Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.

Molecular phylogenetic position and description of a new genus and species of freshwater Chaetonotidae (Gastrotricha: Chaetonotida: Paucitubulatina), and the annotation of its mitochondrial genome.

Chaetonotidae is the most diversified family of the entire phylum Gastrotricha; it comprises ~430 species distributed across 16 genera. The current classification, established mainly on morphological traits, has been challenged in recent years by phylogenetic studies, indicating that the cuticular ornamentations used to discriminate among species may be misleading when used to identify groupings, which has been the practice until now. Therefore, a consensus is developing toward implementing novel approaches to better define species identity and affiliation at a higher taxonomic ranking. Using an integrative morphological and molecular approach, including annotation of the mitogenome, we report on some freshwater gastrotrichs characterised by a mixture of two types of cuticular scales diagnostic of the genera Aspidiophorus and Heterolepidoderma . Our specimens' overall anatomical characteristics find no correspondence in the taxa of these two genera, calling for their affiliation to a new species. Phylogenetic analyses based on the sequence of the ribosomal RNA genes of 96 taxa consistently found the new species unrelated to Aspidiophorus or Heterolepidoderma but allied with Chaetonotus aff. subtilis, as a subset of a larger clade, including mostly planktonic species. Morphological uniqueness and position along the non-monophyletic Chaetonotidae branch advocate erecting a new genus to accommodate the current specimens; consequently, the name Litigonotus ghinii gen. nov., sp. nov. is proposed. The complete mitochondrial genome of the new taxon resulted in a single circular molecule 14,384 bp long, including 13 protein-coding genes, 17 tRNA genes and 2 rRNAs genes, showing a perfect synteny and collinearity with the only other gastrotrich mitogenome available, a possible hint of a high level of conservation in the mitochondria of Chaetonotidae. ZooBank: urn:lsid:zoobank.org:pub:9803F659-306F-4EC3-A73B-8C704069F24A.

An annotated checklist of the chaetonotidan Gastrotricha from India.

India has a long history of research on freshwater and marine Gastrotricha. In more than 110 years of study on Order Chaetonotida, two families consisting of 11 genera and 39 species have been described. Thirty of these species are taxa originally described from other continents, while only nine species (7 freshwater, 2 marine) are only known from India. The large percentage (77%) of so-called cosmopolitan species in India has contributed to the phenomenon known as the meiofauna paradox. However, a careful review of the pertaining literature provides a different biogeographical picture of the chaetonotidan fauna of India. Herein we show that the high incidence of European and North American species reported from India is mainly due to a mixture of misidentification and species lumping. In fact, for only 12 species there are enough data that would make the Indian specimens morphological similar to taxa previously reported from Europe and/or North America. However, without the appropriate molecular sequence data for comparison, there is no way to rule out the possibility of cryptic speciation.We conclude that further sampling throughout India and the use of more powerful microscopical techniques (e.g., DIC optics) and molecular sequencing will reveal more species and improve the quality of re-descriptions of those (9 spp.) that so far appear to be endemic to the subcontinent. Here we recommend six species to be excluded from the fauna of India while another 11 species (non endemic to India) should be considered dubitatively present in the Indian fauna.

Human access impacts biodiversity of microscopic animals in sandy beaches.

Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow "swash" zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity.

The curious and neglected soft-bodied meiofauna: Rouphozoa (Gastrotricha and Platyhelminthes).

Gastrotricha and Platyhelminthes form a clade called Rouphozoa. Representatives of both taxa are main components of meiofaunal communities, but their role in the trophic ecology of marine and freshwater communities is not sufficiently studied. Traditional collection methods for meiofauna are optimized for Ecdysozoa, and include the use of fixatives or flotation techniques that are unsuitable for the preservation and identification of soft-bodied meiofauna. As a result, rouphozoans are usually underestimated in conventional biodiversity surveys and ecological studies. Here, we give an updated outline of their diversity and taxonomy, with some phylogenetic considerations. We describe successfully tested techniques for their recovery and study, and emphasize current knowledge on the ecology, distribution and dispersal of freshwater gastrotrichs and microturbellarians. We also discuss the opportunities and pitfalls of (meta)barcoding studies as a means of overcoming the taxonomic impediment. Finally, we discuss the importance of rouphozoans in aquatic ecosystems and provide future research directions to fill in crucial gaps in the biology of these organisms needed for understanding their basic role in the ecology of benthos and their place in the trophic networks linking micro-, meio- and macrofauna of freshwater ecosystems.

Custom made onlay implants in peek in maxillofacial surgery: a volumetric study.

PURPOSE: Facially malformed patients often present a variable degree of facial imbalance even after basal bone correction, and resolution of the residual hard- and soft-tissue deficiencies and asymmetries of the face are of great importance for achieving a satisfactory post-implant procedure result. The use of polyether ether ketone (PEEK) implants for maxillofacial reconstruction has been documented in the literature, but the number of patients who have received them is limited. The aim of this study was to evaluate the overall volumetric results in patients with facial imbalance after onlay custom implant positioning for mandible and fronto-orbital reconstructions. Analysis was performed by confronting volumes with the use of three-dimensional (3D) photogrammetry. METHODS: Fifteen patients were eligible for PEEK implant placements, eight for mandibular angle reconstruction, and seven for fronto-orbital reconstruction. Pre- and post-surgical 3D images of each patient's face were acquired. Facial asymmetry was analyzed by comparing each face with its mirrored copy. RESULTS: Three-dimensional analyses have shown that some degree of volume imbalance was still present in the patients with only 1.32 ± 1.02 mm residual discrepancy after treatment. CONCLUSION: Results of the study were found to fall within clinically acceptable limits since an asymmetry rate of < 3 mm is considered to fall into the norm.

Correction to: Apoptosis resistance in epithelial tumors is mediated by tumor-cell-derived interleukin-4.

Authors have only now noticed that in the Figure 3a, the immunohistochemical analysis of IL-4Rα on paraffin-embedded sections from breast is incorrect: IL-4 from breast was duplicated and used for the IL-4Rα staining. The correct Figure 3a has been included in the amendment to this paper.An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Integrated data analysis allows the establishment of a new, cosmopolitan genus of marine Macrodasyida (Gastrotricha).

Macrodasyida (phylum Gastrotricha) comprises 365 species distributed across 34 genera and 10 families. However, current classification is under revision due to the contradictory results of molecular and morphological cladistic analyses. Studies aimed at bridging the gaps took advantage of supplementary assessments of poorly known species and particularly from observations of new taxa showing original traits that could help to identify plesiomorphic character states in these anatomically diverse micrometazoa. We follow this path by describing three new interesting macrodasyidan species respectively from Italy, Brazil and Sweden. In many respects, the new species resemble most closely species of the genus Macrodasys; however, details of the external morphology, in combination with the different lay-out of the reproductive system and the tiny spermatozoa lacking a visible flagellum, suggest they belong to a new genus, possibly in the family Macrodasyidae. These hypotheses are supported by the phylogenetic relationships of 47 taxa inferred from analyses of the 18S rRNA gene, which found the new species clustering with Thaidasys tongiorgii in a subset of a larger clade containing Macrodasys. Accordingly, the establishment of the following taxa is proposed: Kryptodasys gen. nov., K. marcocurinii sp. nov., K. carlosrochai sp. nov. and K. ulfjondeliusi sp. nov.

An annotated checklist of the macrodasyidan Gastrotricha from India.

We present a checklist of the macrodasyidan Gastrotricha fauna of India derived from original articles and comprehensive monographies regarding the Indian Fauna. Taxa and specimens described from India are discussed with special attention to their status, especially those species previously known from distant geographic areas. A total of 43 species have been recorded from 4 States and 2 Union territories. A careful taxonomic assessment indicated that many species are in need of re-description as the reported anatomical traits are not sufficient to grant a modern, robust identification. The situation is particularly poor for two species (Macrodasys indicus Govindankutty Nair, 1969 and Paradasys lineatus Rao, 1980), which consequently, are considered here to be species inquirendae; moreover, the Indian records of Tetranchyroderma hystrix and T. massiliense reported from Kerala are doubtful and consequently the two species should not be included among the fauna of the Indian region until proper evidence is found. It is necessary to unravel the true identities of many Indian species through a comparison to topotypical material. We recommend that future comparisons between related species and conspecifics from different populations to include molecular sequence data.

Skeletal stability in orthognathic surgery with the surgery first approach: a systematic review.

The surgery first approach (SFA) is a therapeutic strategy used in orthognathic surgery that is constantly evolving. With this approach, the pre-surgical orthodontic treatment can be eliminated, the maxilla and the mandible are surgically repositioned into the desired position, and the therapy is ended with a short orthodontic phase. Several studies have reported that the SFA is an acceptable approach, but postoperative stability is unclear. In this study, a systematic review on the SFA was performed. The PubMed, Google Scholar, Scopus, LexisNexis, Web of Science, and Cochrane Library databases were accessed. Studies from which data could be extracted on skeletal stability based on specific cephalometric points were included. The search yielded 2766 publications. Application of the selection criteria resulted in a final group of 14 articles. Five hundred and sixty patients with class III malocclusion underwent orthognathic surgery, 339 with the SFA. Study parameters such as evaluation time points and reference planes varied, making it impossible to perform a meta-analysis. The studies suggest that surgery with the SFA is as stable as surgery with the conventional approach. However, all articles described stability using a penultimate time point of 'after surgery' and not 'after debonding'; hence orthodontic movements and consequent mandibular movements could have influenced cephalometric measurements. Thus, to verify the real stability of the SFA, further research with longer follow-up periods is required, with evaluation at the same time points.

Erratum: Author Correction: Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach.

[This corrects the article DOI: 10.1038/s42003-018-0119-2.].

Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach.

Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.

A new species of Turbanellidae (Gastrotricha, Macrodasyida) from Jamaica, with a key to species of Paraturbanella.

The study falls within the framework of a wider research programme aimed at investigating the gastrotrich diversity of the Tropical North-Western Atlantic (TNWA). A new macrodasyidan gastrotrich is described from fine-medium sand collected at Duncans Bay, Jamaica. The description is based on observations carried out on living specimens using differential interference contrast microscopy. Paraturbanella xaymacanasp. n., the third gastrotrich taxon reported from Jamaica, is a mid-sized species, up to 564 µm long, with a feeble peribuccal swelling. The most obvious autapomorphic traits pertain to the testes and the male pore, both of which are located approximately at mid body, rather than at- or near the pharyngo-intestinal junction as occur in the other species of the genus. Additional differences with congeners are discussed and a key to the Paraturbanella species is provided, in the hope it will be useful to both gastrotrich experts and marine ecologists who discover these microscopic metazoans during their research.

Distinctive features of tumor-infiltrating γδ T lymphocytes in human colorectal cancer.

γδ T cells usually infiltrate many different types of cancer, but it is unclear whether they inhibit or promote tumor progression. Moreover, properties of tumor-infiltrating γδ T cells and those in the corresponding normal tissue remain largely unknown. Here we have studied features of γδ T cells in colorectal cancer, normal colon tissue and peripheral blood, and correlated their levels with clinicopathologic hallmarks. Flow cytometry and transcriptome analyses showed that the tumor comprised a highly variable rate of TILs (5-90%) and 4% γδ T cells on average, with the majority expressing Vδ1. Most Vδ1 and Vδ2 T cells showed a predominant effector memory phenotype and had reduced production of IFN- Î³ which was likely due to yet unidentified inhibitory molecules present in cancer stem cell secretome. Transcriptome analyses revealed that patients containing abundant γδ T cells had significantly longer 5-year disease free survival rate, suggesting their efficacy in controlling tumor at very early stage.

Noncanonical GLI1 signaling promotes stemness features and in vivo growth in lung adenocarcinoma.

Aberrant Hedgehog/GLI signaling has been implicated in a diverse spectrum of human cancers, but its role in lung adenocarcinoma (LAC) is still under debate. We show that the downstream effector of the Hedgehog pathway, GLI1, is expressed in 76% of LACs, but in roughly half of these tumors, the canonical pathway activator, Smoothened, is expressed at low levels, possibly owing to epigenetic silencing. In LAC cells including the cancer stem cell compartment, we show that GLI1 is activated noncanonically by MAPK/ERK signaling. Different mechanisms can trigger the MAPK/ERK/GLI1 cascade including KRAS mutation and stimulation of NRP2 by VEGF produced by the cancer cells themselves in an autocrine loop or by stromal cells as paracrine cross talk. Suppression of GLI1, by silencing or drug-mediated, inhibits LAC cells proliferation, attenuates their stemness and increases their susceptibility to apoptosis in vitro and in vivo. These findings provide insight into the growth of LACs and point to GLI1 as a downstream effector for oncogenic pathways. Thus, strategies involving direct inhibition of GLI1 may be useful in the treatment of LACs.

Normal vs cancer thyroid stem cells: the road to transformation.

Recent investigations in thyroid carcinogenesis have led to the isolation and characterisation of a subpopulation of stem-like cells, responsible for tumour initiation, progression and metastasis. Nevertheless, the cellular origin of thyroid cancer stem cells (SCs) remains unknown and it is still necessary to define the process and the target population that sustain malignant transformation of tissue-resident SCs or the reprogramming of a more differentiated cell. Here, we will critically discuss new insights into thyroid SCs as a potential source of cancer formation in light of the available information on the oncogenic role of genetic modifications that occur during thyroid cancer development. Understanding the fine mechanisms that regulate tumour transformation may provide new ground for clinical intervention in terms of prevention, diagnosis and therapy.

Association between CYP2C19 Polymorphisms and Outcomes in Cerebral Endovascular Therapy.

BACKGROUND AND PURPOSE: Differing responses to clopidogrel following endovascular treatment of cerebrovascular diseases may increase the risk of vascular complications. CYP2C19 gene polymorphisms influence clopidogrel activity. We aimed to study the clinical impact of CYP2C19 gene polymorphisms in patients undergoing endovascular treatment. MATERIALS AND METHODS: This was a prospective, longitudinal, observational study. Information on demographics and cerebrovascular status was collected as baseline. Clopidogrel response was tested by the VerifyNow P2Y12 assay. CYP2C19 genotyping was undertaken by polymerase chain reaction-restriction fragment length polymorphism. Three-month follow-up data included vascular complications, mortality, and modified Rankin Scale score. Associations were investigated among CYP2C19 genotypes, clopidogrel responsiveness, and clinical outcomes. RESULTS: One hundred and eight participants were included. Median age was 56 years (interquartile range, 48.8-65.0 years), and 35 (32.4%) were male. Forty-four participants were classified into group 1 (homozygous CYP2C19*1/*1); 31, into group 2 (25 with CYP2C19*1/*2, two with CYP2C19*1/*3, three with CYP2C19*3/*3, one with CYP2C19*2/*3); 28, into group 3 (24 with CYP2C19*1/*17, four with CYP2C19*17/*17); and 5, into group 4 (CYP2C19*2/*17). A significantly higher proportion of participants in group 3 experienced ischemic events (9 of 28, 32.1%) compared with group 1 (5 of 44, 11.4%; P = .04; odds ratio, 3.7; 95% confidence interval, 1.1-12.6). There was no significant difference in clopidogrel response among the 4 genotype groups. CONCLUSIONS: Individuals with CYP2C19*17 may have increased risk of ischemic events following endovascular treatment, independent of clopidogrel responsiveness. Larger studies are required to confirm the influence of CYP2C19*17 on clinical outcomes and to understand the mechanisms for increased ischemic events.

Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins.

BACKGROUND: The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth ~3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines. RESULTS: We report observations from sediments of three DHAB (Urania, Discovery, L'Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTracker(TM) Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L'Atalante normoxic control sediments were fit, while specimens from L'Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L'Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions. CONCLUSIONS: We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time.

Fauna Europaea: Gastrotricha.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Gastrotricha are a meiobenthic phylum composed of 813 species known so far (2 orders, 17 families) of free-living microinvertebrates commonly present and actively moving on and into sediments of aquatic ecosystems, 339 of which live in fresh and brackish waters. The Fauna Europaea database includes 214 species of Chaetonotida (4 families) plus a single species of Macrodasyida incertae sedis. This paper deals with the 224 European freshwater species known so far, 9 of which, all of Chaetonotida, have been described subsequently and will be included in the next database version. Basic information on their biology and ecology are summarized, and a list of selected, main references is given. As a general conclusion the gastrotrich fauna from Europe is the best known compared with that of other continents, but shows some important gaps of knowledge in Eastern and Southern regions.