Video capture and editing as a tool for the storage, distribution, and illustration of morphological characters of nematodes.

Morphological identification and detailed observation of nematodes usually requires permanent slides, but these are never truly permanent and often prevent the same specimens to be used for other purposes. To efficiently record the morphology of nematodes in a format that allows easy archiving, editing, and distribution, we have assembled two micrographic video capture and editing (VCE) configurations. These assemblies allow production of short video clips that mimic multifocal observation of nematode specimens through a light microscope. Images so obtained can be used for training, management, and online access of “virtual voucher specimens” in taxonomic collections, routine screening of fixed or unfixed specimens, recording of ephemeral staining patterns, or recording of freshly dissected internal organs prior to their decomposition. We provide an overview of the components and operation of both of our systems and evaluate their efficiency and image quality. We conclude that VCE is a highly versatile approach that is likely to become widely used in nematology research and teachin

A new nematode genus (Rhabditida: Panagrolaimidae) from pitcher plants

During a visit to Tung-Kai Botanical Garden in Trang Province, near the Isthmus of Kra, Southern Thailand, one of us (HS) sampled the liquid contained within the pitchers of the carnvivorous plant Nepenthes cf. mirabilis (Lour.) Druce, in order to obtain some of the peculiar rotifers recorded from such habitats. No rotifers but some unidentifiable bdelloids were found, but the samples contained abundant material of a large nematode together with some diplogasterids. Some of the unique morphological characters of this nematode make its placement difficult. In order to obtain additional information about the nematode’s identity and position in relation to the other known morphologically related taxa, we reconstructed a molecular phylogenetic history of selected taxa, including this nematode, based on the small subunit (ssu) ribosomal DNA. In this paper, we describe this new genus and species from Nepenthes, and present an emended diagnosis of the family Panagrolaimida

Baujardia mirabilis gen. n., sp n. from pitcher plants and its phylogenetic position within Panagrolaimidae (Nematoda: Rhabditida).

Summary -Measurements, line drawings and scanning electromicrographsare provided of Baujardia mirabilis gen. n., sp. n., isolated from pitcher uid of Nepenthes mirabilis from Thailand. The new genus differs from all known nematodes in having two opposing and offset spermatheca-like pouches at the junction of oviduct and uterus. It also differs from most known Rhabditida in having four cephalic setae instead of papillae. Phylogenetic analysis of small subunit rDNA sequence data robustly places the new genus within Panagrolaimidae as a sister taxon to Panagrellus. These unusual nematodes resemble Panagrellus in body size (1.8-2.7 mm in females, 1.3-1.9 mm in males) and in the monodelphic, prodelphic female reproductive system with thickened vaginal walls and prominent postvulval sac. However, they differ from Panagrellus in the characters mentioned above, in their comparatively longer stegostom and in the shape of the male spicules. Because of its aberrant characters, inclusion of this new genus in Panagrolaimidae requires changes to the family diagnosis

Baujardia mirabilis gen. n., sp. n. from pitcher plants and its phylogenetic position within Panagrolaimidae (Nematoda: Rhabditida)

Summary -Measurements, line drawings and scanning electromicrographsare provided of Baujardia mirabilis gen. n., sp. n., isolated from pitcher uid of Nepenthes mirabilis from Thailand. The new genus differs from all known nematodes in having two opposing and offset spermatheca-like pouches at the junction of oviduct and uterus. It also differs from most known Rhabditida in having four cephalic setae instead of papillae. Phylogenetic analysis of small subunit rDNA sequence data robustly places the new genus within Panagrolaimidae as a sister taxon to Panagrellus. These unusual nematodes resemble Panagrellus in body size (1.8-2.7 mm in females, 1.3-1.9 mm in males) and in the monodelphic, prodelphic female reproductive system with thickened vaginal walls and prominent postvulval sac. However, they differ from Panagrellus in the characters mentioned above, in their comparatively longer stegostom and in the shape of the male spicules. Because of its aberrant characters, inclusion of this new genus in Panagrolaimidae requires changes to the family diagnosis

Marine nematode taxonomy in the DNA age: the present and future of molecular tools to access their biodiversity

Molecular taxonomy is one of the most promising yet challenging fields of biology. Molecular markers such as nuclear and mitochondrial genes are being used in a variety of studies surveying marine nematode taxa. Sequences from more than 600 species have been deposited to date in online databases. These barcode sequences are assigned to 150 nominal species from 104 genera. There are 41 species assigned to Enoplea and 109 species to Chromadorea. Morphology-based surveys are greatly limited by processing speed, while barcoding approaches for nematodes are hampered by difficulties in matching sequence data with morphology-based taxonomy. DNA barcoding is a promising approach because some genes contain variable regions that are useful to discriminate species boundaries, discover cryptic species, quantify biodiversity and analyse phylogeny. We advocate a combination of several approaches in studies of molecular taxonomy, DNA barcoding and conventional taxonomy as a necessary step to enhance the knowledge of biodiversity of marine nematodes

A preliminary faunistic study of soil nematodes from different land uses in Tropical Deciduous Forest in the Costa Chica of Guerrero, Mexico

Tropical Deciduous Forest (TDF) is an important biome threatened globally by climate change and human encroachment. Changes in diversity and abundance of soil nematodes can serve as indicators of soil disturbance due to human activities. Our objective was to present a first inventory of the generic biodiversity of soil nematodes in seven TDF sites subjected to different current or decade-old land uses, located near Copala in the Costa Chica region of Guerrero, Mexico. TDF landscapes are especially heterogeneous in many soil and microclimate parameters, while subsistence agriculture systems in this biome are highly diverse and present great challenges for sampling design with replication. We therefore chose to focus on characterizing the soil nematode fauna, as a first step before undertaking detailed analyses of all potentially relevant biotic and abiotic factors. Genus-level diversity ranged from 12 to 18 taxa for the sampled land uses, or 27 total taxa for all samples combined. Statistical tests for data analysis without replication revealed significant differences in nematode diversity, trophic structure, and abundance between land uses. Four sites, left as fallows for ten years after prior human uses, were statistically different from each other as well as from a forest site undisturbed for at least twenty years. Despite the methodological limitations inherent in this initial study, we hypothesize that some effects on nematode communities may persist for more than a decade after the anthropogenic impacts of subsistence farming in TDF. Thus, future nematode surveys in the TDF biome should not only analyze the current properties of sampling sites, but also document data related to factors from past human use activities. Example factors, suggested by the pattern of nematode abundance from the seven sites in our study, include past levels of trampling by human traffic and grazing, as well as estimates of past amounts of plant debris deposition accumulated by harvesting or weeding.El Bosque Tropical Caducifolio (BTC) es un importante bioma amenazado por el cambio climático y la invasión humana. Los nematodos del suelo pueden ser indicadores de la perturbación del suelo debido a las actividades humanas. Nuestro objetivo fue presentar un primer inventario sobre la biodiversidad de los nematodos en siete sitios sometidos actualmente a diferentes usos del suelo, o con usos anteriores no perturbados durante diez años. Estos sitios están localizados en el BTC cerca de Copala en la región de la Costa Chica de Guerrero, México. Los paisajes del BTC son especialmente heterogéneos en muchos parámetros de suelo y microclima, mientras que los sistemas agrícolas de subsistencia en este bioma son muy diversos y presentan grandes desafíos para el muestreo con replicación. Debido a esto decidimos observar la fauna de nematodos del suelo como un primer paso antes de empezar el análisis de todos los parámetros abióticos potencialmente relevantes. La diversidad a nivel de género osciló entre 12 y 18 taxones para los usos del suelo muestreados, o 27 taxones en total. Las pruebas estadísticas para el análisis de datos sin replicación revelaron diferencias significativas entre los usos del suelo en la diversidad de nematodos, la estructura trófica y la abundancia. Cuatro sitios dejados en descanso por una década después de varios usos fueron estadísticamente diferentes entre sí y con el sitio forestal no perturbado por veinte años. A pesar de las limitaciones metodológicas inherentes a este estudio inicial, planteamos la hipótesis de que, en el BTC, algunos efectos en las comunidades de nematodos pueden persistir durante más de una década después de los impactos antropogénicos de la agricultura de subsistencia. Por lo tanto, las futuras encuestas de nematodos de los ecosistemas derivados de un BTC no solo deberían analizar las propiedades actuales de los sitios de muestreo, sino también documentar los datos relacionados con factores de las actividades humanas en el pasado. Entre estos factores, sugeridos por los resultados de nuestro estudio, se deben incluir niveles ​​de pisoteo humano y pastoreo, así como estimaciones de cantidades de deposición de desechos vegetales acumuladas por cosecha o deshierbe

Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women

Objective To highlight the contribution of the gut microbiota to the modulation of host metabolism by dietary inulin-type fructans (ITF prebiotics) in obese women. Methods A double blind, placebo controlled, intervention study was performed with 30 obese women treated with ITF prebiotics (inulin/oligofructose 50/50 mix; n=15) or placebo (maltodextrin; n=15) for 3 months (16 g/day). Blood, faeces and urine sampling, oral glucose tolerance test, homeostasis model assessment and impedancemetry were performed before and after treatment. The gut microbial composition in faeces was analysed by phylogenetic microarray and qPCR analysis of 16S rDNA. Plasma and urine metabolic profiles were analysed by 1H-NMR spectroscopy. Results Treatment with ITF prebiotics, but not the placebo, led to an increase in Bifidobacterium and Faecalibacterium prausnitzii; both bacteria negatively correlated with serum lipopolysaccharide levels. ITF prebiotics also decreased Bacteroides intestinalis, Bacteroides vulgatus and Propionibacterium, an effect associated with a slight decrease in fat mass and with plasma lactate and phosphatidylcholine levels. No clear treatment clustering could be detected for gut microbial analysis or plasma and urine metabolomic profile analyses. However, ITF prebiotics led to subtle changes in the gut microbiota that may importantly impact on several key metabolites implicated in obesity and/or diabetes. Conclusions ITF prebiotics selectively changed the gut microbiota composition in obese women, leading to modest changes in host metabolism, as suggested by the correlation between some bacterial species and metabolic endotoxaemia or metabolomic signatures

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints

Mediterranean Sea ecosystems are considered as hotspots of biological introductions, exposed to possible negative effects of non-indigenous species. In such temperate marine ecosystems, macroalgae may be dominant, with a great percentage of their diversity represented by introduced species. Their interaction with temperate indigenous benthic organisms have been poorly investigated. To provide new insights, we performed an experimental study on the interaction between the introduced proliferative red alga Asparagopsis taxiformis and the indigenous Mediterranean coral Astroides calycularis. The biological response measurements included meta-barcoding of the associated microbial communities and metabolomic fingerprinting of both species. Significant changes were detected among both associated microbial communities, the interspecific differences decreasing with stronger host interaction. No short term effects of the macroalga on the coral health, neither on its polyp activity or its metabolism, were detected. In contrast, the contact interaction with the coral induced a change in the macroalgal metabolomic fingerprint with a significant increase of its bioactivity against the marine bacteria Aliivibrio fischeri. This induction was related to the expression of bioactive metabolites located on the macroalgal surface, a phenomenon which might represent an immediate defensive response of the macroalga or an allelopathic offense against coral.ERA-NET Biome project "SEAPROLIF"; CNRS; Provence Alpes Cote d'Azur Region; TOTAL Fundation; Fundacao para a Ciencia e a Tecnologia (FCT) [Netbiome/0002/2011]; FCT fellowships [SFRH/BPD/63703/2009, SFRH/BPD/107878/2015]info:eu-repo/semantics/publishedVersio

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

Background Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. Conclusions The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genus-level with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts