From the feces to the genome: a guideline for the isolation and preservation of Strongyloides stercoralis in the field for genetic and genomic analysis of individual worms

Abstract Strongyloidiasis is a soil-borne helminthiasis, which, in spite of the up to 370 million people currently estimated to be infected with its causing agent, the nematode Strongyloides stercoralis, is frequently overlooked. Recent molecular taxonomic studies conducted in Southeast Asia and Australia, showed that dogs can carry the same genotypes of S. stercoralis that also infect humans, in addition to a presumably dog-specific Strongyloides species. This suggests a potential for zoonotic transmission of S. stercoralis from dogs to humans. Although natural S. stercoralis infections have not been reported in any host other than humans, non-human primates and dogs, other as yet unidentified animal reservoirs cannot be excluded. Molecular studies also showed that humans carry rather different genotypes of S. stercoralis. As a result, their taxonomic status and the question of whether they differ in their pathogenic potential remains open. It would therefore be very important to obtain molecular genetic/genomic information about S. stercoralis populations from around the world. One way of achieving this (with little additional sampling effort) would be that people encountering S. stercoralis in the process of their diagnostic work preserve some specimens for molecular analysis. Here we provide a guideline for the isolation, preservation, genotyping at the nuclear 18S rDNA and the mitochondrial cox1 loci, and for whole genome sequencing of single S. stercoralis worms. Since in many cases the full analysis is not possible or desired at the place and time where S. stercoralis are found, we emphasize when and how samples can be preserved, stored and shipped for later analysis. We hope this will benefit and encourage researchers conducting field studies or diagnostics to collect and preserve S. stercoralis for molecular genetic/genomic analyses and either analyze them themselves or make them available to others for further analysis.

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Divergence in plumage, voice, and morphology indicates speciation in Rufous-capped Warblers (Basileuterus rufifrons)

The Auk ◽

10.1093/auk/ukaa029 ◽

2020 ◽

Vol 137 (3) ◽

Cited By ~ 1

Author(s):

Alana D Demko ◽

J Roberto Sosa-López ◽

Richard K Simpson ◽

Stéphanie M Doucet ◽

Daniel J Mennill

Keyword(s):

Species Differences ◽

Genomic Analysis ◽

Taxonomic Status ◽

Morphological Features ◽

Sampling Effort ◽

Field Recordings ◽

Tropical Biodiversity ◽

And Behavior ◽

Accurate Quantification ◽

Comprehensive Study

Abstract The biodiversity of the Neotropics is considerable, but it is likely underestimated owing to gaps in sampling effort and a focus on using morphological features of animals to determine species differences rather than divergence in their mating signals and behavior. Recent multi-trait analyses incorporating morphological, plumage, and vocal data have allowed for more accurate quantification of tropical biodiversity. We present a comprehensive study of morphological features, plumage, and vocalizations of the Neotropical resident Rufous-capped Warbler (Basileuterus rufifrons). This species’ taxonomic status is controversial because the B. r. salvini subspecies is intermediate in plumage coloration between the neighboring B. r. delattrii and B. r. rufifrons subspecies. Using morphological and spectral plumage measurements of field and museum specimens, as well as analyses of vocalizations from field recordings and sound libraries, we compared phenotypes of all 8 currently recognized Rufous-capped Warbler subspecies, with an emphasis on delattrii, rufifrons, and salvini. We found that delattrii and rufifrons differ significantly in morphology and plumage, and that salvini is similar to rufifrons in morphology and some plumage features. Vocalizations fall into 2 distinct groups, delattrii and rufifrons-salvini, which differ in multiple spectro-temporal characteristics with no overlap between them, even among individuals in the delattrii–rufifrons zone of sympatry. Our results therefore suggest that Rufous-capped Warblers comprise 2 distinct groups: Rufous-capped Warblers (B. r. rufifrons and salvini as well as B. r. caudatus, dugesi, and jouyi) and Chestnut-capped Warblers (B. r. delattrii as well as B. r. actuosus and mesochrysus). Future genomic analysis of samples from multiple sites in Mexico and Central America will further refine our assessment of range-wide phenotypic and genetic divergence in this species complex.

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A new slipper lobster of the genus Petrarctus Holthuis, 2002 (Crustacea, Decapoda, Scyllaridae) from Southwest coast of India

Zootaxa ◽

10.11646/zootaxa.4329.5.5 ◽

2017 ◽

Vol 4329 (5) ◽

pp. 477 ◽

Cited By ~ 3

Author(s):

CHIEN-HUI YANG ◽

APPUKUTTANNAIR BIJU KUMAR ◽

TIN-YAM CHAN

Keyword(s):

New Species ◽

Deep Sea ◽

Genetic Information ◽

Anterior Part ◽

Molecular Genetic ◽

Taxonomic Status ◽

Molecular Genetic Analysis ◽

Andaman Sea ◽

Abdominal Somite ◽

A New Species

A new species of slipper lobster of the genus Petrarctus Holthuis, 2002 was discovered from southwestern India during a survey of deep sea crustaceans. The new species closely resembles P. veliger Holthuis, 2002 from the Andaman Sea and western Pacific but differs mainly in the color marking on abdominal somite I, having a relatively lower cardiac tooth but with better developed tubercles on the abdomen, as well as a differently shaped anterior part of the thoracic sternum. Molecular genetic analysis also confirms the distinct taxonomic status of the new species. To fix the identity of the type species of the genus, a neotype of P. rugosus (H. Milne Edwards, 1837) was selected from a recently collected Indian specimen with color and genetic information.

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Dipstick dot ELISA for the detection of Taenia coproantigens in humans

Parasitology ◽

10.1017/s0031182000079439 ◽

1993 ◽

Vol 107 (1) ◽

pp. 79-85 ◽

Cited By ~ 37

Author(s):

J. C. Allan ◽

F. Mencos ◽

J. Garcia-Noval ◽

E. Sarti ◽

A. Flisser ◽

...

Keyword(s):

Sandwich Elisa ◽

Taenia Solium ◽

Field Studies ◽

Diagnostic Techniques ◽

Dipstick Test ◽

Rural Villages ◽

Worm Recovery ◽

Wide Scale ◽

Diagnostic Work ◽

Dot Elisa

SummaryA dipstick dot ELISA for detection of Taenia-specific coproantigens was developed. The test was based on a sandwich ELISA using antibodies raised against adult Taenia solium. Antibodies were adsorbed to nitrocellulose paper previously adhered to acetate plastic to form dipsticks. Once blocked with 5% skimmed milk and dried the antibody-coated dipsticks were stable for several weeks at room temperature. Both micro and dot ELISA formats were genus specific although the dot ELISA was less sensitive than the micro ELISA based on the same antiserum. During field studies, in which the majority of samples were tested in rural villages soon after collection, 3728 samples were tested. All samples were also examined by microscopy using formol ether concentration and individuals questioned to determine whether they were aware of being infected. After the initial diagnostic work individuals were treated with taeniacidal drugs for worm recovery. Use of the coproantigen test significantly increased the number of cases diagnosed. Of the 41 cases diagnosed by the three diagnostic techniques combined 31 were detected by the dipstick assay making it the most sensitive technique employed. The specificity of the dipstick assay was 99·9% with a positive predictive value of 88·%. The combined diagnostic approach did not, however, diagnose all cases. The coproantigen test was fast and easy to use. Further improvements may make the dipstick test suitable for wide-scale use in field studies and diagnostic laboratories.

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Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

International Journal of Molecular Sciences ◽

10.3390/ijms19124039 ◽

2018 ◽

Vol 19 (12) ◽

pp. 4039 ◽

Cited By ~ 5

Author(s):

Mi-Li Liu ◽

Wei-Bing Fan ◽

Ning Wang ◽

Peng-Bin Dong ◽

Ting-Ting Zhang ◽

...

Keyword(s):

Molecular Genetic ◽

Phylogenetic Reconstruction ◽

Sequence Divergence ◽

Genomic Analysis ◽

Repeat Sequence ◽

Biological Research ◽

Comparative Genomic ◽

Sequence Evolution ◽

Evolutionary Analysis ◽

Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

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Genomic analysis of family data reveals additional genetic effects on intelligence and personality

10.1101/106203 ◽

2017 ◽

Cited By ~ 3

Author(s):

W. David Hill ◽

Ruben C. Arslan ◽

Charley Xia ◽

Michelle Luciano ◽

Carmen Amador ◽

...

Keyword(s):

Genetic Variants ◽

Molecular Genetic ◽

Copy Number Variants ◽

Twin Studies ◽

Genomic Analysis ◽

Heritability Estimate ◽

Genetic Effects ◽

Genetic Differences ◽

Substantial Contribution ◽

Nucleotide Polymorphisms

AbstractPedigree-based analyses of intelligence have reported that genetic differences account for 50-80% of the phenotypic variation. For personality traits these effects are smaller, with 34-48% of the variance being explained by genetic differences. However, molecular genetic studies using unrelated individuals typically report a heritability estimate of around 30% for intelligence and between 0% and 15% for personality variables. Pedigree-based estimates and molecular genetic estimates may differ because current genotyping platforms are poor at tagging causal variants, variants with low minor allele frequency, copy number variants, and structural variants. Using ∼20 000 individuals in the Generation Scotland family cohort genotyped for ∼700 000 single nucleotide polymorphisms (SNPs), we exploit the high levels of linkage disequilibrium (LD) found in members of the same family to quantify the total effect of genetic variants that are not tagged in GWASs of unrelated individuals. In our models, genetic variants in low LD with genotyped SNPs explain over half of the genetic variance in intelligence, education, and neuroticism. By capturing these additional genetic effects our models closely approximate the heritability estimates from twin studies for intelligence and education, but not for neuroticism and extraversion. We then replicated our finding using imputed molecular genetic data from unrelated individuals to show that ∼50% of differences in intelligence, and ∼40% of the differences in education, can be explained by genetic effects when a larger number of rare SNPs are included. From an evolutionary genetic perspective, a substantial contribution of rare genetic variants to individual differences in intelligence and education is consistent with mutation-selection balance.

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Cytogenetics and molecular genetics

Oxford Textbook of Endocrinology and Diabetes ◽

10.1093/med/9780199235292.003.9050 ◽

2011 ◽

pp. 1375-1380

Author(s):

Dieter Meschede ◽

Frank Tüttelmann

Keyword(s):

Clinical Skills ◽

Single Gene ◽

Molecular Genetic ◽

Practical Importance ◽

Cell Lineage ◽

Diagnostic Process ◽

Meiotic Pairing ◽

Molecular Tests ◽

Endocrine Disturbances ◽

Diagnostic Work

Genetic aberrations are important causes of spermatogenic and endocrine testicular failure. Often, clinical skills are insufficient to demonstrate the primary genetic nature of a gonadal disorder, and cytogenetic and molecular tests should be considered for the diagnostic process (Table 9.5.3.1) (1–7). They are helpful, not only for establishing the basic aetiology of certain types of male endocrine disturbances, but also in that karyotyping and some DNA tests have attained a pivotal role in genetic risk counselling for severely infertile couples. Also, the diagnosis of a chromosomal abnormality or single gene mutation in an infertile man can have repercussions for other members of his family. They may carry the same type of genetic aberration, and thus be at increased risk for inadvertent reproductive outcomes. The most time-honoured method in male endocrinology is the analysis of banded metaphase chromosome preparations from blood lymphocytes, which remains of undiminished practical importance (8, 9). This technique allows for the direct visualization of the complete set of chromosomes in a somatic cell lineage and provides information on both chromosome number and structure. However, a regular karyotype in somatic cells, such as lymphocytes, does not necessarily translate into normal meiotic pairing and segregation of the chromosomes in the germ cell lineage. Meiotic cell preparations and ejaculated spermatozoa may thus be included in the diagnostic work-up of an infertile man. The place of these techniques is more in the realm of research than of daily clinical practice, as discussed below. In contrast, several molecular genetic tests are firmly established as valuable diagnostic tools. Details concerning the two most important tests, mutation analysis of the CFTR gene and screening for Y-chromosomal microdeletions, are given below.

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Analysis of non-morphometric morphological characters used in the taxonomy of the genus Pseudechiniscus (Tardigrada: Echiniscidae)

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz097 ◽

2019 ◽

Cited By ~ 3

Author(s):

Denis V Tumanov

Keyword(s):

Species Delimitation ◽

Taxonomic Status ◽

Electron Microscopic Examination ◽

Morphological Characters ◽

Electron Microscopic ◽

The Family ◽

Scanning Electron Microscopic ◽

Claw Morphology ◽

Taxonomic Studies ◽

A New Species

Abstract Pseudechiniscus, the second-largest genus of the family Echiniscidae (Tardigrada: Heterotardigrada: Echiniscoidea), is notoriously difficult for taxonomic studies. In this study, I performed a morphological analysis of a new species from Croatia, based on a light microscopic and scanning electron microscopic examination of 45 specimens from the same sample. Furthermore, I have summarized all available data on Pseudechiniscus species, including their original descriptions, and have analysed the following complexes of morphological characters: (1) arrangement and morphology of dorsal cuticular plates, (2) ventral sculpture, (3) morphology of cephalic, trunk and leg sensory organs and (4) claw morphology. The applicability of these characters in the taxonomy and their distribution in the genus are discussed. Some of the characters traditionally used for species delimitation were shown to be unsuitable and others in need of a thorough reinvestigation. The meaning of the old term ‘faceted’, commonly used but often misapplied, has been clarified, based on the initial definition. Several characters of the claw structure were suggested as potentially useful for species delimitation. The taxonomic status of several old forms and species was discussed.

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Scinax nebulosus (Spix, 1824) (Amphibia: Hylidae): review of distribution and new record from Sergipe, Brazil

Check List ◽

10.15560/11.3.1660 ◽

2015 ◽

Vol 11 (3) ◽

pp. 1660

Author(s):

Eduardo José Dos Reis Dias ◽

Rony Peterson Santos Almeida ◽

Maria Aldenise Xavier ◽

Mayara De Lima Mota ◽

Adriano Da Cunha Lima ◽

...

Keyword(s):

Tropical Forests ◽

Atlantic Forest ◽

New Record ◽

Taxonomic Status ◽

Dorsal Surface ◽

First Record ◽

Careful Evaluation ◽

Temporary Water Bodies ◽

Temporary Water ◽

Taxonomic Studies

We present the first record of Scinax nebulosus for the State of Sergipe, in the Atlantic Forest, Brazil. Scinax nebulosus is a small hylid which inhabits the Amazon and Atlantic Forest. Its main microhabitat is temporary water bodies in tropical forests. This species can be recognized by the presence of many scattered glandules on the dorsal surface, especially on the head, upper eyelids and margins of the members. Some taxonomic studies and vocals records suggest careful evaluation of the taxonomic status of S. nebulosus along its geographical distribution.

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Genetic typing and phylogeny of the Leishmania donovani complex by restriction analysis of PCR amplified gp63 intergenic regions

Parasitology ◽

10.1017/s0031182001007466 ◽

2001 ◽

Vol 122 (4) ◽

pp. 393-403 ◽

Cited By ~ 55

Author(s):

I. L. MAURICIO ◽

M. W. GAUNT ◽

J. R. STOTHARD ◽

M. A. MILES

Keyword(s):

Leishmania Donovani ◽

Restriction Analysis ◽

Taxonomic Status ◽

Logarithmic Phase ◽

Strongly Correlated ◽

Causative Agents ◽

Intergenic Regions ◽

Genetic Clusters ◽

Major Surface ◽

Taxonomic Studies

Protozoan parasites of the Leishmania donovani complex (L. donovani, L. infantum/L. chagasi) are causative agents of visceral leishmaniasis. To understand phylogeny and taxonomy within this group better we have developed 2 new polymerase chain reaction-linked restriction fragment length polymorphism (PCR–RFLP) analyses of the major surface protease (msp or gp63) intergenic (ITG) regions. We have named this approach msp intergenic region RFLP typing (MIRT). One intergenic region lies between the constitutive msp (mspC) and stationary phase msp (mspS4) genes (ITG/CS) and the other between multicopy logarithmic phase msp (mspL) genes (ITG/L). The markers generated robust and congruent phylogenies, identifying 5 genetic clusters within L. donovani. One cluster was synonymous with L. infantum (L. chagasi); clusters strongly correlated with isoenzyme typing and some with geographical origin. These genetic groups may be important for epidemiological and clinical studies. The congruence of the groups identified indicates suitability of these genomic targets for taxonomic studies. Furthermore, subgroups of L. donovani were of equivalent phylogenetic status to L. infantum. No evidence was found to support the existence of L. archibaldi. It is likely to be necessary in future to re-evaluate the taxonomic status of L. donovani or of L. infantum, as discrete species.

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In Myelodysplastic/Myeloproliferative Neoplasms Aberrant Antigen Expression As Assessed by Multiparameter Flow Cytometry Is Related to Molecular Genetic Mutations

Blood ◽

10.1182/blood.v118.21.5152.5152 ◽

2011 ◽

Vol 118 (21) ◽

pp. 5152-5152

Author(s):

Wolfgang Kern ◽

Susanne Schnittger ◽

Tamara Alpermann ◽

Claudia Haferlach ◽

Torsten Haferlach

Keyword(s):

Myeloproliferative Neoplasms ◽

Molecular Genetic ◽

Antigen Expression ◽

Multiparameter Flow Cytometry ◽

Employment Equity ◽

Aberrant Expression ◽

Equity Ownership ◽

Diagnostic Work ◽

Work Up ◽

Diagnostic Work Up

Abstract Abstract 5152 Background: Immunophenotyping by multiparameter flow cytometry (MFC) is increasingly used in the diagnostic work-up of patients with cytopenias and suspected myelodysplastic syndromes (MDS). Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) comprise a group of diseases with some features of MDS and is separately classified in the current WHO system. While the immunophenotype of chronic myelomonocytic leukemia has been described in detail, data is scarce on the use of MFC in myelodysplastic/myeloproliferative neoplasms, unclassifiable (MDS/MPNu) as well as on refractory anemia with ring sideroblasts and thrombocytosis (RARS-T), which is a provisional entity in the current WHO classification. Aim: To assess patients with MDS/MPNu and RARS-T for MDS-related aberrant immunophenotypes in the context of a comprehensive diagnostic work-up including cytomorphology, cytogenetics, and molecular genetics. Patients and Methods: A total of 91 patients were analyzed in parallel by cytomorphology, cytogenetics, and MFC applying an antibody panel designed to diagnose MDS. MFC was used to detect expression of mature antigens in myeloid progenitors; abnormal CD13-CD16- and CD11b-CD16-expression patterns, aberrant expression of myeloid markers and reduced side scatter signal in granulocytes; reduced expression of myelomonocytic markers in monocytes; aberrant expression of CD71 in erythroid cells; as well as expression of lymphoid markers in all myeloid cell lines. In 77/91 patients molecular genetic markers were investigated. The median age of the patients was 75.1 years (range, 35.3–87.4). The male/female ratio was 60/31. Six patients had RARS-T and 85 had MDS/MPNu. Results: In 54/91 (59.3%) patients MFC identified an MDS-immunophenotype. This was true in 4/6 (66.7%) RARS-T and in 50/85 (58.8%) MDS/MPNu (n.s.). Cases with MDS-immunophenotype displayed aberrancies significantly more frequently than those without as follows: in myeloid progenitor cells (number of aberrantly expressed antigens, mean±SD: 0.5±0.6 vs. 0.2±0.4, p=0.002), granulocytes (2.7±1.3 vs. 1.2±1.1, p<0.001), and monocytes (1.7±1.2 vs. 0.5±0.7, p<0.001). Accordingly, there was a significant difference in the total number of aberrantly expressed antigens (4.9±2.4 vs. 2.0±1.4, p<0.001). The presence of an aberrant karyotype was not related to an MDS-immunophenotype which was observed in 11/18 (61.1%) cases with aberrant karyotype and in 43/73 (58.9%) with normal karyotype (n.s.). Mutations in RUNX1 and TET2 as well as FLT3-ITD were predominantly present in cases with an MDS-immunophenotype (10/33, 30.3%) and occurred less frequently in cases without (1/7, 9.1%, n.s.). In detail, RUNX1 mutations were present in 4/26 (10.3%) vs. 0/2, TET2 mutations were present in 4/6 (66.7%) vs. 1/2 (50%), and FLT3-ITD was present in 3/29 (10.3%) vs. 0/5. Accordingly, in cases with RUNX1 or TET2 mutations or with FLT3-ITD a significantly higher number of aberrantly expressed antigens was observed as compared to cases with none of these mutations (mean±SD, 6.4±2.0 vs. 4.4±2.5, p=0.024). In contrast, JAK2V617F mutations occurred at identical frequencies in patients with and without MDS-immunophenotype (11/38, 28.9% vs. 9/31, 29.0%). Regarding prognosis, the presence of an MDS-immunophenotype had no impact on overall survival. Conclusions: These data demonstrates that MDS-related aberrant antigen expression is present in the majority of patients with RARS-T and MDS/MPNu. While there is no association between the presence of an MDS-immunophenotype and the detection of JAK2 mutations cases with an MDS-immunophenotype tended to more frequently carry mutations in RUNX1 and TET2 as well as FLT3-ITDs. These data therefore suggests that MDS/MPNu may be subdivided based on molecular genetics and on the immunophenotype into cases with MDS-related features and those without. Further analyses are needed to validate these findings and their potential significance in RARS-T. Disclosures: Kern: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Alpermann:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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