Palaeobiogeographic affinities of the reef faunas from the earliest Pragian in the Cantabrian Zone (NW Spain)

Devonian reef faunas in the Cantabrian Zone are well known through several works done by the Research Group on Devonian Reefs from Oviedo University. This Group has established up to seven Devonian reef episodes of different magnitude and some of them were widely studied (Méndez-Bedia et al., 1994, Fernández et al., 1997, among others). The first episode was developed during the earliest Pragian and is recorded in some thin-bedded biostromal limestones with a rich fauna of corals and stromatoporoids. This interval has been studied within the context of the project CGL2005-03715/BTE and the results are currently in press. The aim of this work is to display the palaeobiogeographical affinities shown by the corals and stromatoporoids occurring in this first reef episode

Earliest Pragian (Early Devonian) corals and stromatoporoids from reefal settings in the Cantabrian Zone (N Spain)

p. 301-323The oldest reefal episode in the Cantabrian Zone (earliest Pragian) consists of small biostromal patch reefs, mainly built by corals and stromatoporoids, and developed on a storm-dominated ramp. Four outcrops provide the stratigraphic framework in which these reef facies developed, and these permitted an interpretation of their depositional setting in terms of a relatively distal or protected shelf. We systematically describe three species of rugose corals, five species of tabulate corals, and six species of stromatoporoids. This fauna is allocated to three Pragian fossil associations. Association 1 is mainly composed of massive tabulate corals and stromatoporoids. Association 2 contains dominant branching rugose and tabulate corals. Finally, association 3 is represented by tiny massive tabulate corals. Each association occurs at a specific location within a framework of high-frequency deepening upward cycles, being related to a specific depositional setting. This mode of occurrence suggests that their development was tuned by relative base-level oscillations, forming during rises that took the sea-bottom to relatively deep or sheltered conditions, with rare reworking by storm-related currents. Finally, a comparison of this reefal fauna with examples of similar age from elsewhere is presented in order to explore their affinities.S

First record of chambered hexactinellid sponges from the Palaeozoic

p. 129-130Most chambered sponges (the polyphyletic group of "Sphinctozoa") are hypercalcified types and most of them probably belong to the Demospongia. "Spinctozoa" occur from the Cambrian to the Recent and are the most abundant sponges in Late Palaeozoic and Triassic reefs and shallow water limestones. Among hexactinellid sponges, chambered forms are very rare including taxa only from the Late Jurassic and the Late Triassic of Europe, Russia, Tadjikistan, Iran or China. There are five genera described Casearia Quenstedt, Caucasocoelia Boiko, Dracolychnos Wu & Xiao, Pseudo-verticillites Boiko and Innaecoelia Boiko, the latter of which is synomised with Casearia by most authors.S

Strong-LAMP: A LAMP Assay for Strongyloides spp. Detection in Stool and Urine Samples. Towards the Diagnosis of Human Strongyloidiasis Starting from a Rodent Model

[EN]Background: Strongyloides stercoralis, the chief causative agent of human strongyloidiasis, is a nematode globally distributed but mainly endemic in tropical and subtropical regions. Chronic infection is often clinically asymptomatic but it can result in severe hyperinfection syndrome or disseminated strongyloidiasis in immunocompromised patients. There is a great diversity of techniques used in diagnosing the disease, but definitive diagnosis is accomplished by parasitological examination of stool samples for morphological identification of parasite. Until now, no molecular method has been tested in urine samples as an alternative to stool samples for diagnosing strongyloidiasis. This study aimed to evaluate the use of a new molecular LAMP assay in a well-established Wistar rat experimental infection model using both stool and, for the first time, urine samples. The LAMP assay was also clinically evaluated in patients´ stool samples. Methodology/Principal Findings: Stool and urine samples were obtained daily during a 28-day period from rats infected subcutaneously with different infective third-stage larvae doses of S. venezuelensis. The dynamics of parasite infection was determined by daily counting the number of eggs per gram of feces from day 1 to 28 post-infection. A set of primers for LAMP assay based on a DNA partial sequence in the 18S rRNA gene from S. venezuelensis was designed. The set up LAMP assay (namely, Strong-LAMP) allowed the sensitive detection of S. venezuelensis DNA in both stool and urine samples obtained from each infection group of rats and was also effective in S. stercoralis DNA amplification in patients´ stool samples with previously confirmed strongyloidiasis by parasitological and real-time PCR tests. Conclusions/Significance: Our Strong-LAMP assay is an useful molecular tool in research of a strongyloidiasis experimental infection model in both stool and urine samples. After further validation, the Strong-LAMP could also be potentially applied for effective diagnosis of strongyloidiasis in a clinical setting. © 2016 Fernández-Soto et al

Assessment of the SmMIT-LAMP technique for the molecular detection of Schistosoma mansoni DNA in urine samples

Background: Human schistosomiasis, is one of the most common parasitic diseases worldwide. Parasitological and serological techniques have different shortcomings to control this illness. Therefore, the development of new diagnostic methods to detect infection in acute phase is required. Loop-mediated isothermal amplification technique (LAMP) could be a good choice. Methodology / Results: Firstly, experimental model was used to obtain urine samples from mice infected with cercariae of S. mansoni. The samples were collected weekly from week 0 to 8th post-infection. Finally, SmMIT-LAMP technique was performed to analyse urine samples DNA of S. mansoni was detected since 3rd week post-infection, Conclusions / Significance: We have detected, for the first time in acute phase, DNA of the S. mansoni in urine samples of infected mice, using a simple, rapid, inexpensive, and potentially applicable method to the diagnosis of schistosomiasis in endemic areas.Antecedentes: La esquistosomosis humana, es una de las enfermedades parasitarias más frecuentes en todo el mundo. Su principal problema reside en el control de la enfermedad debido a las limitaciones de las técnicas parasitológicas y serológicas. Por ello, es necesario el desarrollo de nuevos métodos de diagnóstico capaces de detectar la infección en fase aguda. Un enfoque prometedor es la técnica de amplificación isotérmica de ácidos nucleicos tipo LAMP (Loop-mediated isothermal amplification). Metodología / Resultados: Se utilizó un modelo murino de Schistosoma mansoni para obtener muestras de orina a partir de ratones infectados con cercarias de S. mansoni. Las muestras se recogieron semanalmente desde la semana 0 hasta la semana 8ª después de la infección. Posteriormente se realizó al análisis de las muestras de orina mediante la técnica SmMIT-LAMP, consiguiendo detectar ADN de S. mansoni desde la 3ª semana post-infección (p.i). Conclusiones / Importancia: Hemos logrado, por primera vez la detección de ADN de S. mansoni en muestras de orina en fase aguda de la infección producida por S. mansoni mediante un método molecular sencillo, rápido, económico y potencialmente aplicable en zonas endémicas

A Trypanosoma cruzi Genome Tandem Repetitive Satellite DNA Sequence as a Molecular Marker for a LAMP Assay for Diagnosing Chagas' Disease

Chagas' disease is a neglected tropical disease caused by Trypanosoma cruzi which is endemic throughout Latin America and is spread by worldwide migration. Diagnosis is currently limited to serological and molecular techniques having variations regarding their sensitivity and specificity. This work was aimed at developing a new sensitive, applicable, and cost-effective molecular diagnosis technique for loop-mediated isothermal amplification-based detection of T. cruzi (Tc-LAMP). The results led to determining a highly homologous satellite repeat region (231 bp) among parasite strains as a molecular marker for diagnosing the disease. Tc-LAMP was performed correctly for detecting parasite DNA (5 fg for the CL Brener strain and 50 fg for the DM28, TcVI, and TcI strains). Assay results proved negative for DNA from 16 helminth species and 7 protozoa, including Leishmania spp. Tc-LAMP based on the highly repeated T. cruzi satellite region is thus proposed as an important alternative for diagnosing T. cruzi infection, overcoming other methods' limitations such as their analytic capability, speed, and requiring specialized equipment or highly trained personnel. Tc-LAMP could be easily adapted for point-of-care testing in areas having limited resources

Application of the Strong-LAMP method for the molecular detection of Strongyloides stercoralis in a population of Porto Iguazú, Misiones, Argentina.

Strongiloides stercoralis is a nematode globally distributed and the chief causative agent of human Strongyloidiasis. Chronic infection is clinically asymptomatic, but, it can cause Hyperinfection Syndrome in immunocompromised patients. At present, the lack of a standardized diagnosis generates an underestimation of the prevalence of the disease. Coprological test, considered as the gold-standard, has a very low sensitivity. An alternative is the specific and sensitive LAMP method for the detection of S.stercoralis, the Strong-LAMP. In the present study, it have been used a total of 100 stool samples collected from a population of Porto Iguazú, Misiones (Argentina) and stored on filter paper until analysis. When Strong-LAMP was applied for the detection of Strongyloides spp. DNA, up to 39 samples (39%) were positive, including 5 positive obtained by coprological test, compared to 7 positive samples (7%) obtained by parasitological test. Therefore, Strong-LAMP has demonstrated more sensitive method for the detection of Strongyloides stercoralis in stool samples stored in filter paper than parasitological diagnostic methods and could be used in combination with parasitological methods in endemic areas to establish with greater reliability the real prevalence of the disease.Strongiloides stercoralis es un parásito nematodo de distribución global y el principal agente causal de la Estrongiloidiasis. La infección crónica presenta un curso asintomático, sin embargo, puede producir Síndrome de Hiperinfección en pacientes inmunodeprimidos. En la actualidad, la falta de un diagnóstico estandarizado genera una subestimación de la prevalencia de la enfermedad. El análisis coprológico, considerado como el gold-standard, presenta una muy baja sensibilidad. Una alternativa es el método LAMP específico y sensible para la detección de S.stercoralis, el Strong-LAMP. En el presente estudio, se ha utilizado un total de 100 muestras de heces recolectadas de una población de Porto Iguazú, Misiones (Argentina) y almacenadas en papel de filtro hasta su analisis. Cuando se aplicó el Strong-LAMP para la detección de ADN de Strongyloides spp., hasta 39 muestras (39%) resultaron positivas, incluyendo 5 positivas al análisis coprológico, frente a 7 muestras(7%) positivas obtenidas por análisis parasitológico. Por tanto, el Strong-LAMP ha demostrado ser un método más sensible para la detección de Strongyloides stercoralis en muestras de heces almacenadas en papel de filtro que los métodos de diagnóstico parasitológicos y podría utilizarse en combinación con los métodos parasitológicos en áreas endémicas para establecer con mayor fiabilidad la prevalencia real de la enfermedad

Combinatorial formulas for Kazhdan-Lusztig polynomials with respect to W-graph ideals

In \cite{y1} Yin generalized the definition of $W$-graph ideal $E_J$ in weighted Coxeter groups and introduced the weighted Kazhdan-Lusztig polynomials $\left \{ P_{x,y} \mid x,y\in E_J\right \}$, where $J$ is a subset of simple generators $S$. In this paper, we study the combinatorial formulas for those polynomials, which extend the results of Deodhar \cite{v3} and Tagawa \cite{h1}.Comment: 16 page

Strong-LAMP Assay Based on a Strongyloides spp.-Derived Partial Sequence in the 18S rRNA as Potential Biomarker for Strongyloidiasis Diagnosis in Human Urine Samples

Human strongyloidiasis a soil-transmitted infection caused by Strongyloides stercoralis is one of the most neglected amongst the so-called Neglected Tropical Diseases (NTDs). S. stercoralis is a nematode, which is distributed worldwide; it has been estimated that it could affect millions of people, mainly in tropical and subtropical endemic regions. The difficulties of diagnosis lead to infection rates being underreported. Asymptomatic patients have chronic infections that can lead to severe hyperinfection syndrome or disseminated strongyloidiasis in immunocompromised patients. Strongyloidiasis can easily be misdiagnosed because conventional faecal-based techniques lack of sensitivity for the morphological identification of infective larvae in faeces. None of the currently used molecular methods have used urine samples as an alternative to faecal samples for diagnosing strongyloidiasis. This study was thus aimed at comparing, for the first time, the use of a new loop-mediated isothermal amplification (LAMP) molecular assay (Strong-LAMP) to traditional methods on patients' urine samples. Twenty-four urine samples were taken from patients included in a study involving two Spanish hospitals for strongyloidiasis screening using parasitological and serological tests. Strongyloides larvae were found in 11 patients' faecal samples, thereby ascertaining that they had the disease. Other patients had high antibody titres but no larvae were found in their faeces. All urine samples were analysed by PCR and Strong-LAMP assay. No amplification occurred when using PCR. Strong-LAMP led to detecting S. stercoralis DNA in urine samples from patients having previously confirmed strongyloidiasis by parasitological tests and/or a suspicion of being infected by serological ones. The Strong-LAMP assay is a useful molecular tool for research regarding strongyloidiasis in human urine samples. After further validation, the Strong-LAMP assay could also be used for complementary and effective diagnosis of strongyloidiasis in a clinical setting