altitude tropical populations did not act as trans-equatorial ‘stepping-stones’, but rather were derived from later dispersal events. All arrivals to the Antarctic region occurred well before the Last Glacial Maximum and previous glaciations, suggesting that, despite the harsh climate during these past glacial maxima, plants have had a much longer presence in this southern region than previously thought.

scholarly journals Progression in Neuroimaging of Normal Pressure Hydrocephalus

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Yin ◽  
Junxian Wen ◽  
Junji Wei
Keyword(s):  
Future Development ◽  
Normal Pressure Hydrocephalus ◽  
Large Scale ◽  
Elderly Population ◽  
Normal Pressure ◽  
The Elderly ◽  
Rapid Identification ◽  
Clinical Syndrome ◽  
Surgical Interventions ◽  
Large Scale Screening

Normal-pressure hydrocephalus is a clinical syndrome that mainly targets the elderly population. It features dementia, impaired walking, and the malfunction of sphincters. The rapid identification and large-scale screening of patients with normal-pressure hydrocephalus (NPH) are of great significance as surgical interventions can greatly improve or even reverse the symptoms. This review aims to summarize the traditional parameters used to diagnose NPH and the emerging progression in neuroimaging of the disease, hoping to provide an up-to-date overall perspective and summarize the possible direction of its future development.

scholarly journals MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies

2019 ◽  
Vol 36 (2) ◽  
pp. 356-363 ◽  
Author(s):  
Terry Ma ◽  
Di Xiao ◽  
Xin Xing
Keyword(s):  
Large Scale ◽  
Empirical Studies ◽  
Nonnegative Matrix ◽  
Rapid Identification ◽  
Strain Level ◽  
Bacterial Strains ◽  
Binary Matrix ◽  
Next Generation Sequencing Technology ◽  
Microbial Species ◽  
Reference Genomes

Abstract Motivation Metagenomics studies microbial genomes in an ecosystem such as the gastrointestinal tract of a human. Identification of novel microbial species and quantification of their distributional variations among different samples that are sequenced using next-generation-sequencing technology hold the key to the success of most metagenomic studies. To achieve these goals, we propose a simple yet powerful metagenomic binning method, MetaBMF. The method does not require prior knowledge of reference genomes and produces highly accurate results, even at a strain level. Thus, it can be broadly used to identify disease-related microbial organisms that are not well-studied. Results Mathematically, we count the number of mapped reads on each assembled genomic fragment cross different samples as our input matrix and propose a scalable stratified angle regression algorithm to factorize this count matrix into a product of a binary matrix and a nonnegative matrix. The binary matrix can be used to separate microbial species and the nonnegative matrix quantifies the species distributions in different samples. In simulation and empirical studies, we demonstrate that MetaBMF has a high binning accuracy. It can not only bin DNA fragments accurately at a species level but also at a strain level. As shown in our example, we can accurately identify the Shiga-toxigenic Escherichia coli O104: H4 strain which led to the 2011 German E.coli outbreak. Our efforts in these areas should lead to (i) fundamental advances in metagenomic binning, (ii) development and refinement of technology for the rapid identification and quantification of microbial distributions and (iii) finding of potential probiotics or reliable pathogenic bacterial strains. Availability and implementation The software is available at https://github.com/didi10384/MetaBMF.

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