scholarly journals Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 337-347 ◽  
Author(s):  
Barnabas H. Daru ◽  
Michelle van der Bank ◽  
Abubakar Bello ◽  
Kowiyou Yessoufou
Keyword(s):  
Dna Barcode ◽  
Poor Performance ◽  
Species Level ◽  
Discriminatory Power ◽  
Species Boundaries ◽  
Species Discrimination ◽  
Data Set ◽  
As Species ◽  
History Of ◽  
Combined Data

Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.

scholarly journals DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns

2021 ◽  
Vol 9 ◽  
Author(s):  
Parvin Aghayeva ◽  
Salvatore Cozzolino ◽  
Donata Cafasso ◽  
Valida Ali-zade ◽  
Silvia Fineschi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Species Level ◽  
Floristic Survey ◽  
Barcoding Gap ◽  
Plant Groups ◽  
History Of ◽  
Nuclear Its ◽  
Species Assignment ◽  
Assignment Success

DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.

DNA barcoding of a complex genus, Aesculus L. (Sapindaceae) reveals lack of species-level resolution

Botany ◽  
2019 ◽  
Vol 97 (9) ◽  
pp. 503-512 ◽  
Author(s):  
Deniz Aygoren Uluer ◽  
Rahma Alshamrani
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Its Region ◽  
Species Level ◽  
Species Discrimination ◽  
Phylogenetic Studies ◽  
Taxonomic Confusion ◽  
Low Levels ◽  
Trees And Shrubs ◽  
Small Genus

Aesculus L. is a small genus of horticulturally important trees and shrubs, comprising 13–19 species. Frequent hybridization among species, particularly in cultivation, has contributed to taxonomic confusion and difficulties in the identification of plants. In this study, we evaluated three widely employed plant DNA barcode loci, matK, and the entire ITS region (ITS1+5.8S+ITS2) as well as subunit ITS2 for 50 individuals representing 13 species of Aesculus, excluding only A. wangii (=A. assamica). In contrast to the plastid matK region, both the ITS and ITS2 loci displayed low levels of species discrimination, especially in our “first hit” BLASTn searches. We also presented the phylogeny of Aesculus based on matK and the entire ITS region, with additional matK and ITS sequences from GenBank. Our results show that Aesculus chinensis, A. flava, A. glabra, A. pavia, and A. sylvatica are probably not monophyletic. Furthermore, with the widest taxon coverage until now, the current study highlights the importance of sampling multiple individuals, not only for DNA barcoding, but also for phylogenetic studies.

scholarly journals DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

ZooKeys ◽  
2020 ◽  
Vol 921 ◽  
pp. 141-157 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt ◽  
Leif Aarvik ◽  
Kai Berggren ◽  
Oleksiy Bidzilya ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Barcode ◽  
Species Level ◽  
Coi Gene ◽  
Species Discrimination ◽  
Nominal Species ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
First Time

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

scholarly journals How the Central American Seaway and an ancient northern passage affected flatfish diversification

2018 ◽  
Author(s):  
Lisa Byrne ◽  
François Chapleau ◽  
Stéphane Aris-Brosou
Keyword(s):  
Molecular Data ◽  
Central American ◽  
Molecular Clocks ◽  
Data Set ◽  
As Species ◽  
Central American Seaway ◽  
History Of ◽  
Clock Models ◽  
Current Species ◽  
Northern Species

AbstractWhile the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the Equator diverged during the closure of CAS, while those with a northern range diverged after this, hereby suggesting the existence of a post-CAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.

Selection of children with ultra-severe traumatic brain injury for neurosurgical intervention

2019 ◽  
Vol 23 (6) ◽  
pp. 670-679
Author(s):  
Krista Greenan ◽  
Sandra L. Taylor ◽  
Daniel Fulkerson ◽  
Kiarash Shahlaie ◽  
Clayton Gerndt ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Decision Tree ◽  
Prediction Model ◽  
Severe Traumatic Brain Injury ◽  
Pupillary Response ◽  
Data Set ◽  
Robust Model ◽  
Gcs Score ◽  
Combined Data

OBJECTIVEA recent retrospective study of severe traumatic brain injury (TBI) in pediatric patients showed similar outcomes in those with a Glasgow Coma Scale (GCS) score of 3 and those with a score of 4 and reported a favorable long-term outcome in 11.9% of patients. Using decision tree analysis, authors of that study provided criteria to identify patients with a potentially favorable outcome. The authors of the present study sought to validate the previously described decision tree and further inform understanding of the outcomes of children with a GCS score 3 or 4 by using data from multiple institutions and machine learning methods to identify important predictors of outcome.METHODSClinical, radiographic, and outcome data on pediatric TBI patients (age < 18 years) were prospectively collected as part of an institutional TBI registry. Patients with a GCS score of 3 or 4 were selected, and the previously published prediction model was evaluated using this data set. Next, a combined data set that included data from two institutions was used to create a new, more statistically robust model using binomial recursive partitioning to create a decision tree.RESULTSForty-five patients from the institutional TBI registry were included in the present study, as were 67 patients from the previously published data set, for a total of 112 patients in the combined analysis. The previously published prediction model for survival was externally validated and performed only modestly (AUC 0.68, 95% CI 0.47, 0.89). In the combined data set, pupillary response and age were the only predictors retained in the decision tree. Ninety-six percent of patients with bilaterally nonreactive pupils had a poor outcome. If the pupillary response was normal in at least one eye, the outcome subsequently depended on age: 72% of children between 5 months and 6 years old had a favorable outcome, whereas 100% of children younger than 5 months old and 77% of those older than 6 years had poor outcomes. The overall accuracy of the combined prediction model was 90.2% with a sensitivity of 68.4% and specificity of 93.6%.CONCLUSIONSA previously published survival model for severe TBI in children with a low GCS score was externally validated. With a larger data set, however, a simplified and more robust model was developed, and the variables most predictive of outcome were age and pupillary response.

A Fierce Green Fire

2016 ◽  
Author(s):  
Marybeth Lorbiecki
Keyword(s):  
Life Story ◽  
Environmental Literature ◽  
Aldo Leopold ◽  
Paradigm Shifts ◽  
Ripple Effects ◽  
Ecological Vision ◽  
As Species ◽  
Wilderness Areas ◽  
The Face ◽  
History Of

For anyone interested in wildlife, birds, wilderness areas, parks, ecology, conservation, environmental literature, and ethics, the name Aldo Leopold is sure to pop up. Since first publication, Aldo Leopold: A Fierce Green Fire has remained the classic short, inspiring biography of Leopold--the perfect companion to reading his ever popular A Sand County Almanac. Winning numerous awards, this comprehensive account of his life story is dynamic and readable, written in the context of the history of American conservation and illustrated with historic photographs. Marybeth Lorbiecki has now enriched A Fierce Green Fire in a way no other biography on Leopold has, adding numerous chapters on the ripple effects of his ideas, books, ecological vision, land ethic, and Shack, as well as of the ecological contributions of his children, graduate students, contemporary scholars, and organizations--and the wilderness lands he helped preserve. Lorbiecki weaves these stories and factual information into the biography in a compelling way that keeps both lay and academic readers engaged. In the introduction to this edition, Lorbiecki makes it clear how much better our lives are because Leopold lived and why today we so radically need what he left us to bring about paradigm shifts in our ethical, economic, and cultural thinking. Instead of losing relevance, Leopold's legacy has gained ever more necessity and traction in the face of contemporary national and world challenges, such as species loss and climate change. Even the phenological studies he started at as a hobby are proving valuable, showing the climatic shifts that have occurred at the Shack lands since the 1930s, recognized by the plants and animals.

scholarly journals Evaluating Metagenomic Analysis for Pathogen Transmission in Healthcare Settings

2020 ◽  
Vol 41 (S1) ◽  
pp. s224-s224
Author(s):  
Curt Hewitt ◽  
Katharina Weber ◽  
Danielle LeSassier ◽  
Anthony Kappell ◽  
Kathleen Schulte ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Dna Analysis ◽  
Pathogen Transmission ◽  
Species Level ◽  
Metagenomic Analysis ◽  
Skin Microbiome ◽  
Limited Information ◽  
Culture Methods ◽  
Data Set ◽  
Skin Contact

Background: The prevalence of healthcare-acquired infections (HAIs) and rising levels of antimicrobial resistance place a significant burden on modern healthcare systems. Cultures are typically used to track HAIs; however, culture methods provide limited information and are not applicable to all pathogens. Next-generation sequencing (NGS) can detect and characterize pathogens present within a sample, but few research studies have explored how NGS could be used to detect pathogen transmission events under HAI-relevant scenarios. The objective of this CDC-funded project was to evaluate and correlate sequencing approaches for pathogen transmission with standard culture-based analysis. Methods: We modeled pathogen transfer via hand contact using synthetic skin. These skin coupons were seeded with a community of commensal organisms to mimic the human skin microbiome. Pathogens were added at physiologically relevant high or low levels prior to skin-to-skin contact. The ESKAPE pathogens: E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp plus C. difficile were employed because they are the most common antibiotic resistant HAIs. Pathogen transfer between skin coupons was measured following direct skin contact and fomite surface transmission. The effects of handwashing or fomite decontamination were also evaluated. Transferred pathogens were enumerated via culture to establish a robust data set against which DNA and RNA sequence analyses of the same samples could be compared. These data also provide a quantitative assessment of individual ESKAPE+C pathogen transfer rates in skin contact scenarios. Results: Metagenomic and metatranscriptomic analysis using custom analysis pipelines and reference databases successfully identified the commensal and pathogenic organisms present in each sample at the species level. This analysis also identified antibiotic resistance genes and plasmids. Metatranscriptomic analysis permitted not only gene identification but also confirmation of gene expression, a critical factor in the evaluation of antibiotic resistance. DNA analysis does not require cell viability, a key differentiator between sequencing and culturing reflected in simulated handwashing data. Sensitivity remains a key limitation of metagenomic analysis, as shown by the poor species identification and gene content characterization of pathogens present at low abundance within the simulated microbial community. Species level identification typically failed as ratios fell below 1:1,000 pathogen CFU:total community CFU. Conclusions: These findings demonstrate the strengths and weaknesses of NGS for molecular epidemiology. The data sets produced for this study are publicly available so they can be employed for future metagenomic benchmarking studies.Funding: NoneDisclosures: None

Economics of respiratory disease in dairy replacement heifers

2020 ◽  
Vol 21 (2) ◽  
pp. 143-148
Author(s):  
Michael W. Overton
Keyword(s):  
Respiratory Disease ◽  
Milk Production ◽  
Incident Case ◽  
Data Set ◽  
Dairy Heifers ◽  
The Usa ◽  
History Of ◽  
On Farm ◽  
The Impact ◽  
Selective Culling

AbstractBovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

Characteristics and Care of U.S. Nursing Home Residents with a History of Chronic Mental Illness

2000 ◽  
Vol 19 (S2) ◽  
pp. 1-17 ◽  
Author(s):  
Charles D. Phillips ◽  
Kathleen M. Spry
Keyword(s):  
Nursing Home ◽  
Nursing Home Residents ◽  
Minimum Data Set ◽  
Chronic Mental Illness ◽  
Data Set ◽  
Minimum Data ◽  
Troubles Mentaux ◽  
History Of ◽  
Resident Assessment ◽  
Medicaments Psychotropes

RÉSUMÉTrès peu de recherches ont été effectuées sur les pensionnaires des maisons de soins ayant manifestés des troubles mentaux chroniques sans démence avant leur entrée en institution. Les données du Minimum Data Set for Nursing Home Resident Assessment and Care Screening (MDS) de 1993 ont été utilisées pouranalyser les différences dans les caractéristiques et les soins se rapportant à ce type de pensionnaires par rapport aux autres pensionnaires. Cette enquête portait sur 70 000 pensionnaires du Kansas, du Maine, du Mississippi et du Dakota du Sud. Les caractéristiques des pensionnaires qui éprouvaient ce type de troubles mentaux chroniques étaient plus fréquemment les suivantes: sexe masculin, 65 ans et plus, bénéficiaires de Medicaid, moins médicalement inaptes et niveau plus élevé de problèmes de comportements. Ces pensionnaires reçoivent aussi davantage de médicaments psychotropes et suivant une thérapie, la prévalence de la thérapie étant cependant moins éleveé. Les informations recueillies pourraient laisser croire que les soins accordés à ces pensionnaires ne sont pas des plus appropriés.

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